Project Information

SUMMARY

 

We recently initiated a large genome resequencing project (led by Josh Udall, with Daojun Yuan and Thiru Ramaraj) funded by the National Science Foundation Plant Genome Program.  In this project, we are addressing biological questions of broad relevance to polyploid plant genomes, while at the same time generating detailed information on genomic and phylogeographic patterns of diversity in wild and domesticated cotton, advancing our capacity to utilize an expanded gene pool for cotton improvement.

  • Yuan D, Grover CE, Hu G, Pan M, Miller ER, Conover JL, Hunt SP, Udall JA, Wendel JF. Parallel and intertwining threads of domestication in allopolyploid cotton. Adv. Sci. 2021 Mar 15; 2003634:1-17.
The two cultivated allopolyploid cottons, Gossypium hirsutum and G. barbadense, represent a remarkable example of parallel independent domestication, both involving dramatic morphological transformations under selection from wild perennial plants to annualized row crops. We combine deep resequencing of 643 newly sampled accessions spanning the wild-todomesticated continuum of both species, and their allopolyploid relatives, with existing data to ... [more]
Project Information

A comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV).

Cotton Cluster File Request

Name: 
Ezekiel Visconti
Email Address: 
Storkower Strasse 65
Email Address: 
Storkower Strasse 65
Organization: 
Ezekiel Ltd
Acknowledgement: 
0
Acknowledgement4: 
0

G. armourianum D21 ISU v1.0 (13 chrom. and 1,349 scaffolds)

Human-Readable NameG. armourianum D21 ISU v1.0 (13 chrom. and 1,349 scaffolds)
Database Path/mainlab/web/temp/db/cottongen/G.armourianum_D2-1_genome_ISU_v1_genome.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for G.armourianum_D2-1_v1
RegEx/^(\S+).*/
Link-out Typejbrowse

-- G. armourianum D21 ISU v1.0 CDs (25,464)

Human-Readable Name-- G. armourianum D21 ISU v1.0 CDs (25,464)
Database Path/mainlab/web/temp/db/cottongen/G.armourianum_D2-1_genome_ISU_v1.transcripts.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

-- G. armourianum D21 ISU v1.0 proteins (25,464)

Human-Readable Name-- G. armourianum D21 ISU v1.0 proteins (25,464)
Database Path/mainlab/web/temp/db/cottongen/G.armourianum_D2-1_genome_ISU_v1.pep.faa
Database Typeprotein
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

G. harknessii D22 ISU v1.0 Genome (13 chrom. and 2,572 scaffolds)

Human-Readable NameG. harknessii D22 ISU v1.0 Genome (13 chrom. and 2,572 scaffolds)
Database Path/mainlab/web/temp/db/cottongen/G.harknessii_D22_ISU_v1.0_genome.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for D22_ISU_v1.0
RegEx/^(\S+).*/
Link-out Typejbrowse

-- G. harknessii D22 ISU v1.0 CDs (31,153)

Human-Readable Name-- G. harknessii D22 ISU v1.0 CDs (31,153)
Database Path/mainlab/web/temp/db/cottongen/G.harknessii_D22_ISU_v1.0.transcripts.fas
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

-- G. harknessii D22 ISU v1.0 proteins (31,153)

Human-Readable Name-- G. harknessii D22 ISU v1.0 proteins (31,153)
Database Path/mainlab/web/temp/db/cottongen/G.harknessii_D22_ISU_v1.0.pep.faa
Database Typeprotein
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink