Gossypium hirsutum (AD1) 'Jin668' T2T genome HAU_v1.0
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Overview
Here, we assembled a complete telomere-to-telomere (T2T) genome of Upland cotton genotype Jin668 and a high-quality genome of YZ1. Comparative genomics, chromatin accessibility and gene expression analyses shed light on the key gene regulatory networks that facilitate the ability of Jin668 to achieve regeneration. Additionally, we conducted a comprehensive evaluation of the impact of genetic variation between genotypes on the precision of CRISPR-based genome editing, emphasizing the importance of high-quality genome assembly for individual genotypes to ensure accurate genome editing for functional gene research and molecular breeding.
Supplementary Table 3 Statistics for the Jin668 genome after assembly with Hi-C reads.
Publication: Xu ZP, Wang GY, et al., Genome assembly of two allotetraploid cotton germplasms reveals mechanisms of somatic embryogenesis and enables precise genome editing. Nat Genet (2025). Assembly
The chromosomes (pseudomolecules) for G. hrisutum 'Jin668' T2T genome. These files belong to the Gossypium hirsutum (AD1) 'Jin668' T2T genome HAU Assembly v1.0
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Functional Analysis
Functional annotation files for the Gossypium hirsutum Jin668 Genome v1.0 are available for download below. The Gossypium hirsutum Jin668 Genome v1.0 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
Genes
The predicted gene model, their alignments, and proteins for G. hirsutum 'Jin668' T2T genome. These files belong to the Gossypium hirsutum (AD1) 'Jin668' T2T genome HAU Assembly v1.0
Homology
Homology of the Gossypium hirsutum Jin668 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-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2025-02), and UniProtKB/TrEMBL (Release 2025-02) databases. The best hit reports are available for download in Excel format. Protein Homologs
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 Jin668 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. 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 Jin668 HAU genome 1.0 assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3.
Links
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