Gossypium hirsutum (AD1) 'TM-1' genome WHU_updated v1

Overview
Analysis NameGossypium hirsutum (AD1) 'TM-1' genome WHU_updated v1
MethodUltra-depth PacBio long-reads and Hi-C technologies
SourceGhirsutum_TM-1_WHU_genome.standard
Date performed2020-04-04

About the assembly

The new assembly of Gossypium hirsutum genome (genetic standard line TM-1) was released from the Institute for Advanced Studies, Wuhan University, Wuhan, China (IAS-WHU). The assembly were sequenced using high-depth SMRT long reads resulting in 81.6-fold genome coverage (~205 Gb). The genome assembly was corrected by using accurate Illumina paired-end reads. The resulting assembled genome size was 2,290 Mb with 99.17% of all sequences anchored on 26 chromosomes (A-subgenome, 1,449 Mb; D-subgenome, 822 Mb). The N50 of the new assembled genome is 5,020 kb, with significantly fewer gaps compared with previously published genome assemblies. The new genome assembly has substantial improvements with high completeness and accuracy. In addition, the new assembly filled a lot of genome gaps existed in previous assemblies. The new assembly also showed high congruence and good collinear relationships in quantity among cotton genomes. Our continuing efforts to assemble the high-resolution and chromosome-scale G. hirsutum reference genome will further facilitate the translation of genomics to cotton breeding and genetics.

Summary of Assembly Gossypium hirsutum TM-1
Total PacBio reads (Gb)

205

Number of total contigs 1,235
N50 of contigs (kb) 5,020
Anchored and oriented contigs (Mb) 2,271
Number of total scaffolds 342
Total assembled genome size (Mb) 2,290
Percentage of anchoring and ordering (%) 99.17
Transposable elements (TEs) proportion (%) 64.06
Number of annotated protein-coding genes 74,350

Publication

Huang, G. et al., Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics. 2020. doi.org/10.1038/s41588-020-0607-4

Properties
Additional information about this analysis:
Property NameValue
Short NameAD1_WHU
Analysis Typewhole_genome
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/Gh_TM1_WHU_v1&loc=
Assembly

The chromosomes (pseudomolecules) and scaffolds for Gossypium hirsutum (AD1) 'TM1' genome. These files belong to the WHU Updated Assembly v1.0

Chromosomes & scaffolds (FASTA format) Ghirsutum_TM-1_WHU_genome.standard.fa.gz
Transposable Elements (GFF format) Ghirsutum_TM-1_WHU_transposableElements.CHRplus.gff.gz
Downloads

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.

Functional Analysis

Functional annotation files for the Gossypium hirsutum WHU Genome v1.0 are available for download below. The Gossypium hirsutum WHU Genome proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan Gh_TM1_WHU_v1_a1_genes2GO.xlsx.gz
IPR assignments from InterProScan Gh_TM1_WHU_v1_a1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Gh_TM1_WHU_v1_a1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Gh_TM1_WHU_v1_a1_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for Gossypium hirsutum (AD1) 'TM1' genome. These files belong to the WHU Assembly v1.0

Predicted gene models with exons (GFF3 format) Ghirsutum_TM-1_WHU_standard.gene.gff3.gz
Coding sequences, CDS (FASTA format) Ghirsutum_TM-1_WHU_standard.gene.cds.fa.gz
Protein sequences (FASTA format) Ghirsutum_TM-1_WHU_standard.gene.pep.fa.gz
Homology

Homology of the Gossypium hirsutum WHU Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

G.hirsutumi WHU Genome v1.0 proteins with NCBI nr homologs (EXCEL file) Gh_TM1_WHU_v1_a1_vs_nr.xlsx.gz
G.hirsutumi WHU Genome v1.0 proteins with NCBI nr (FASTA file) Gh_TM1_WHU_v1_a1_vs_nr_hit.fasta.gz
G.hirsutumi WHU Genome v1.0 proteins without NCBI nr (FASTA file) Gh_TM1_WHU_v1_a1_vs_nr_noHit.fasta.gz
G.hirsutumi WHU Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Gh_TM1_WHU_v1_a1_vs_tair.xlsx.gz
G.hirsutumi WHU Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Gh_TM1_WHU_v1_a1_vs_tair_hit.fasta.gz
G.hirsutumi WHU Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Gh_TM1_WHU_v1_a1_vs_tair_noHit.fasta.gz
G.hirsutumi WHU Genome v1.0 proteins with SwissProt homologs (EXCEL file) Gh_TM1_WHU_v1_a1_vs_swissprot.xlsx.gz
G.hirsutumi WHU Genome v1.0 proteins with SwissProt (FASTA file) Gh_TM1_WHU_v1_a1_vs_swissprot_hit.fasta.gz
G.hirsutumi WHU Genome v1.0 proteins without SwissProt (FASTA file) Gh_TM1_WHU_v1_a1_vs_swissprot_noHit.fasta.gz
G.hirsutumi WHU Genome v1.0 proteins with TrEMBL homologs (EXCEL file) Gh_TM1_WHU_v1_a1_vs_trembl.xlsx.gz
G.hirsutumi WHU Genome v1.0 proteins with TrEMBL (FASTA file) Gh_TM1_WHU_v1_a1_vs_trembl_hit.fasta.gz
G.hirsutumi WHU Genome v1.0 proteins without TrEMBL (FASTA file) Gh_TM1_WHU_v1_a1_vs_trembl_noHit.fasta.gz

 

Markers
Marker alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map marker sequences from CottonGen to the Gossypium hirsutum genome assembly. Markers required 90% identity over 97% of their length. For SSRs & RFLPs, gap size was restricted to 1000bp or less with less than 2 gaps. For dbSNPs and Indels gap size was restricted to 2bp with less than 2 gaps. The available files are in GFF3 format. Markers available in CottonGen are linked to JBrowse.
 
CottonGen SNP markers mapped to genome G.hirsutumi_WHU-AD1_SNP
CottonGen InDel markers mapped to genome G.hirsutumi_WHU-AD1_InDel
CottonGen RFLP markers mapped to genome G.hirsutumi_WHU-AD1_RFLP
CottonGen SSR markers mapped to genome G.hirsutumi_WHU-AD1_SSR

 

Transcript Alignments
Transcript alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the G. hirsutum genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.

 

G. arboreum CottonGen RefTrans v1 G.hirsutumi_WHU-AD1_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.hirsutumi_WHU-AD1_G.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.hirsutumi_WHU-AD1_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.hirsutumi_WHU-AD1_g.raimondii_cottongen_reftransV1