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Overview
| Analysis Name | Gossypium hirsutum (AD1) 'TM-1' T2T genome JZU_v1.0 |
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| Method | Oxford Nanopore PromethION; PacBio Sequel (HiFiasm v. 0.7) |
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| Source | (1.0) |
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| Date performed | 2025-03-11 |
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Upland cotton (Gossypium hirsutum) accounts for more than 90% of the world’s cotton production and, as an allotetraploid, is a model plant for polyploid crop domestication. In the present study, we reported a complete telomere-to-telomere (T2T) genome assembly of Upland cotton accession Texas Marker-1 (T2T-TM-1), which has a total size of 2,299.6 Mb, and annotated 79,642 genes. Based on T2T-TM-1, interspecific centromere divergence was detected between the A- and D-subgenomes and their corresponding diploid progenitors. Centromere-associated repetitive sequences (CRCs) were found to be enriched for Gypsy-like retroelements. Centromere size expansion, repositioning and structure variations occurred post-polyploidization. It is interesting that CRC homologs were transferred from the diploid D-genome progenitor to the D-subgenome, invaded the A-subgenome and then underwent post-tetraploidization proliferation. This suggests an evolutionary advantage for the CRCs of the D-genome progenitor, presents a D-genome-adopted inheritance of centromere repeats after polyploidization and shapes the dynamic centromeric landscape during polyploidization in polyploid species.
Table 1. Assembly and annotation of the gap-free genome sequences
| Genomic feature |
TM-1-T2T |
| Genome size (Mb) |
2299.6 |
| No. of gaps |
0 |
| No. of centromeres |
26 |
| No. of telomeres |
47 |
| Percentage of TE |
66.05 |
| Number of genes |
79,642 |
| Hi-C rate (%) |
99.71 |
| BUSCOs (%) |
99.5 |
publication: Yan, H., Han, J., Jin, S. et al. Post-polyploidization centromere evolution in cotton. Nat Genet (2025). https://doi.org/10.1038/s41588-025-02115-3
Assembly
The chromosomes (pseudomolecules) and scaffolds for G. hrisutum 'TM-1' T2T genome. These files belong to the Gossypium hirsutum (AD1) 'TM-1' T2T genome ZJU_v1.0
| Chromosomes & scaffolds (FASTA format) |
G.hirsutum_ZJU-TM1_T2T_v1.0.fasta.gz |
Functional Analysis
Functional annotation files for the Gossypium hirsutum TM1 T2T ZJU genome 1.0 are available for download below. The Gossypium hirsutum TM1 T2T ZJU genome 1.0 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
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 TM-1 T2T ZJU v1.0 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.
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 TM1 T2T ZJU genome 1.0 assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
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