G.barbadense ZJU v1.1 Genome (26 chrom. and 11,324 scaffolds)

Human-Readable NameG.barbadense ZJU v1.1 Genome (26 chrom. and 11,324 scaffolds)
Database Path/mainlab/web/temp/db/cottongen/G.barbadense_ZJU_v1.1.genome.fas
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for G.barbadense_ZJU_v1.1
RegEx/^(\S+).*/
Link-out Typejbrowse

-- G.barbadense ZJU v1.1 CDs (75,071)

Human-Readable Name-- G.barbadense ZJU v1.1 CDs (75,071)
Database Path/mainlab/web/temp/db/cottongen/G.barbadense_ZJU_v1.1.cds.fas
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

-- G.barbadense ZJU v1.1 proteins (75,071)

Human-Readable Name-- G.barbadense ZJU v1.1 proteins (75,071)
Database Path/mainlab/web/temp/db/cottongen/G.barbadense_ZJU_v1.1.pep.fas
Database Typeprotein
FASTA Header Formatdefault
External DatabaseJBrowse for G.barbadense_ZJU_v1.1
RegEx/^(\S+).*/
Link-out Typejbrowse

-- G.hirsutum ZJU v2.1 proteins (72,761)

Human-Readable Name-- G.hirsutum ZJU v2.1 proteins (72,761)
Database Path/mainlab/web/temp/db/cottongen/G.hirsutum_ZJU_v2.1.pep.fas
Database Typeprotein
FASTA Header Formatdefault
External DatabaseJBrowse for G.hirsutum_ZJU_v2.1
RegEx/^(\S+).*/
Link-out Typejbrowse

-- G.hirsutum ZJU v2.1 CDs (72,761)

Human-Readable Name-- G.hirsutum ZJU v2.1 CDs (72,761)
Database Path/mainlab/web/temp/db/cottongen/G.hirsutum_ZJU_v2.1.cds.fas
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typejbrowse

G.hirsutum ZJU v2.1 Genome (26 chrom. and 12,072 scaffolds)

Human-Readable NameG.hirsutum ZJU v2.1 Genome (26 chrom. and 12,072 scaffolds)
Database Path/mainlab/web/temp/db/cottongen/G.hirsutum_ZJU_v2.1.genome.fas
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for G.hirsutum_ZJU_v2.1
RegEx/^(\S+).*/
Link-out Typejbrowse

Genomes of AD2 Hai7124 & improved AD1 TM-1 published (3/18/19)

New genome data of  AD2 Hai7124 and an improved assembly and annotation of AD1 TM-1, contributed by Zhejiang University, China, Published in Nature Genetics on 18 March 2019. Data available at CottonGen Download, CottonGen JBrowse and CottonGen BLAST.

About the assembly

We adopted a hierarchical approach to perform the chromosome-scale assembly. The 800 Gb high-quality data (>330× genome coverage) generated from a series of PCR-free libraries, mate paired-end read (MP) libraries and 10× GemCode library were assembled using the software package DenovoMAGIC3 (NRGene, Nes Ziona, Israel). Initially, the assembly of G. barbadense cv. Hai7124 that captured 2.23 Gb was generated. Thereafter, the initial scaffolds were further corrected and merged using optical mapping data (BioNano Genomics). Finally, we used three-dimensional proxim... [more]

Resource Titles: 
Assembly
Genes
Downloads
Resource Blocks: 

The chromosomes (pseudomolecules) and scaffolds for G. barbadense 'Hai7124' genome. These files belong to the ZJU assembly v1.1

Chromosomes & scaffolds (FASTA format) G.barbadense_ZJU-AD2_assembly_v1.1.fasta.gz

The predicted gene model, their alignments and proteins for G. barbadense 'Hai7124' genome. These files belong to the ZJU assembly v1.1 & annotation a1

Predicted gene models with exons (GFF3 format) G.barbadense_ZJU-AD2_v1.1_a1.0_functional.gff.gz
Coding sequences, CDS (FASTA format) G.barbadense_ZJU-AD2_v1.1_a1.0_cds.fasta.gz
Protein sequences (FASTA format) G.barbadense_ZJU-AD2_v1.1_a1.0_pep.fasta.gz

All annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.  Alternatively, you can use the FTP repository for bulk download.

About the assembly

An improved de novo assembled genome of Texas Marker-1 (TM-1) was produced by using the software package DenovoMAGIC3 (NRGene, Nes Ziona, Israel).  Thereafter, the initial scaffolds were further corrected and merged using optical mapping data (BioNano Genomics).  Finally, three-dimensional proximity information obtained by Hi-C and our updated ultra-dense genetic map with single-nucleotide polymorphisms (SNPs) was used to check, order and orient these super-scaffolds. 

... [more]
Resource Titles: 
Assembly
Genes
Downloads
Resource Blocks: 

The chromosomes (pseudomolecules) and scaffolds for G. hrisutum 'TM-1' genome. These files belong to the ZJU Improved Assembly v2.1

Chromosomes & scaffolds (FASTA format) G.hirsutum_ZJU-AD1_assembly_v2.1.fasta.gz

The predicted gene model, their alignments and proteins for G. hirsutum 'TM-1' genome. These files belong to the ZJU Improved Assembly v2.1 & Annotation a1.0

Predicted gene models with exons (GFF3 format) G.hirsutum_ZJU-AD1_v2.1_a1.0_functional.gff.gz
Coding sequences, CDS (FASTA format) G.hirsutum_ZJU-AD1_v2.1_a1.0_cds.fasta.gz
Protein sequences (FASTA format) G.hirsutum_ZJU-AD1_v2.1_a1.0_pep.fasta.gz

All annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.  Alternatively, you can use the FTP repository for bulk download.