Gossypium hirsutum (AD1) 'TX2094' genome ISU_v2
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Overview
TX-2094 (PI 501501) is a wild accession of Gossypium hirsutum collected from the Yucatan peninsula of Mexico and maintained in the GRIN NPGS Cotton Collection (USA). Known aliases include PS-19, TEX 2094, and TX 2094 Yucatanense. This accession has brown lint and brown fuzz. Wild cottons from the Yucatan region are considered especially important in understanding the early stages of cotton domestication, and TX-2094 represents this historically significant native gene pool. Assembly To maximize resequencing mapping quality, we generated a high-quality de novo reference genome assembly for the Yucatán accession TX-2094 of G. hirsutum (NCBI: PRJNA1045685), which was used for all comparative genomic analyses reported here. In brief, PacBio sequencing data were assembled into 3,035 contigs, which were scaffolded using Hi-C into 26 pseudochromosomes (2.30 Gb total), yielding a scaffold N50 of 108.0 Mb and a maximum scaffold length of 127.8 Mb. BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis indicated 99.3% completeness, with 97.1% duplicated, as expected for a polyploid.
Table S1. The assembled genome of TX2094
♱Scaffold metrics reported are after manual scaffolding
Assembly
The chromosomes (pseudomolecules) for Gossypium hirsutum var TX-2094 genome. These files belong to the Gossypium hirsutum (AD1) 'TX2094' genome ISU_v2.0
Contact
Functional Analysis
Functional annotation files for the Gossypium hirsutum TX2094 ISU v2.0.a1 protein sequences are available for download below. Protein sequences were analyzed using InterProScan v5.72 to assign InterPro domains and Gene Ontology (GO) terms. Pathway analysis was performed using the KEGG Automatic Annotation Server (KAAS) v2.1. Downloads
Genes
The predicted gene model, their alignments and proteins for Gossypium hirsutum var TX2094 genome. These files belong to the Gossypium hirsutum (AD1) 'TX2094' genome ISU_v2.0
Homology
Homology of the Gossypium hirsutum TX2094 ISU v2.0.a1 protein sequences was determined by pairwise sequence comparison using the BLASTp algorithm against various protein databases. An E-value cutoff of 10-6 was applied for Arabidopsis thaliana (Araport11, 2022-09), UniProtKB/Swiss-Prot (Release date: 2026-01-28), and UniProtKB/TrEMBL (Release date: 2026-01-28) databases. The best-hit reports are available for download in Excel format. Protein Homologs
Markers
Marker alignments were performed by the CottonGen Team of the Main Bioinformatics Lab (WSU). The alignment tool 'BLAT' was used to map marker sequences from CottonGen to the Gossypium hirsutum TX2094 ISU v2.0.a1 assembly. Markers required 90% identity over 97% of their length. For SSRs & RFLPs, gap size was restricted to 1000 bp or less with ewer than 2 gaps. For dbSNPs and indels, gap size was restricted to 2 bp with fewer than 2 gaps. The available files are in GFF3 format. Markers available in CottonGen are linked to JBrowse.
Links
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