Seagrasses

2022-05-06T02:04:53Z

Philippbayer: /* Amphibolis antarctica */

Seagrasses

2022-05-06T02:04:44Z

Philippbayer:

Seagrasses

2022-05-06T02:04:33Z

Philippbayer:

Seagrasses

2022-05-06T01:53:11Z

Philippbayer:

This page collects assemblies, annotations, and supplementary data for the Amphibolis antarctica and Posidonia australis genome assemblies.

The raw reads are deposited in the SRA under BioProject PRJNA835502

== Posidonia australis ==

Draft genome assembly:

[http://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.fasta.gz P_australis_genome_bigger1kbp.fasta.gz]

MAKER annotation:

GFF of all evidence: [http://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.gff.gz P_australis_genome_bigger1kbp.all.gff.gz]
GFF of gene models only: [http://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.gene_models.gff.gz P_australis_genome_bigger1kbp.all.gene_models.gff.gz]

Proteins (fasta): [http://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.maker.proteins.fasta.gz P_australis_genome_bigger1kbp.all.maker.proteins.fasta.gz]
Transcripts/CDS (fasta): [http://appliedbioinformatics.com.au/download/P_australis_genome_bigger1kbp.all.maker.transcripts.fasta.gz P_australis_genome_bigger1kbp.all.maker.transcripts.fasta.gz]

== Amphibolis antarctica ==

Draft genome assembly:

[http://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.fasta.gz A_antarctica_genome_bigger1kbp.fasta.gz]

MAKER annotation:

GFF of all evidence: [http://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.gff.gz A_antarctica_genome_bigger1kbp.all.gff.gz]
GFF of gene models only: [http://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.gene_models.gff.gz A_antarctica_genome_bigger1kbp.all.gene_models.gff.gz]

Proteins (fasta): [http://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.maker.proteins.fasta.gz A_antarctica_genome_bigger1kbp.all.maker.proteins.fasta.gz]
Transcripts/CDS (fasta): [http://appliedbioinformatics.com.au/download/A_antarctica_genome_bigger1kbp.all.maker.transcripts.fasta.gz A_antarctica_genome_bigger1kbp.all.maker.transcripts.fasta.gz]

== EDTA results ==

These are EDTA TE libraries, annotated using TEfinder using rexdb-plant. I renamed the TE names, if TEfinder had no hit, I used the EDTA name.

For example, this is the TEfinder output:

>TE_00000000#Unknown TE_00000000#DNA/DTC

Saying that TEfinder does not know the class, but EDTA has it under DNA/DTC based on the tool that predicted it.

This is the final name:

>TE_00000000#DNA/DTC TE_00000000#DNA/DTC

Zostera muelleri: [http://appliedbioinformatics.com.au/download/Zmu_v1_scaffolds.big1k.merged_scaffolds.renamed.fa.mod.EDTA.TElib.fa.rexdb.cls.renamed.lib.fa.gz Zmu_v1_scaffolds.big1k.merged_scaffolds.renamed.fa.mod.EDTA.TElib.fa.rexdb.cls.renamed.lib.fa.gz ]

Zostera marina: [http://appliedbioinformatics.com.au/download/Zostera_marina.mainGenome.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz Zostera_marina.mainGenome.fasta.mod.EDTA.TElib.fa.rexdb-plant.cls.renamed.lib.fa.gz ]

Seagrasses

2022-05-06T01:44:48Z

Philippbayer:

2019-11-13T03:33:38Z

Philippbayer: /* Academic history */

Alumni

2019-11-13T02:43:27Z

Philippbayer:

'''PhD graduates'''

[[Andy Yuan]]

[[Armin Scheben]]

[[Bhavna Hurgobin]]

[[Juan Montenegro]]

[[Seyedehmahsa Mousaviderazmahalleh (Mahsa Mousavi)]]

[[Jenny (HueyTyng) Lee]]

[[Agnieszka Golicz]]

[[Paul Visendi Muhindira]]

[[Paula Andrea Martinez]]

[[Philipp Bayer]]

[[Pradeep Ruperao]]

[[Michal Lorenc]]

[[Kaitao Lai]]

[[Paul Berkman]]

Chris Duran

Mike Imelfort

Jatinder Kaur

Christopher Love

'''Masters graduates'''

Patricia Angelica Vera

Nikki Appleby (MSc)

'''Senior researchers and postdocs'''

[[Kenneth Chan]]

Terry Clark

[[Pradeep Ruperao]]

Hong Ching Lee

[[Jenny (HueyTyng) Lee]]

Edmund Ling

Daniel Marshall

Jiri Stiller

Ping Zhang

'''Research assistants'''

Sahana Manoli

Adam Skarshewski

Sonika Tyagi

Yang Liu (Ben)

'''Interns'''

Tristan de Jong

Thomas Schumann

Lars Smits

Nikolay Terentyev

Tek-Jun Ling

[[Oliver Schliebs]]

Brent Verpaalen

Main Page

2019-11-13T02:42:43Z

Philippbayer: /* PhD students */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SNParrayDB]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]
:[http://daisychain.appliedbioinformatics.com.au Daisychain]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

===Publicly available data sets:===

:[[Sample data]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Ricky Hu]]

[[Clementine Merce]]

[[Monica Danilevicz]]

[[Robyn Anderson]]

[[Cassandria Tay Fernandez]]

[[Jacob Marsh]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

2019-11-03T10:07:46Z

Philippbayer: Created page with "This page collects RGAugury results for all published Brassicaceae. The archive contains, for each assembly, a fasta file each for RLKs, RLPs, and NLR genes. Files ending in ...."

Main Page

2019-10-30T03:24:29Z

Philippbayer: /* Genome annotation and visualisation */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found on [https://scholar.google.com.au/citations?user=AxsOkqYAAAAJ&hl=en Google Scholar]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome Seagrass genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SNParrayDB]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]
:[http://daisychain.appliedbioinformatics.com.au Daisychain]

===Knowledge networks===

:[[QTLNetMiner collaboration with Rothamstead Research]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Seagrass]]

:[[Other legumes]]

:[[Metagenomics]]

===Publicly available data sets:===

:[[Sample data]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Philipp Bayer]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Habib Rijzaani]]

[[Andy Yuan]]

[[Armin Scheben]]

[[Ricky Hu]]

[[Clementine Merce]]

[[Monica Danilevicz]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions available at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

SGSGeneLoss

2019-04-16T05:12:15Z

Philippbayer: /* Plotting results */

Darmor Tapidor

2018-06-15T15:07:59Z

Philippbayer:

This page collects the files for Bayer et al. B. napus Darmor/Tapidor genome paper

== Software ==

Collinearity analysis - parses MCScanX results and checks for missing genes in expected regions [http://appliedbioinformatics.com.au/download/DarmorTapidor/Collinearity_scripts.zip Collinearity_scripts.zip]

LASTZSorter.py - sorts contigs based on LASTZ alignment with reference [http://appliedbioinformatics.com.au/download/DarmorTapidor/LASTZSorter.py LASTZSorter.py]

contigPlacer - places contigs based on recombination patterns [https://github.com/philippbayer/contigplacer contigPlacer]

R-scripts used for plotting - Venn-diagrams, boxplots [http://appliedbioinformatics.com.au/download/DarmorTapidor/R_plotting_scripts.zip R_plotting_scripts.zip]

The SkimGBS pipeline is available here: http://appliedbioinformatics.com.au/index.php/SkimGBS

== Results ==

[http://appliedbioinformatics.com.au/download/DarmorTapidor/MSTMap_Results.txt.gz Tapidor genetic map from MSTMap (txt)] - [http://appliedbioinformatics.com.au/download/DarmorTapidor/MSTMap_Input.zip MSTMap_Input.zip] Input file for MSTMap

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_Tapidor_Ningyou_SNPs.zip Darmor SNPs anchored on Darmor v8.1 reference (gff3)]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_Tapidor_Ningyou_SNPs.zip Tapidor SNPs anchored on Tapidor v6.3 reference (gff3)]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Repetitive_Collapsed_Genes.zip Repetitive_Collapsed_Genes.zip] List of genes in repetitive and collapsed regions

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Repetitive_Collapsed_Regions.zip Repetitive_Collapsed_Regions.zip] Coordinates of repetitive and collapsed regions in Darmor and Tapidor (bed)

[http://appliedbioinformatics.com.au/download/DarmorTapidor/SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip] Pfam and Swissprot results for repetitive and collapsed genes

== Annotation ==

[http://appliedbioinformatics.com.au/download/DarmorTapidor/ListOfBadPfamDomains.txt List of Transposase related PFAM IDs used for filtering]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/GO_Arabidopsis_Terms.zip GO_Arabidopsis_Terms.zip] Swiss-Prot/''Arabidopsis'' based GO terms for Darmor and Tapidor annotation

=== Tapidor v6.3 ===

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v6.3_contig_order.zip Tapidor_v6.3_contig_order.zip] - contig positions in assembly as gff3

==== Unfiltered annotation ====

Straight from AUGUSTUS, with MAKER's AED scores

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz Tapidor_v63_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz] - annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz] - predicted proteins

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz] - predicted transcripts

==== Filtered annotation ====

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz Tapidor_v63_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz] - filtered predicted annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz] - filtered predicted transcripts

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz] - filtered predicted proteins

=== Darmor v8.1 ===

WARNING - the Brassica community annotation standard says to number the genes by their order on the pseudomolecules. I've done this here as well. Since we tried to place as many contigs as possible that means that the order shifted a lot, so you 'cannot' just look for the same gene numbers when you compare with the v4.1 annotation, you have to use BLAST or similar to search for your candidate genes.

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.fasta.gz Darmor_v81_assembly_fasta.gz] - assembly as pseudo-molecules

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v8.1_contig_order.zip Darmor_v8.1_contig_order.zip] - order of contigs as gff3 files

==== Unfiltered annotation ====

Straight from AUGUSTUS, with MAKER's AED scores

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz Darmor_v81_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz] - annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz] - proteins, fasta

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz] - transcripts, fasta

==== Filtered annotation ====

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz Darmor_v81_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz] - filtered predicted annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz] - filtered predicted transcripts

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz] - filtered predicted proteins

Darmor Tapidor

2018-05-16T04:07:55Z

Philippbayer: /* Annotation */

This page collects the files for Bayer et al. B. napus Darmor/Tapidor genome paper

== Software ==

Collinearity analysis - parses MCScanX results and checks for missing genes in expected regions [http://appliedbioinformatics.com.au/download/DarmorTapidor/Collinearity_scripts.zip Collinearity_scripts.zip]

LASTZSorter.py - sorts contigs based on LASTZ alignment with reference [http://appliedbioinformatics.com.au/download/DarmorTapidor/LASTZSorter.py LASTZSorter.py]

contigPlacer - places contigs based on recombination patterns [https://github.com/philippbayer/contigplacer contigPlacer]

R-scripts used for plotting - Venn-diagrams, boxplots [http://appliedbioinformatics.com.au/download/DarmorTapidor/R_plotting_scripts.zip R_plotting_scripts.zip]

The SkimGBS pipeline is available here: http://appliedbioinformatics.com.au/index.php/SkimGBS

== Results ==

[http://appliedbioinformatics.com.au/download/DarmorTapidor/MSTMap_Results.txt.gz Tapidor genetic map from MSTMap (txt)] - [http://appliedbioinformatics.com.au/download/DarmorTapidor/MSTMap_Input.zip MSTMap_Input.zip] Input file for MSTMap

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_Tapidor_Ningyou_SNPs.zip Darmor SNPs anchored on Darmor v8.1 reference (gff3)]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_Tapidor_Ningyou_SNPs.zip Tapidor SNPs anchored on Tapidor v6.3 reference (gff3)]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Repetitive_Collapsed_Genes.zip Repetitive_Collapsed_Genes.zip] List of genes in repetitive and collapsed regions

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Repetitive_Collapsed_Regions.zip Repetitive_Collapsed_Regions.zip] Coordinates of repetitive and collapsed regions in Darmor and Tapidor (bed)

[http://appliedbioinformatics.com.au/download/DarmorTapidor/SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip] Pfam and Swissprot results for repetitive and collapsed genes

== Annotation ==

[http://appliedbioinformatics.com.au/download/DarmorTapidor/ListOfBadPfamDomains.txt List of Transposase related PFAM IDs used for filtering]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/GO_Arabidopsis_Terms.zip GO_Arabidopsis_Terms.zip] Swiss-Prot/''Arabidopsis'' based GO terms for Darmor and Tapidor annotation

=== Tapidor v6.3 ===

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v6.3_contig_order.zip Tapidor_v6.3_contig_order.zip] - contig positions in assembly as gff3

==== Unfiltered annotation ====

Straight from AUGUSTUS, with MAKER's AED scores

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz Tapidor_v63_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz] - annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz] - predicted proteins

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz] - predicted transcripts

==== Filtered annotation ====

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz Tapidor_v63_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz] - filtered predicted annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz] - filtered predicted transcripts

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz] - filtered predicted proteins

=== Darmor v8.1 ===

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.fasta.gz Darmor_v81_assembly_fasta.gz] - assembly as pseudo-molecules

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v8.1_contig_order.zip Darmor_v8.1_contig_order.zip] - order of contigs as gff3 files

==== Unfiltered annotation ====

Straight from AUGUSTUS, with MAKER's AED scores

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz Darmor_v81_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz] - annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz] - proteins, fasta

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz] - transcripts, fasta

==== Filtered annotation ====

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz Darmor_v81_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz] - filtered predicted annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz] - filtered predicted transcripts

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz] - filtered predicted proteins

Darmor Tapidor

2018-05-16T03:52:18Z

Philippbayer: /* Annotation */

This page collects the files for Bayer et al. B. napus Darmor/Tapidor genome paper

== Software ==

Collinearity analysis - parses MCScanX results and checks for missing genes in expected regions [http://appliedbioinformatics.com.au/download/DarmorTapidor/Collinearity_scripts.zip Collinearity_scripts.zip]

LASTZSorter.py - sorts contigs based on LASTZ alignment with reference [http://appliedbioinformatics.com.au/download/DarmorTapidor/LASTZSorter.py LASTZSorter.py]

contigPlacer - places contigs based on recombination patterns [https://github.com/philippbayer/contigplacer contigPlacer]

R-scripts used for plotting - Venn-diagrams, boxplots [http://appliedbioinformatics.com.au/download/DarmorTapidor/R_plotting_scripts.zip R_plotting_scripts.zip]

The SkimGBS pipeline is available here: http://appliedbioinformatics.com.au/index.php/SkimGBS

== Results ==

[http://appliedbioinformatics.com.au/download/DarmorTapidor/MSTMap_Results.txt.gz Tapidor genetic map from MSTMap (txt)] - [http://appliedbioinformatics.com.au/download/DarmorTapidor/MSTMap_Input.zip MSTMap_Input.zip] Input file for MSTMap

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_Tapidor_Ningyou_SNPs.zip Darmor SNPs anchored on Darmor v8.1 reference (gff3)]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_Tapidor_Ningyou_SNPs.zip Tapidor SNPs anchored on Tapidor v6.3 reference (gff3)]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Repetitive_Collapsed_Genes.zip Repetitive_Collapsed_Genes.zip] List of genes in repetitive and collapsed regions

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Repetitive_Collapsed_Regions.zip Repetitive_Collapsed_Regions.zip] Coordinates of repetitive and collapsed regions in Darmor and Tapidor (bed)

[http://appliedbioinformatics.com.au/download/DarmorTapidor/SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip] Pfam and Swissprot results for repetitive and collapsed genes

== Annotation ==

[http://appliedbioinformatics.com.au/download/DarmorTapidor/ListOfBadPfamDomains.txt List of Transposase related PFAM IDs used for filtering]

[http://appliedbioinformatics.com.au/download/DarmorTapidor/GO_Arabidopsis_Terms.zip GO_Arabidopsis_Terms.zip] Swiss-Prot/''Arabidopsis'' based GO terms for Darmor and Tapidor annotation

=== Tapidor v6.3 ===

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v6.3_contig_order.zip Tapidor_v6.3_contig_order.zip] - contig positions in assembly as gff3
==== Filtered annotation ====

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.augustus_masked_filtered.gff.gz Tapidor_v63_assembly.augustus_masked_filtered.gff.gz] - filtered predicted annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz] - filtered predicted transcripts

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz] - filtered predicted proteins

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz] - PFam results for filtered predicted proteins

=== Darmor v8.1 ===

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.fasta.gz Darmor_v81_assembly_fasta.gz] - assembly as pseudo-molecules

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v8.1_contig_order.zip Darmor_v8.1_contig_order.zip] - order of contigs as gff3 files

==== Unfiltered annotation ====

Straight from AUGUSTUS, with MAKER's AED scores

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz Darmor_v81_assembly.augustus_masked.propermodels.sorted.renamed.gff.gz] - annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.fasta.gz] - proteins, fasta

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.fasta.gz] - transcripts, fasta

==== Filtered annotation ====

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz Darmor_v81_assembly.augustus_masked.propermodels.sorted_filtered.renamed.gff.gz] - filtered predicted annotation in GFF format

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.transcripts.renamed.filtered.fasta.gz] - filtered predicted transcripts

[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz Darmor_v81_assembly.all.maker.augustus_masked.proteins.renamed.filtered.fasta.gz] - filtered predicted proteins

Repeats Tables

2018-02-08T03:04:47Z

Philippbayer:

Supplementary Table S1: Repeats and count of R-gene domains contained therein

{| class="wikitable"
! Repeat name
! Species
! Year last updated in Repbase
! PF00931 NB-ARC domain
! PF01582 TIR domain
! PF13676 TIR domain
! PF13855 Leucine rich repeat
! PF13516 Leucine Rich Repeat
! PF00560 Leucine Rich Repeat
! PF14580 Leucine-rich repeat
! PF08263 Leucine rich repeat N-terminal domain
|-
| Helitron-3_PTr
| Populus trichocarpa
| 2012
| 1
|
|
|
|
|
|
|
|-
| Helitron-1_Mad
| Malus domestica
| 2010
| 2
| 1
|
|
| 1
|
|
|
|-
| Helitron-N68_OS
| Oryza sativa
| 2016
|
|
|
|
|
|
|
| 1
|-
| REP-6_CCri
| Chondrus crispus
| 2013
| 1
|
|
|
|
|
|
|
|-
| Gypsy-112_GM-I
| Glycine max
| 2012
|
|
|
| 3
|
|
|
| 1
|-
| MuDR-N10_ALy
| Arabidopsis lyrata
| 2011
|
|
|
|
| 1
|
|
|
|-
| Gypsy-8_PX-I
| Gypsy Pyrus x bretschneideri
| 2012
|
|
|
| 2
|
| 1
|
| 1
|-
| MU4_ZM
| Zea mays
| 2004
|
|
|
| 1
|
|
|
|
|-
| REP-5_CCri
| Chondrus crispus
| 2013
| 1
|
| 1
|
|
|
|
|
|-
| REP-7_CCri
| Chondrus crispus
| 2013
| 1
|
|
|
|
|
|
|
|-
| hAT-7_ATr
| Amborella trichopoda
| 2014
|
|
|
| 1
|
|
|
|
|-
| DNA-18_CCri
| Chondrus crispus
| 2013
|
|
|
|
|
|
| 1
|
|-
| EnSpm-19_CCri
| Chondrus crispus
| 2013
|
|
|
|
|
|
| 1
|
|}

Supplementary Table S2: Names of R-gene candidates in the four assemblies

{| class="wikitable"
! Brassica napus Darmor-bzh v4.1
!
! Brassica napus Darmor-bzh v4.1 repeatmasked
!
! Brassica napus Darmor-bzh v8.1
!
! Brassica napus Tapidor
!
! Brassica rapa v1.5
!
! Brassica rapa v1.5 repeat-masked
!
! Brassica rapa v2.1
!
|-
| R-gene
| Class
| R-gene
| Class
| R-gene
| Class
| R-gene
| Class
| R-gene
| Class
| R-gene
| Class
| R-gene
| Class
|-
| BnaA01g01450D
| TNL
| BnaA01g15270D
| CNL
| BnaA01g01400.1D2
| TN
| BnaA01g00100.1T
| TN
| Bra000758
| N
| Bra002495
| CNL
| BraA01000263
| TNL
|-
| BnaA01g01460D
| TNL
| BnaA01g16260D
| CN
| BnaA01g01410.1D2
| TN
| BnaA01g00110.1T
| TNL
| Bra000759
| TNL
| Bra005270
| N
| BraA01000264
| TNL
|-
| BnaA01g03580D
| RN
| BnaA01g19950D
| CN
| BnaA01g03380.1D2
| RN
| BnaA01g00460.1T
| RN
| Bra001160
| TNL
| Bra005273
| CN
| BraA01000507
| RN
|-
| BnaA01g09840D
| N
| BnaA01g19960D
| N
| BnaA01g09430.1D2
| N
| BnaA01g08320.1T
| N
| Bra001161
| TNL
| Bra005278
| N
| BraA01001130
| N
|-
| BnaA01g09850D
| N
| BnaA01g23040D
| CNL
| BnaA01g09440.1D2
| N
| BnaA01g08500.1T
| TNL
| Bra001162
| TNL
| Bra008055
| Other
| BraA01001131
| N
|-
| BnaA01g10040D
| TNL
| BnaA01g28560D
| N
| BnaA01g15480.1D2
| CN
| BnaA01g11700.1T
| CN
| Bra001175
| TNL
| Bra008977
| N
| BraA01001163
| TNL
|-
| BnaA01g15270D
| CNL
| BnaA01g35670D
| CNL
| BnaA01g19610.1D2
| CN
| BnaA01g20650.1T
| N
| Bra002117
| TNL
| Bra009434
| RN
| BraA01001262
| CN
|-
| BnaA01g16260D
| CN
| BnaA02g23810D
| NL
| BnaA01g19620.1D2
| N
| BnaA01g20660.1T
| CN
| Bra002153
| TNL
| Bra009882
| ANL
| BraA01001263
| N
|-
| BnaA01g18700D
| Other
| BnaA02g24000D
| CN
| BnaA01g21730.1D2
| Other
| BnaA01g22490.1T
| N
| Bra002154
| TNL
| Bra012116
| N
| BraA01001376
| CNL
|-
| BnaA01g19940D
| N
| BnaA02g25160D
| CNL
| BnaA01g32850.1D2
| N
| BnaA01g27860.1T
| N
| Bra002495
| CNL
| Bra013947
| CNL
| BraA01002293
| Other
|-
| BnaA01g19950D
| CN
| BnaA03g52640D
| CN
| BnaA01g34280.1D2
| N
| BnaA02g03480.1T
| N
| Bra003863
| Other
| Bra015597
| CNL
| BraA01003840
| N
|-
| BnaA01g19960D
| N
| BnaA05g07900D
| CN
| BnaA02g04280.1D2
| N
| BnaA02g04160.1T
| TN
| Bra003864
| TN
| Bra016781
| CN
| BraA02000452
| N
|-
| BnaA01g21960D
| Other
| BnaA06g02940D
| CNL
| BnaA02g16960.1D2
| N
| BnaA02g21520.1T
| NL
| Bra003866
| TN
| Bra016785
| NL
| BraA02002337
| Other
|-
| BnaA01g23040D
| CNL
| BnaA06g08270D
| CN
| BnaA02g24190.1D2
| Other
| BnaA02g22130.1T
| Other
| Bra003867
| TNL
| Bra018198
| N
| BraA02004043
| RN
|-
| BnaA01g28560D
| N
| BnaA06g28070D
| RNL
| BnaA02g24220.1D2
| NL
| BnaA02g23490.1T
| NL
| Bra003997
| TNL
| Bra018804
| NL
| BraA02004178
| CN
|-
| BnaA01g32130D
| TNL
| BnaA06g29870D
| CN
| BnaA02g24240.1D2
| N
| BnaA02g23500.1T
| NL
| Bra004192
| TNL
| Bra018810
| N
| BraA03000948
| N
|-
| BnaA01g33710D
| TN
| BnaA06g29890D
| CN
| BnaA02g24250.1D2
| NL
| BnaA02g23520.1T
| NL
| Bra005270
| N
| Bra018834
| CNL
| BraA03002936
| N
|-
| BnaA01g33750D
| TNL
| BnaA06g31950D
| Other
| BnaA02g24300.1D2
| TN
| BnaA03g30810.1T
| N
| Bra005271
| CN
| Bra018980
| N
| BraA03002937
| NL
|-
| BnaA01g33780D
| TNL
| BnaA07g12270D
| N
| BnaA02g24410.1D2
| Other
| BnaA03g30820.1T
| TNL
| Bra005273
| CN
| Bra019413
| N
| BraA03004422
| CN
|-
| BnaA01g33930D
| TN
| BnaA07g22930D
| TN
| BnaA02g30810.1D2
| N
| BnaA03g32490.1T
| Other
| Bra005277
| CN
| Bra019752
| NL
| BraA03004509
| N
|-
| BnaA01g35670D
| CNL
| BnaA08g11840D
| RN
| BnaA02g31850.1D2
| N
| BnaA03g35160.1T
| N
| Bra005278
| N
| Bra019754
| NL
| BraA03005210
| NL
|-
| BnaA02g03780D
| Other
| BnaA08g20150D
| TN
| BnaA02g31870.1D2
| N
| BnaA03g40130.1T
| NL
| Bra006094
| TNL
| Bra021130
| Other
| BraA03005211
| TNL
|-
| BnaA02g03790D
| TNL
| BnaA08g24860D
| NL
| BnaA02g31890.1D2
| N
| BnaA03g40140.1T
| TNL
| Bra006095
| NL
| Bra021980
| NC
| BraA03005442
| T2N
|-
| BnaA02g03810D
| TN
| BnaA08g26370D
| CN
| BnaA02g31900.1D2
| CN
| BnaA04g25410.1T
| N
| Bra006146
| TNL
| Bra025290
| Other
| BraA03005714
| NL
|-
| BnaA02g03830D
| TN
| BnaA08g26380D
| N
| BnaA02g31910.1D2
| N
| BnaA05g11370.1T
| Other
| Bra006452
| TNL
| Bra025956
| N
| BraA05000920
| RNL
|-
| BnaA02g04080D
| NL
| BnaA08g26400D
| CN
| BnaA02g31920.1D2
| CN
| BnaA05g19410.1T
| CNL
| Bra006487
| TN
| Bra026368
| CN
| BraA05001948
| CN
|-
| BnaA02g16190D
| TN
| BnaA08g26410D
| NL
| BnaA02g31940.1D2
| N
| BnaA05g19420.1T
| N
| Bra006556
| TNL
| Bra026923
| N
| BraA05001954
| CN
|-
| BnaA02g22600D
| TN
| BnaA09g07700D
| Other
| BnaA02g31970.1D2
| N
| BnaA06g16320.1T
| TNL
| Bra008053
| TN
| Bra026924
| N
| BraA05001956
| CN
|-
| BnaA02g23780D
| TNL
| BnaA09g10520D
| CNL
| BnaA03g25010.1D2
| N
| BnaA06g21980.1T
| N
| Bra008055
| Other
| Bra026977
| CNL
| BraA05001961
| N
|-
| BnaA02g23800D
| NL
| BnaA09g13850D
| CNL
| BnaA03g37030.1D2
| N
| BnaA07g08130.1T
| N
| Bra008056
| TN
| Bra026978
| NL
| BraA05001962
| CN
|-
| BnaA02g23810D
| NL
| BnaA09g44880D
| N
| BnaA03g37480.1D2
| CN
| BnaA07g08140.1T
| RN
| Bra008060
| TN
| Bra026979
| CNL
| BraA05001969
| N
|-
| BnaA02g23840D
| Other
| BnaA09g44910D
| N
| BnaA03g37490.1D2
| N
| BnaA07g16000.1T
| N
| Bra008977
| N
| Bra027097
| CNL
| BraA05001971
| CN
|-
| BnaA02g23850D
| TN
| BnaA09g46490D
| N
| BnaA03g42720.1D2
| NL
| BnaA07g28850.1T
| NL
| Bra009141
| TN
| Bra030778
| CNL
| BraA05001972
| CN
|-
| BnaA02g24000D
| CN
| BnaA09g47220D
| CNL
| BnaA03g44490.1D2
| T2N
| BnaA08g01570.1T
| N
| Bra009434
| RN
| Bra030779
| CNL
| BraA05001978
| CN
|-
| BnaA02g24510D
| Other
| BnaA09g47240D
| CNL
| BnaA03g46970.1D2
| NL
| BnaA08g01580.1T
| CN
| Bra009882
| RNL
| Bra030997
| Other
| BraA05002460
| CNL
|-
| BnaA02g24520D
| NL
| BnaA10g04980D
| CN
| BnaA05g07820.1D2
| CN
| BnaA08g12530.1T
| N
| Bra010496
| TNL
| Bra031482
| CNL
| BraA05002461
| N
|-
| BnaA02g24530D
| NL
| BnaA10g13140D
| CN
| BnaA05g07830.1D2
| N
| BnaA09g03220.1T
| Other
| Bra010551
| TNL
| Bra036045
| CN
| BraA06000225
| Other
|-
| BnaA02g24540D
| TNL
| BnaA10g21210D
| N
| BnaA05g07850.1D2
| CN
| BnaA09g03820.1T
| Other
| Bra010552
| TNL
| Bra036053
| N
| BraA06000253
| N
|-
| BnaA02g24560D
| TNL
| BnaA10g25550D
| RN
| BnaA05g07860.1D2
| N
| BnaA09g11190.1T
| N
| Bra010588
| Other
| Bra036054
| CN
| BraA06000257
| Other
|-
| BnaA02g25160D
| CNL
| BnaAnng28610D
| N
| BnaA05g07880.1D2
| CN
| BnaA09g14420.1T
| NL
| Bra010589
| TNL
| Bra037139
| Other
| BraA06000259
| NL
|-
| BnaA02g25170D
| NL
| BnaC01g04860D
| RN
| BnaA05g07890.1D2
| N
| BnaA09g14430.1T
| N
| Bra010590
| TNL
| Bra040843
| N
| BraA06000261
| NL
|-
| BnaA02g25180D
| N
| BnaC01g04900D
| N
| BnaA05g07930.1D2
| CN
| BnaA09g19220.1T
| N
| Bra010663
| TNL
|
|
| BraA06000794
| NL
|-
| BnaA02g30250D
| Other
| BnaC01g19360D
| N
| BnaA05g12530.1D2
| TNL
| BnaA09g21870.1T
| NL
| Bra011432
| RN
|
|
| BraA06000978
| N
|-
| BnaA02g30300D
| TNL
| BnaC01g24770D
| CN
| BnaA05g25750.1D2
| CNL
| BnaA09g23910.1T
| N
| Bra011665
| TNL
|
|
| BraA06002781
| CN
|-
| BnaA02g31380D
| RN
| BnaC01g27900D
| N
| BnaA05g25760.1D2
| N
| BnaA09g23930.1T
| CNL
| Bra011666
| TNL
|
|
| BraA06002782
| CN
|-
| BnaA02g32570D
| N
| BnaC01g29260D
| N
| BnaA06g02900.1D2
| N
| BnaA09g28400.1T
| N
| Bra012114
| N
|
|
| BraA06002785
| CN
|-
| BnaA02g32580D
| N
| BnaC01g35850D
| N
| BnaA06g28360.1D2
| RN
| BnaA09g33210.1T
| TN
| Bra012116
| N
|
|
| BraA06002789
| CN
|-
| BnaA02g32620D
| N
| BnaC02g07560D
| NL
| BnaA06g30810.1D2
| CN
| BnaA10g07620.1T
| N
| Bra012540
| TNL
|
|
| BraA06003004
| RNL
|-
| BnaA02g32660D
| CN
| BnaC02g07680D
| N
| BnaA06g30820.1D2
| CN
| BnaA10g07640.1T
| N
| Bra012541
| TNL
|
|
| BraA06004215
| Other
|-
| BnaA02g32670D
| N
| BnaC02g21630D
| TN
| BnaA06g32820.1D2
| N
| BnaA10g13060.1T
| N
| Bra012688
| TNL
|
|
| BraA06004225
| RN
|-
| BnaA02g32710D
| N
| BnaC02g46990D
| Other
| BnaA06g32960.1D2
| Other
| BnaA10g16570.1T
| CN
| Bra012689
| TNL
|
|
| BraA07001692
| N
|-
| BnaA02g35050D
| TN
| BnaC02g47150D
| TNL
| BnaA07g11690.1D2
| RN
| BnaA10g26110.1T
| N
| Bra013134
| N
|
|
| BraA07001694
| N
|-
| BnaA03g03260D
| TNL
| BnaC02g47400D
| N
| BnaA07g11700.1D2
| RN
| BnaA10g29530.1T
| RN
| Bra013213
| CN
|
|
| BraA07001695
| N
|-
| BnaA03g03270D
| TN
| BnaC02g48740D
| N
| BnaA07g34310.1D2
| NL
| BnaC01g01250.1T
| N
| Bra013372
| N
|
|
| BraA07002488
| NL
|-
| BnaA03g03830D
| TNL
| BnaC03g44590D
| NL
| BnaA08g02170.1D2
| N
| BnaC01g08790.1T
| Other
| Bra013373
| N
|
|
| BraA07002973
| N
|-
| BnaA03g07040D
| TNL
| BnaC03g69970D
| N
| BnaA08g02180.1D2
| CN
| BnaC01g18750.1T
| N
| Bra013400
| TNL
|
|
| BraA07002974
| NL
|-
| BnaA03g14540D
| TNL
| BnaC04g15810D
| N
| BnaA08g08210.1D2
| NL
| BnaC01g18780.1T
| N
| Bra013947
| CNL
|
|
| BraA07003658
| N
|-
| BnaA03g24930D
| NL
| BnaC04g15820D
| Other
| BnaA08g11350.1D2
| RN
| BnaC01g18790.1T
| N
| Bra013959
| TNL
|
|
| BraA07004170
| N
|-
| BnaA03g25330D
| TNL
| BnaC04g20050D
| CN
| BnaA08g14930.1D2
| TN
| BnaC01g22430.1T
| Other
| Bra014241
| CN
|
|
| BraA08000671
| CN
|-
| BnaA03g29130D
| TN
| BnaC04g32140D
| N
| BnaA08g14940.1D2
| N
| BnaC01g26190.1T
| CN
| Bra015597
| CNL
|
|
| BraA08001335
| RN
|-
| BnaA03g29300D
| TNL
| BnaC05g09540D
| N
| BnaA08g14950.1D2
| TNL
| BnaC01g27780.1T
| NL
| Bra016027
| TN
|
|
| BraA08001421
| CN
|-
| BnaA03g29580D
| TNL
| BnaC05g09600D
| N
| BnaA08g19560.1D2
| TN
| BnaC01g27790.1T
| NL
| Bra016029
| TN
|
|
| BraA08002117
| TNL
|-
| BnaA03g38510D
| N
| BnaC05g11810D
| N
| BnaA08g19610.1D2
| TN
| BnaC02g12910.1T
| N
| Bra016311
| TN
|
|
| BraA08002118
| NL
|-
| BnaA03g44080D
| TN
| BnaC05g11820D
| N
| BnaA08g22160.1D2
| N
| BnaC02g26050.1T
| TN
| Bra016314
| TN
|
|
| BraA08003020
| Other
|-
| BnaA03g44090D
| TNL
| BnaC05g12120D
| CN
| BnaA09g08110.1D2
| N
| BnaC02g26450.1T
| NL
| Bra016594
| TNL
|
|
| BraA08003021
| TN
|-
| BnaA03g45000D
| TN
| BnaC05g51110D
| N
| BnaA09g08270.1D2
| Other
| BnaC02g26470.1T
| N
| Bra016781
| CN
|
|
| BraA08003024
| TN
|-
| BnaA03g45020D
| Other
| BnaC06g03300D
| CN
| BnaA09g14610.1D2
| N
| BnaC02g26520.1T
| TN
| Bra016782
| CNL
|
|
| BraA08003334
| NL
|-
| BnaA03g45040D
| TN
| BnaC06g03790D
| CN
| BnaA09g17050.1D2
| N
| BnaC02g26600.1T
| CN
| Bra016785
| NL
|
|
| BraA08003834
| CN
|-
| BnaA03g45970D
| T2N
| BnaC06g03820D
| N
| BnaA09g20500.1D2
| NL
| BnaC02g26620.1T
| CN
| Bra017542
| TNL
|
|
| BraA09000931
| TN
|-
| BnaA03g46200D
| NL
| BnaC06g03840D
| N
| BnaA09g20690.1D2
| TNL
| BnaC02g28910.1T
| N
| Bra017544
| TN
|
|
| BraA09001684
| N
|-
| BnaA03g48510D
| NL
| BnaC06g04820D
| CNL
| BnaA09g20710.1D2
| TN
| BnaC03g01050.1T
| N
| Bra017572
| Other
|
|
| BraA09003304
| Other
|-
| BnaA03g52640D
| CN
| BnaC06g05500D
| N
| BnaA09g20740.1D2
| TNL
| BnaC03g01950.1T
| NL
| Bra017807
| TNL
|
|
| BraA09003305
| TNL
|-
| BnaA03g56180D
| TNL
| BnaC06g25360D
| N
| BnaA09g24240.1D2
| TN
| BnaC03g01970.1T
| N
| Bra018037
| TNL
|
|
| BraA09003373
| CN
|-
| BnaA03g57650D
| CN
| BnaC06g34010D
| TN
| BnaA09g29330.1D2
| TN
| BnaC03g10050.1T
| TNL
| Bra018196
| N
|
|
| BraA09003651
| TNL
|-
| BnaA04g04710D
| NL
| BnaC06g34040D
| TN
| BnaA09g29340.1D2
| TNL
| BnaC03g10060.1T
| NL
| Bra018198
| N
|
|
| BraA09003652
| NL
|-
| BnaA04g11150D
| Other
| BnaC06g40800D
| NL
| BnaA09g31750.1D2
| CN
| BnaC03g19180.1T
| CN
| Bra018245
| CNL
|
|
| BraA09004788
| N
|-
| BnaA04g11170D
| TNL
| BnaC07g02790D
| NL
| BnaA09g32190.1D2
| N
| BnaC03g19190.1T
| N
| Bra018448
| N
|
|
| BraA09004814
| N
|-
| BnaA04g11180D
| Other
| BnaC07g16470D
| Other
| BnaA09g32210.1D2
| Other
| BnaC03g33810.1T
| N
| Bra018804
| NL
|
|
| BraA09004816
| TNL
|-
| BnaA04g11350D
| TN
| BnaC07g24530D
| Other
| BnaA09g37230.1D2
| N
| BnaC03g35740.1T
| CNL
| Bra018810
| N
|
|
| BraA09005580
| TNL
|-
| BnaA04g18550D
| TNL
| BnaC08g15420D
| NL
| BnaA09g45370.1D2
| TN
| BnaC03g41000.1T
| RN
| Bra018834
| CNL
|
|
| BraA09005583
| NL
|-
| BnaA04g27840D
| TNL
| BnaC08g15510D
| N
| BnaA10g09460.1D2
| N
| BnaC03g41040.1T
| N
| Bra018835
| CNL
|
|
| BraA09005584
| TNL
|-
| BnaA04g28100D
| TNL
| BnaC08g15930D
| N
| BnaA10g13610.1D2
| CN
| BnaC03g49000.1T
| N
| Bra018863
| CNL
|
|
| BraA09005999
| CN
|-
| BnaA05g07870D
| CN
| BnaC08g37610D
| N
| BnaA10g20770.1D2
| N
| BnaC03g49330.1T
| NL
| Bra018980
| N
|
|
| BraA09006040
| N
|-
| BnaA05g07880D
| CN
| BnaC08g37620D
| N
| BnaA10g24980.1D2
| Other
| BnaC03g50030.1T
| NL
| Bra019063
| NL
|
|
| BraA09006908
| N
|-
| BnaA05g07900D
| CN
| BnaC08g37650D
| TN
| BnaC01g04330.1D2
| N
| BnaC03g50060.1T
| TN
| Bra019273
| TNL
|
|
| BraA10001174
| RN
|-
| BnaA05g07930D
| CN
| BnaC08g40550D
| NL
| BnaC01g04350.1D2
| N
| BnaC03g50070.1T
| N
| Bra019305
| T2N
|
|
| BraA10001175
| RN
|-
| BnaA05g12020D
| NL
| BnaC08g40560D
| N
| BnaC01g10550.1D2
| TNL
| BnaC03g52330.1T
| RN
| Bra019409
| TNL
|
|
|
|
|-
| BnaA05g12030D
| TNL
| BnaC08g41340D
| CN
| BnaC01g10590.1D2
| NL
| BnaC03g54210.1T
| N
| Bra019410
| Other
|
|
|
|
|-
| BnaA05g24990D
| CN
| BnaC08g41420D
| CN
| BnaC01g10600.1D2
| N
| BnaC03g54220.1T
| CN
| Bra019413
| N
|
|
|
|
|-
| BnaA05g25000D
| N
| BnaC08g41430D
| NL
| BnaC01g10890.1D2
| N
| BnaC04g03230.1T
| N
| Bra019752
| NL
|
|
|
|
|-
| BnaA05g33170D
| TNL
| BnaC08g41710D
| CN
| BnaC01g17680.1D2
| CN
| BnaC04g30980.1T
| N
| Bra019754
| NL
|
|
|
|
|-
| BnaA06g02940D
| CNL
| BnaC09g07690D
| Other
| BnaC01g22960.1D2
| CN
| BnaC05g23300.1T
| RN
| Bra019755
| CNL
|
|
|
|
|-
| BnaA06g02950D
| N
| BnaC09g10760D
| CNL
| BnaC01g22970.1D2
| N
| BnaC05g25790.1T
| CN
| Bra020568
| RN
|
|
|
|
|-
| BnaA06g08260D
| CNL
| BnaC09g10770D
| CNL
| BnaC01g25630.1D2
| CN
| BnaC05g25810.1T
| CN
| Bra020693
| Other
|
|
|
|
|-
| BnaA06g08270D
| CN
| BnaC09g11510D
| N
| BnaC01g25650.1D2
| N
| BnaC05g38140.1T
| CN
| Bra020861
| TNL
|
|
|
|
|-
| BnaA06g28070D
| RNL
| BnaC09g13250D
| CN
| BnaC01g26020.1D2
| Other
| BnaC05g38150.1T
| N
| Bra021130
| Other
|
|
|
|
|-
| BnaA06g29860D
| N
| BnaC09g13260D
| N
| BnaC02g09410.1D2
| N
| BnaC06g19940.1T
| N
| Bra021754
| TNL
|
|
|
|
|-
| BnaA06g29870D
| CN
| BnaC09g15010D
| CN
| BnaC02g17220.1D2
| Other
| BnaC06g28130.1T
| N
| Bra021952
| TNL
|
|
|
|
|-
| BnaA06g29890D
| CN
| BnaC09g15110D
| N
| BnaC02g18990.1D2
| N
| BnaC06g30970.1T
| NL
| Bra021953
| TNL
|
|
|
|
|-
| BnaA06g31950D
| Other
| BnaC09g18900D
| TNL
| BnaC02g21980.1D2
| N
| BnaC07g02070.1T
| NL
| Bra021956
| Other
|
|
|
|
|-
| BnaA06g35960D
| TNL
| BnaC09g20620D
| N
| BnaC02g29700.1D2
| TN
| BnaC07g15880.1T
| Other
| Bra021957
| TN
|
|
|
|
|-
| BnaA06g39650D
| N
| BnaC09g35960D
| CN
| BnaC02g29720.1D2
| NL
| BnaC07g16720.1T
| NL
| Bra021980
| Other
|
|
|
|
|-
| BnaA07g12270D
| N
| BnaC09g36260D
| CN
| BnaC02g30040.1D2
| N
| BnaC07g16730.1T
| CN
| Bra022034
| TNL
|
|
|
|
|-
| BnaA07g12280D
| RN
| BnaCnng20410D
| CN
| BnaC02g30130.1D2
| N
| BnaC07g16740.1T
| N
| Bra022035
| Other
|
|
|
|
|-
| BnaA07g15400D
| TNL
| BnaCnng24770D
| TN
| BnaC02g31500.1D2
| Other
| BnaC07g16750.1T
| N
| Bra022036
| NL
|
|
|
|
|-
| BnaA07g17000D
| CNL
| BnaCnng41120D
| N
| BnaC03g07660.1D2
| TNL
| BnaC07g18220.1T
| N
| Bra022037
| TNL
|
|
|
|
|-
| BnaA07g22910D
| Other
| BnaCnng50000D
| N
| BnaC03g07670.1D2
| TN
| BnaC07g18230.1T
| N
| Bra022039
| TNL
|
|
|
|
|-
| BnaA07g22930D
| TN
| BnaCnng50410D
| N
| BnaC03g16790.1D2
| TNL
| BnaC07g21420.1T
| RN
| Bra022071
| TNL
|
|
|
|
|-
| BnaA07g22940D
| TNL
| BnaCnng50420D
| NL
| BnaC03g25820.1D2
| CN
| BnaC07g21430.1T
| RN
| Bra022850
| TNL
|
|
|
|
|-
| BnaA07g24260D
| TNL
| BnaCnng57760D
| N
| BnaC03g25830.1D2
| N
| BnaC07g21450.1T
| Other
| Bra023350
| TN
|
|
|
|
|-
| BnaA07g26100D
| TNL
| BnaCnng57770D
| N
| BnaC03g25970.1D2
| Other
| BnaC07g22610.1T
| CN
| Bra023631
| TN
|
|
|
|
|-
| BnaA07g30480D
| N
| BnaUnng00420D
| CNL
| BnaC03g26780.1D2
| NL
| BnaC07g24180.1T
| RNL
| Bra023646
| Other
|
|
|
|
|-
| BnaA07g30500D
| TN
| BnaUnng00640D
| NL
| BnaC03g39710.1D2
| CN
| BnaC07g29190.1T
| NL
| Bra023647
| TNL
|
|
|
|
|-
| BnaA07g34770D
| TN
|
|
| BnaC03g39840.1D2
| N
| BnaC07g29210.1T
| NL
| Bra023648
| TN
|
|
|
|
|-
| BnaA07g35000D
| TNL
|
|
| BnaC03g40440.1D2
| N
| BnaC07g29250.1T
| NL
| Bra023649
| TN
|
|
|
|
|-
| BnaA07g38520D
| TN
|
|
| BnaC03g42310.1D2
| CNL
| BnaC07g29270.1T
| NL
| Bra023670
| TNL
|
|
|
|
|-
| BnaA08g02210D
| CN
|
|
| BnaC03g56130.1D2
| N
| BnaC08g08280.1T
| TN
| Bra023671
| TNL
|
|
|
|
|-
| BnaA08g09210D
| TNL
|
|
| BnaC03g56140.1D2
| NL
| BnaC08g08330.1T
| TN
| Bra023710
| TN
|
|
|
|
|-
| BnaA08g09220D
| TNL
|
|
| BnaC03g56160.1D2
| N
| BnaC08g15060.1T
| N
| Bra024651
| TNL
|
|
|
|
|-
| BnaA08g10100D
| TNL
|
|
| BnaC03g56180.1D2
| TNL
| BnaC08g15070.1T
| N
| Bra024652
| TNL
|
|
|
|
|-
| BnaA08g11840D
| RN
|
|
| BnaC03g57380.1D2
| NL
| BnaC08g15080.1T
| CN
| Bra025290
| Other
|
|
|
|
|-
| BnaA08g14760D
| TNL
|
|
| BnaC03g57400.1D2
| TN
| BnaC08g24020.1T
| NL
| Bra025467
| TN
|
|
|
|
|-
| BnaA08g15160D
| TNL
|
|
| BnaC03g57420.1D2
| TNL
| BnaC08g29100.1T
| Other
| Bra025493
| Other
|
|
|
|
|-
| BnaA08g15180D
| TNL
|
|
| BnaC03g57430.1D2
| NL
| BnaC08g35830.1T
| N
| Bra025639
| TNL
|
|
|
|
|-
| BnaA08g15560D
| TNL
|
|
| BnaC03g60240.1D2
| N
| BnaC09g13610.1T
| CN
| Bra025956
| N
|
|
|
|
|-
| BnaA08g16300D
| TNL
|
|
| BnaC03g62040.1D2
| CN
| BnaC09g13670.1T
| CN
| Bra026094
| CNL
|
|
|
|
|-
| BnaA08g20150D
| TN
|
|
| BnaC03g62050.1D2
| N
| BnaC09g13690.1T
| N
| Bra026368
| CN
|
|
|
|
|-
| BnaA08g20170D
| TN
|
|
| BnaC04g09490.1D2
| CN
| BnaC09g15120.1T
| N
| Bra026682
| CNL
|
|
|
|
|-
| BnaA08g23030D
| TNL
|
|
| BnaC04g29920.1D2
| N
| BnaC09g15130.1T
| CN
| Bra026923
| N
|
|
|
|
|-
| BnaA08g24860D
| NL
|
|
| BnaC05g18690.1D2
| TN
| BnaC09g15470.1T
| N
| Bra026924
| N
|
|
|
|
|-
| BnaA08g26370D
| CN
|
|
| BnaC05g18710.1D2
| TNL
| BnaC09g15490.1T
| NL
| Bra026977
| CNL
|
|
|
|
|-
| BnaA08g26380D
| N
|
|
| BnaC05g34670.1D2
| CN
| BnaC09g15530.1T
| TNL
| Bra026978
| NL
|
|
|
|
|-
| BnaA08g26400D
| CN
|
|
| BnaC05g34680.1D2
| N
| BnaC09g15540.1T
| TNL
| Bra026979
| CNL
|
|
|
|
|-
| BnaA08g26410D
| NL
|
|
| BnaC06g04440.1D2
| N
| BnaC09g15570.1T
| NL
| Bra026985
| NL
|
|
|
|
|-
| BnaA09g02670D
| N
|
|
| BnaC06g20380.1D2
| TN
| BnaC09g15580.1T
| N
| Bra027097
| CNL
|
|
|
|
|-
| BnaA09g07530D
| N
|
|
| BnaC06g28990.1D2
| TN
| BnaC09g15620.1T
| N
| Bra027122
| NL
|
|
|
|
|-
| BnaA09g07700D
| Other
|
|
| BnaC06g34410.1D2
| NL
| BnaC09g17330.1T
| N
| Bra027332
| CNL
|
|
|
|
|-
| BnaA09g10520D
| CNL
|
|
| BnaC07g01710.1D2
| N
| BnaC09g17370.1T
| TNL
| Bra027333
| N
|
|
|
|
|-
| BnaA09g11190D
| TNL
|
|
| BnaC07g11660.1D2
| N
| BnaC09g24150.1T
| NL
| Bra027510
| TNL
|
|
|
|
|-
| BnaA09g11200D
| N
|
|
| BnaC07g13300.1D2
| Other
| BnaC09g26800.1T
| TN
| Bra027595
| TNL
|
|
|
|
|-
| BnaA09g11650D
| TNL
|
|
| BnaC07g14020.1D2
| RN
| BnaC09g31210.1T
| N
| Bra027598
| Other
|
|
|
|
|-
| BnaA09g11730D
| TNL
|
|
| BnaC07g15020.1D2
| NL
| BnaC09g31690.1T
| N
| Bra027599
| TNL
|
|
|
|
|-
| BnaA09g11740D
| Other
|
|
| BnaC07g15030.1D2
| Other
| BnaC09g33520.1T
| Other
| Bra027660
| Other
|
|
|
|
|-
| BnaA09g11760D
| TNL
|
|
| BnaC07g20530.1D2
| Other
| BnaC09g39090.1T
| CN
| Bra027772
| TNL
|
|
|
|
|-
| BnaA09g13850D
| CNL
|
|
| BnaC07g20550.1D2
| Other
| BnaC09g41850.1T
| TNL
| Bra027774
| TN
|
|
|
|
|-
| BnaA09g14320D
| TNL
|
|
| BnaC07g20570.1D2
| RN
| BnaC09g48550.1T
| RN
| Bra027775
| TNL
|
|
|
|
|-
| BnaA09g14420D
| N
|
|
| BnaC07g20580.1D2
| Other
| BnaU01g00960.1T
| N
| Bra027778
| TNL
|
|
|
|
|-
| BnaA09g14560D
| N
|
|
| BnaC07g22610.1D2
| CN
| BnaU01g04230.1T
| N
| Bra027779
| TNL
|
|
|
|
|-
| BnaA09g14680D
| N
|
|
| BnaC07g31040.1D2
| NL
|
|
| Bra027780
| TNL
|
|
|
|
|-
| BnaA09g16680D
| TNL
|
|
| BnaC07g31050.1D2
| TNL
|
|
| Bra027790
| TNL
|
|
|
|
|-
| BnaA09g17850D
| Other
|
|
| BnaC07g31080.1D2
| NL
|
|
| Bra027791
| TNL
|
|
|
|
|-
| BnaA09g18010D
| TN
|
|
| BnaC07g31090.1D2
| N
|
|
| Bra027834
| N
|
|
|
|
|-
| BnaA09g18030D
| TNL
|
|
| BnaC07g31110.1D2
| N
|
|
| Bra027843
| N
|
|
|
|
|-
| BnaA09g20940D
| NL
|
|
| BnaC07g32990.1D2
| T2N
|
|
| Bra027866
| CN
|
|
|
|
|-
| BnaA09g21200D
| NL
|
|
| BnaC07g35090.1D2
| NL
|
|
| Bra028499
| TNL
|
|
|
|
|-
| BnaA09g21220D
| TNL
|
|
| BnaC07g39890.1D2
| NL
|
|
| Bra028500
| TNL
|
|
|
|
|-
| BnaA09g29600D
| TN
|
|
| BnaC07g39910.1D2
| TNL
|
|
| Bra029405
| CN
|
|
|
|
|-
| BnaA09g29610D
| TNL
|
|
| BnaC08g17790.1D2
| N
|
|
| Bra029431
| TNL
|
|
|
|
|-
| BnaA09g31620D
| CN
|
|
| BnaC08g19640.1D2
| CN
|
|
| Bra029432
| NL
|
|
|
|
|-
| BnaA09g31990D
| TNL
|
|
| BnaC08g24510.1D2
| N
|
|
| Bra029454
| NL
|
|
|
|
|-
| BnaA09g32080D
| TNL
|
|
| BnaC08g33210.1D2
| N
|
|
| Bra030778
| CNL
|
|
|
|
|-
| BnaA09g32090D
| Other
|
|
| BnaC09g07280.1D2
| N
|
|
| Bra030779
| CNL
|
|
|
|
|-
| BnaA09g44880D
| N
|
|
| BnaC09g07460.1D2
| RN
|
|
| Bra030994
| TN
|
|
|
|
|-
| BnaA09g44890D
| TNL
|
|
| BnaC09g07480.1D2
| Other
|
|
| Bra030995
| TN
|
|
|
|
|-
| BnaA09g44910D
| N
|
|
| BnaC09g14090.1D2
| CN
|
|
| Bra030997
| Other
|
|
|
|
|-
| BnaA09g44930D
| TN
|
|
| BnaC09g16540.1D2
| N
|
|
| Bra030998
| Other
|
|
|
|
|-
| BnaA09g44940D
| TN
|
|
| BnaC09g17130.1D2
| N
|
|
| Bra031482
| CNL
|
|
|
|
|-
| BnaA09g46490D
| N
|
|
| BnaC09g17150.1D2
| N
|
|
| Bra032045
| TNL
|
|
|
|
|-
| BnaA09g47220D
| CNL
|
|
| BnaC09g17190.1D2
| TNL
|
|
| Bra032996
| TN
|
|
|
|
|-
| BnaA09g47240D
| CNL
|
|
| BnaC09g17200.1D2
| TN
|
|
| Bra033939
| TN
|
|
|
|
|-
| BnaA09g47300D
| NL
|
|
| BnaC09g17220.1D2
| NL
|
|
| Bra034079
| TNL
|
|
|
|
|-
| BnaA09g53220D
| NL
|
|
| BnaC09g17240.1D2
| NL
|
|
| Bra034556
| RN
|
|
|
|
|-
| BnaA10g04980D
| CN
|
|
| BnaC09g18750.1D2
| N
|
|
| Bra034631
| CNL
|
|
|
|
|-
| BnaA10g10380D
| N
|
|
| BnaC09g18770.1D2
| TNL
|
|
| Bra035103
| TN
|
|
|
|
|-
| BnaA10g13140D
| CN
|
|
| BnaC09g21340.1D2
| NL
|
|
| Bra035126
| TNL
|
|
|
|
|-
| BnaA10g13740D
| CN
|
|
| BnaC09g21890.1D2
| N
|
|
| Bra035424
| Other
|
|
|
|
|-
| BnaA10g16870D
| TNL
|
|
| BnaC09g35490.1D2
| TN
|
|
| Bra036019
| TNL
|
|
|
|
|-
| BnaA10g21210D
| N
|
|
| BnaC09g45980.1D2
| RN
|
|
| Bra036045
| CN
|
|
|
|
|-
| BnaA10g24700D
| TN
|
|
| BnaU01g00650.1D2
| Other
|
|
| Bra036053
| N
|
|
|
|
|-
| BnaA10g25550D
| RN
|
|
| BnaU01g03730.1D2
| N
|
|
| Bra036054
| CN
|
|
|
|
|-
| BnaAnng03870D
| CN
|
|
| BnaU01g12500.1D2
| N
|
|
| Bra036206
| N
|
|
|
|
|-
| BnaAnng08730D
| TNL
|
|
| BnaU01g22180.1D2
| N
|
|
| Bra036413
| TNL
|
|
|
|
|-
| BnaAnng14860D
| TNL
|
|
| BnaU01g22190.1D2
| N
|
|
| Bra036417
| Other
|
|
|
|
|-
| BnaAnng15960D
| TN
|
|
|
|
|
|
| Bra036432
| TN
|
|
|
|
|-
| BnaAnng18140D
| TN
|
|
|
|
|
|
| Bra036790
| Other
|
|
|
|
|-
| BnaAnng18220D
| CNL
|
|
|
|
|
|
| Bra036791
| TNL
|
|
|
|
|-
| BnaAnng20930D
| TNL
|
|
|
|
|
|
| Bra036799
| TNL
|
|
|
|
|-
| BnaAnng21180D
| TN
|
|
|
|
|
|
| Bra036845
| CN
|
|
|
|
|-
| BnaAnng27760D
| TN
|
|
|
|
|
|
| Bra036995
| CNL
|
|
|
|
|-
| BnaAnng28610D
| N
|
|
|
|
|
|
| Bra037123
| N
|
|
|
|
|-
| BnaAnng30420D
| CN
|
|
|
|
|
|
| Bra037139
| Other
|
|
|
|
|-
| BnaC01g04860D
| RN
|
|
|
|
|
|
| Bra037448
| CN
|
|
|
|
|-
| BnaC01g04900D
| N
|
|
|
|
|
|
| Bra037451
| CN
|
|
|
|
|-
| BnaC01g11830D
| TNL
|
|
|
|
|
|
| Bra037453
| Other
|
|
|
|
|-
| BnaC01g11870D
| Other
|
|
|
|
|
|
| Bra038872
| TNL
|
|
|
|
|-
| BnaC01g18040D
| NL
|
|
|
|
|
|
| Bra039560
| Other
|
|
|
|
|-
| BnaC01g19360D
| N
|
|
|
|
|
|
| Bra039798
| TNL
|
|
|
|
|-
| BnaC01g24770D
| CN
|
|
|
|
|
|
| Bra040208
| N
|
|
|
|
|-
| BnaC01g24790D
| N
|
|
|
|
|
|
| Bra040210
| TN
|
|
|
|
|-
| BnaC01g27870D
| CN
|
|
|
|
|
|
| Bra040841
| CN
|
|
|
|
|-
| BnaC01g27900D
| N
|
|
|
|
|
|
| Bra040843
| N
|
|
|
|
|-
| BnaC01g28360D
| Other
|
|
|
|
|
|
| Bra040891
| CN
|
|
|
|
|-
| BnaC01g29260D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g31430D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g35850D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g39050D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g40270D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g40280D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g40310D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g40460D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC01g40930D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g03820D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g07390D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g07560D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g07600D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g07630D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g07660D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g07680D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g08020D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g08030D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g08220D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g12880D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g16530D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g18370D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g21630D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g21650D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g21660D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g26460D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g32310D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g32370D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g32780D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g38690D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g46990D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g47150D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g47230D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g47330D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g47380D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g47400D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g47450D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g47510D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC02g48740D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g04690D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g05380D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g08650D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g08660D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g08900D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g08920D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g12220D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g15650D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g18920D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g29290D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g34840D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g44460D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g44590D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g45320D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g45730D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g47360D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g47400D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g56070D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g59890D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g61670D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g61680D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g61980D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g61990D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g62010D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g62020D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g62030D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g63230D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g63240D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g63280D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g63290D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g64750D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g68520D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g69970D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC03g76220D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g08930D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g12970D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g15810D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g15820D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g18730D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g20030D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g20050D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g20460D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g20540D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g27190D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g31910D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g32140D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC04g32150D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g09540D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g09570D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g09600D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g11810D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g11820D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g12120D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g19440D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g19500D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g39120D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g39130D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g41750D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g47400D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g47420D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC05g51110D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g03300D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g03340D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g03790D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g03820D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g03840D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g04820D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g05500D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g13520D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g13540D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g23910D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g23920D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g23930D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g23940D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g23970D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g23980D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g24000D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g24010D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g25350D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g25360D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g25370D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g27830D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g34000D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g34010D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g34030D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g34040D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g34060D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g34070D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g34080D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g39660D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g39930D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g40800D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC06g41410D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g02790D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g14550D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g16470D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g18270D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g18280D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g18310D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g19200D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g24530D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g24570D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g24600D
| RN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g24610D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g26860D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g34000D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g35890D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g35900D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g35920D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g35930D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g35950D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g35960D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g37000D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g37010D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g38210D
| T2N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g38450D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g40790D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g44370D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g46000D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC07g46010D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g11460D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g11510D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g11590D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g15420D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g15510D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g15930D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g17450D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g20450D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g21550D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g22370D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g22900D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g28290D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g37590D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g37610D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g37620D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g37650D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g37660D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g40550D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g40560D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g41330D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g41340D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g41420D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g41430D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g41710D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC08g48650D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g02130D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g06020D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g07440D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g07660D
| RN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g07690D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g10760D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g10770D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g11490D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g11510D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g11530D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g11620D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g11670D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g12560D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g12570D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g12630D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g12650D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g12670D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g12760D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g13250D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g13260D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g14870D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g15010D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g15110D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g17030D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g18870D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g18900D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g18950D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g18980D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g19000D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g19010D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g19040D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g19160D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g19380D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g19410D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g19420D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g20620D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g20640D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g20650D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g23580D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g35960D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g36260D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g39430D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g39460D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g39890D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g40030D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g44520D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g49630D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g50760D
| RN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g51410D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g51450D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g51750D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaC09g51800D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng06850D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng06890D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng11240D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng14160D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng20410D
| CN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng24770D
| TN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng26470D
| RN
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng30760D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng39060D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng41120D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng49910D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng50000D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng50410D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng50420D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng57760D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng57770D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng59870D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng62690D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng63440D
| N
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng64090D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng66530D
| Other
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaCnng76010D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaUnng00420D
| CNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaUnng00480D
| TNL
|
|
|
|
|
|
|
|
|
|
|
|
|-
| BnaUnng00640D
| NL
|
|
|
|
|
|
|
|
|
|
|
|
|}

Repeats Tables

2018-02-08T03:02:30Z

Philippbayer: Created page with "Supplementary Table S1: Repeats and count of R-gene domains contained therein {| class="wikitable" ! Repeat name ! Species ! Year last updated in Repbase ! PF00931 NB-ARC dom..."

Philipp Bayer

2017-10-07T01:31:51Z

Philippbayer: /* Academic history */

=== Research interests ===

Pan-genomics, Graph databases & knowledge networks, genotyping by sequencing, genome assembly assessment, genome assembly improvement

I started to focus on bioinformatics during my BSc Biology in Germany, where I worked on the evolution of HIV/SIV and heat shock resistance in sea-grasses (''Zostera marina'' and ''Posidonia oceanica''). I then came to Australia to work on my IT skills, which culminated in a Master IT with a short stint doing SQL consulting for a web design company. At the same time I co-founded and worked on openSNP.org, an open repository for human genotyping datasets from customers of direct-to-consumer genotyping companies like 23andMe. I did my PhD at the University of Queensland in the Edwards group developing a novel low-coverage genotyping by sequencing pipeline, and used the pipeline to assess genome assembly quality in ''Brassica napus'' and ''Cicer arietinum''.

I now work as a post-doc in the same group focusing on knowledge networks, the assembly, annotation and analysis of pan-genomes of several crop species (currently mostly legumes and Brassicas), genome-wide association studies, population genetics, and more.

I am also involved in organising and teaching the Bioinformatics courses for Masters students and am an active poster on biostars.org. I'm also a certified and active Software and Data Carpentry instructor and have set up as well as taught at several workshops.

==Academic history==
{| class="wikitable"
! Authors || Title || Publication || Volume || Number || Pages || Year || Publisher
|-
| Hane, James K; Ming, Yao; Kamphuis, Lars G; Nelson, Matthew N; Garg, Gagan; Atkins, Craig A; Bayer, Philipp E; Bravo, Armando; Bringans, Scott; Cannon, Steven; || A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution || Plant biotechnology journal || 15 || 3 || 318-330 || 2017 ||
|-
| Kaur, Parwinder; Bayer, Philipp E; Milec, Zbyněk; Vrána, Jan; Yuan, Yuxuan; Appels, Rudi; Edwards, David; Batley, Jacqueline; Nichols, Phillip; Erskine, William; || An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance || Plant biotechnology journal || || || || 2017 ||
|-
| Montenegro, Juan D; Golicz, Agnieszka A; Bayer, Philipp E; Hurgobin, Bhavna; Lee, HueyTyng; Chan, Chon‐Kit Kenneth; Visendi, Paul; Lai, Kaitao; Doležel, Jaroslav; Batley, Jacqueline; || The pangenome of hexaploid bread wheat || The Plant Journal || 90 || 5 || 1007-1013 || 2017 ||
|-
| Yuan, Yuxuan; Bayer, Philipp E; Batley, Jacqueline; Edwards, David; || Improvements in genomic technologies: application to crop genomics || Trends in Biotechnology || || || || 2017 || Elsevier Current Trends
|-
| Bayer, Philipp E; Hurgobin, Bhavna; Golicz, Agnieszka A; Chan, Chon‐Kit Kenneth; Yuan, Yuxuan; Lee, HueyTyng; Renton, Michael; Meng, Jinling; Li, Ruiyuan; Long, Yan; || Assembly and comparison of two closely related Brassica napus genomes || Plant biotechnology journal || || || || 2017 ||
|-
| Yuan, Yuxuan; Bayer, Philipp E; Lee, Huey-Tyng; Edwards, David; || runBNG: a software package for BioNano genomic analysis on the command line || Bioinformatics || 33 || 19 || 3107-3109 || 2017 || Oxford University Press
|-
| Yuan, Yuxuan; Bayer, Philipp E; Scheben, Armin; Chan, Chon-Kit Kenneth; Edwards, David; || BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data || BMC bioinformatics || 18 || 1 || 323 || 2017 || BioMed Central
|-
| Kaur, Parwinder; Appels, Rudi; Bayer, Philipp E; Keeble-Gagnere, Gabriel; Wang, Jiankang; Hirakawa, Hideki; Shirasawa, Kenta; Vercoe, Philip; Stefanova, Katia; Durmic, Zoey; || Climate clever clovers: New paradigm to reduce the environmental footprint of ruminants by breeding low methanogenic forages utilizing haplotype variation || Frontiers in Plant Science || 8 || || || 2017 || Frontiers Media SA
|-
| Bayer, Philipp Emanuel; || Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies || Plant Bioinformatics: Methods and Protocols || || || 285-292 || 2016 || Springer New York
|-
| Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel AP; Chèvre, Anne-Marie; Batley, Jacqueline; || Centromere locations in Brassica A and C genomes revealed through half-tetrad analysis || Genetics || 202 || 2 || 513-523 || 2016 || Genetics
|-
| Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; || An efficient approach to BAC based assembly of complex genomes || Plant methods || 12 || 1 || 2 || 2016 || BioMed Central
|-
| Bayer, Philipp Emanuel; || Genomics of Salinity || Plant Genomics and Climate Change || || || 179-194 || 2016 || Springer New York
|-
| Lee, HueyTyng; Golicz, Agnieszka A; Bayer, Philipp; Jiao, Yuannian; Tang, Haibao; Paterson, Andrew H; Sablok, Gaurav; Krishnaraj, Rahul R; Chan, Chon-Kit Kenneth; Batley, Jacqueline; || The genome of a southern hemisphere seagrass species (Zostera muelleri) || Plant physiology || || || pp. 00868.2016 || 2016 || American Society of Plant Biologists
|-
| Barash, Mark; Bayer, Philipp E; van Daal, Angela; || Candidate gene scan for Single Nucleotide Polymorphisms involved in the determination of normal variability in human craniofacial morphology || bioRxiv || || || 60814 || 2016 || Cold Spring Harbor Labs Journals
|-
| Golicz, Agnieszka A; Bayer, Philipp E; Barker, Guy C; Edger, Patrick P; Kim, HyeRan; Martinez, Paula A; Chan, Chon Kit Kenneth; Severn-Ellis, Anita; McCombie, W Richard; Parkin, Isobel AP; || The pangenome of an agronomically important crop plant Brassica oleracea || Nature communications || 7 || || 13390 || 2016 || Nature Publishing Group
|-
| Gacek, Katarzyna; Bayer, Philipp E; Bartkowiak-Broda, Iwona; Szala, Laurencja; Bocianowski, Jan; Edwards, David; Batley, Jacqueline; || Genome-wide association study of genetic control of seed fatty acid biosynthesis in Brassica napus || Frontiers in plant science || 7 || || || 2016 || Frontiers Media SA
|-
| Lee, HueyTyng; Golicz, Agnieszka A; Bayer, Philipp E; Jiao, Yuannian; Tang, Haibao; Paterson, Andrew H; Sablok, Gaurav; Krishnaraj, Rahul R; Chan, Chon-Kit Kenneth; Batley, Jacqueline; || The Genome of a Southern Hemisphere Seagrass || || || || || 2016 ||
|-
| Lai, Kaitao; Lorenc, Michał T; Lee, Hong Ching; Berkman, Paul J; Bayer, Philipp Emanuel; Visendi, Paul; Ruperao, Pradeep; Fitzgerald, Timothy L; Zander, Manuel; Chan, Chon‐Kit Kenneth; || Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat || Plant biotechnology journal || 13 || 1 || 97-104 || 2015 ||
|-
| Golicz, Agnieszka A; Bayer, Philipp E; Edwards, David; || Skim-based genotyping by sequencing || Plant Genotyping: Methods and Protocols || || || 257-270 || 2015 || Springer New York
|-
| Bayer, Philipp E; Ruperao, Pradeep; Mason, Annaliese S; Stiller, Jiri; Chan, Chon-Kit Kenneth; Hayashi, Satomi; Long, Yan; Meng, Jinling; Sutton, Tim; Visendi, Paul; || High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus || Theoretical and Applied Genetics || 128 || 6 || 1039-1047 || 2015 || Springer Berlin Heidelberg
|-
| Greshake, Bastian; Bayer, Philipp; Rausch, Helge; Reda, Julia; || openSNP–personal genomics and the public domain || F1000Research || 4 || || || 2015 ||
|-
| Greshake, Bastian; Bayer, Philipp E; Rausch, Helge; Reda, Julia; || openSNP–a crowdsourced web resource for personal genomics || PLoS One || 9 || 3 || e89204 || 2014 || Public Library of Science
|-
| Mason, Annaliese S; Batley, Jacqueline; Bayer, Philipp Emanuel; Hayward, Alice; Cowling, Wallace A; Nelson, Matthew N; || High‐resolution molecular karyotyping uncovers pairing between ancestrally related Brassica chromosomes || New Phytologist || 202 || 3 || 964-974 || 2014 || Wiley Online Library
|-
| Chalhoub, Boulos; Denoeud, France; Liu, Shengyi; Parkin, Isobel AP; Tang, Haibao; Wang, Xiyin; Chiquet, Julien; Belcram, Harry; Tong, Chaobo; Samans, Birgit; || Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome || Science || 345 || 6199 || 950-953 || 2014 || American Association for the Advancement of Science
|-
| Dattolo, Emanuela; Gu, Jenny; Bayer, Philipp E; Mazzuca, Silvia; Serra, Ilia A; Spadafora, Antonia; Bernardo, Letizia; Natali, Lucia; Cavallini, Andrea; Procaccini, Gabriele; || Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles || Frontiers in plant science || 4 || || || 2013 || Frontiers Media SA
|-
| Golicz, Agnieszka A; Bayer, Philipp E; Martinez, Paula A; Lai, Kaitao; Lorenc, Michal T; Alamery, Salman; Hayward, A; Tollenaere, Reece; Batley, Jacqueline; Edwards, David; || Characterising diversity in the Brassica genomes || VI International Symposium on Brassicas and XVIII Crucifer Genetics Workshop 1005 || || || 33-47 || 2012 ||
|-
| Alamery, Salman; Tirnaz, Soodeh; Bayer, Philipp; Tollenaere, Reece; Chalhoub, Boulos; Edwards, David; Batley, Jacqueline; || Genome wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus || || || || || ||
|}

=== Contact ===

University of Western Australia

Crawley, Australia

Tel: +61 (0)8 6488 4311

email: philipp.bayer@uwa.edu.au

Twitter: [http://twitter.com/philippbayer @PhilippBayer]

Homepage: http://philipp-bayer.net

GitHub: https://github.com/philippbayer/