Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1

Analysis NameGossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1
MethodHiSeq and NovaSeq and PacBio SEQUEL and RSII platforms
Source (assembly v2.0 annotation a2.1)
Date performed2020-04-22

Please Note: This genome assembly is made available through a "Reserved Analyses" restriction. Please see the Restrictions on Dataset Usage for further details.



The v2.1 annotation release is on genome assembly v2.0, a high-quality version of the Gossypium hirsutum genome sequenced from high-quality large-molecule genomic DNA of G. hirsutum L. acc. TM-1, the same genotype that was used to construct the physical map and sequence BAC ends (Saski et al. 2017). The genome was sequenced with a combination of PACBIO RSII long reads, Illumina read pairs and HiC data. An additional 110 offsprings from a TM-1 x 3-79 (Gossypium barbadense L. acc. 3-79) cross were resequenced with Illumina. The release utilized synteny from the published G. hirsutum assembly (Zhang et al. 2015) and included integration of BAC end sequences and physical maps (Saski et al. 2017) and additional screening of small repetitive scaffolds.

How was the assembly generated?

This release is a high-quality version of the Gossypium hirsutum genome. Main assembly consisted of 94.06x of PacBio coverage (8,106 bp average read size), and was assembled using MECAT and the resulting sequence was polished using QUIVER. A total of 148,239 unique, non-repetitive, non-overlapping 1 KB sequences were generated using the published NBI Gossypium hirsutum assembly and aligned to the polished G. hirsutum assembly. Scaffold breaks were identified as an abrupt change in the G. hirsutum linkage group. A total of 70 breaks were made. The resulting broken assembly was then scaffolded using 40x of HiC data using the JUICER pipeline. Small rearrangements were made using the JUICEBOX interface, and 2 additional breaks were executed on the scaffold assembly. Both the G. barbadense and G. hirsutum were scaffolded using JUICER at the same time. When G. barbadense and G. hirsutum were compared to one another it was noted that the chromosome arms were highly syntenic, however in the region around the centromere there were discrepancies between the two assemblies. These rearrangements were corrected in both the G. barbadense and G. hirsutum by leveraging the contiguity of G. barbadense relative to G. hirsutum. A set of 5,275 finished clones (474.3 Mb) was used to patch remaining gaps in the G. hirsutum assembly. A total of 626 gaps were patched resulting in 1,871,050 bp to the assembly. Scaffolds were then oriented, ordered, and assembled into 26 chromosomes. A total of 6 joins were made during this process. Care was taken to ensure that telomere was properly oriented in the chromosomes, and the resulting sequence was screened for retained vector and/or contaminants.

Finally, homozygous SNPs and INDELs were corrected in the release sequence using ~50x of Illumina reads (2x150, 400bp insert).

Completeness of the euchromatic portion of the genome assembly was assessed by aligning genes from the v2.0 G. raimondii annotated genes. In the case of alternative splicing, the longest alternative splice was selected. The alignments were screened, and alignments less than 90% identity and 85% coverage were excluded. This is a routine test to determine whether we are missing significant portions of the genome. The final results are given below:

Summary of the Assembly  
Estimate of genome size (bp) 2,305,241,538
Number of scaffolds 1,025
Total length of scaffolds (Mb) 2,305.20
Scaffold N50L (Mb) 108.1
Number of contigs 6,733
Total length of contigs (Mb) and gap (%)a 2,302.3 (0.1%)
Contig N50L (Mb) 0.7839
Genome in chromosomes (%) 98.9
Number of genes 75,376
Repeat sequences (%) 73.21

 aA gap is a representation of the assembled sequence with unknown sequence information. bp, base pair; Mb, megabase pairs.

Publication: Chen et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement Nat Genet 20 April 2020.

Restrictions on Dataset Usage

Gossypium hirsutum genome v2.1 data is made available before scientific publication according to the Ft. Lauderdale Accord. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by principal investigators of a comprehensive genome analysis without the consent of project's investigators listed in Contacts below. ("Reserved Analyses"). "Reserved analyses" include the identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome- scale comparisons with other species. The embargo on publication of Reserved Analyses by researchers outside of the Gossypium hirsutum Genome Sequencing Project is expected to extend until the publication of the results of the sequencing project is accepted. Studies of any type on the reserved data sets that are not in direct competition with those planned by the principle investigators may also be undertaken after an agreement with project's principle investigators. The assembly and sequence data should not be redistributed or repackaged without permission from the project's principle investigators.

We request that potential users of this sequence assembly contact the individuals listed under Contacts with their plans to ensure that proposed usage of sequence data are not considered Reserved Analyses.


Principal Investigators:
Z. Jeffrey Chen (University of Texas at Austin) (email: zjchen@austin.utexas.edu)
Jane Grimwood (HudsonAlpha Institute for Biotechnology) (email: jgrimwood@hudsonalpha.org)



Additional information about this analysis:
Property NameValue
Short NameAD1_UTX
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/Gh_TM1_UTX_v2.1&loc=
Analysis Typewhole_genome

The chromosomes (pseudomolecules) for Gossypium hirsutum TM-1 genome. These files belong to the Phytozome Gossypium hirsutum v2.1

Chromosomes (FASTA format) G.hirsutum_UTX-TM1_v2.0.fa.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.

Functional Analysis

Functional annotation files for the Gossypium hirsutum UTX Genome v2.1 are available for download below. The Gossypium hirsutum UTX 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).


GO assignments from InterProScan Gh_TM1_UTX_v2.1_genes2GO.xlsx.gz
IPR assignments from InterProScan Gh_TM1_UTX_v2.1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Gh_TM1_UTX_v2.1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Gh_TM1_UTX_v2.1_KEGG-pathways.xlsx.gz



The predicted gene model, their alignments and proteins for Gossypium hirsutum TM-1 genome. These files belong to the Phytozome Gossypium hirsutum v2.1

Predicted gene models with exons (GFF3 format) G.hirsutum_UTX-TM1_v2.1_genes_with_exon_gff3.gz
Predicted gene models (GFF3 format) G.hirsutum_UTX-TM1_v2.1_genes_gff3.gz
CDS sequences (FASTA format) G.hirsutum_UTX-TM1_v2.1_CDS.fa.gz
Transcript sequences (FASTA format) G.hirsutum_UTX-TM1_v2.1_transcript.fa.gz
Protein sequences (FASTA format) G.hirsutum_UTX-TM1_v2.1_protein.fa.gz

Homology of the Gossypium hirsutum UTX Genome v2.1 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.hirsutum UTX Genome v2.1 proteins with NCBI nr homologs (EXCEL file) Gh_TM1_UTX_v2.1_vs_nr.xlsx.gz
G.hirsutum UTX Genome v2.1 proteins with NCBI nr (FASTA file) Gh_TM1_UTX_v2.1_vs_nr_hit.fasta.gz
G.hirsutum UTX Genome v2.1 proteins without NCBI nr (FASTA file) Gh_TM1_UTX_v2.1_vs_nr_noHit.fasta.gz
G.hirsutum UTX Genome v2.1 proteins with arabidopsis (Araport11) homologs (EXCEL file) Gh_TM1_UTX_v2.1_vs_tair.xlsx.gz
G.hirsutum UTX Genome v2.1 proteins with arabidopsis (Araport11) (FASTA file) Gh_TM1_UTX_v2.1_vs_tair_hit.fasta.gz
G.hirsutum UTX Genome v2.1 proteins without arabidopsis (Araport11) (FASTA file) Gh_TM1_UTX_v2.1_vs_tair_noHit.fasta.gz
G.hirsutum UTX Genome v2.1 proteins with SwissProt homologs (EXCEL file) Gh_TM1_UTX_v2.1_vs_swissprot.xlsx.gz
G.hirsutum UTX Genome v2.1 proteins with SwissProt (FASTA file) Gh_TM1_UTX_v2.1_vs_swissprot_hit.fasta.gz
G.hirsutum UTX Genome v2.1 proteins without SwissProt (FASTA file) Gh_TM1_UTX_v2.1_vs_swissprot_noHit.fasta.gz
G.hirsutum UTX Genome v2.1 proteins with TrEMBL homologs (EXCEL file) Gh_TM1_UTX_v2.1_vs_trembl.xlsx.gz
G.hirsutum UTX Genome v2.1 proteins with TrEMBL (FASTA file) Gh_TM1_UTX_v2.1_vs_trembl_hit.fasta.gz
G.hirsutum UTX Genome v2.1 proteins without TrEMBL (FASTA file) Gh_TM1_UTX_v2.1_vs_trembl_noHit.fasta.gz


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_UTX-AD1_SNP
CottonGen InDel markers mapped to genome G.hirsutumi_UTX-AD1_InDel
CottonGen RFLP markers mapped to genome G.hirsutumi_UTX-AD1_RFLP
CottonGen SSR markers mapped to genome G.hirsutumi_UTX-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_UTX-AD1_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.hirsutumi_UTX-AD1_G.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.hirsutumi_UTX-AD1_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.hirsutumi_UTX-AD1_g.raimondii_cottongen_reftransV1