Gossypium arboreum (A2) 'SXY1' genome HAU_v2
Wang, M. et al. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat. Genet. 2022 Dec;54(12):1959-1971. doi: 10.1038/s41588-022-01237-2. Epub 2022 Dec 6. .
Functional annotation files for the Gossypium arboreum HAU Genome v2.0 are available for download below. The Gossypium arboreum HAU Genome v2.0 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).
The predicted gene model, their alignments and proteins for Gossypium arboreum (A2) genome. These files belong to the HAU G. arboreum 'ShiXiYa-1' Assembly v2.0.
Homology of the Gossypium arboreum HAU Genome v2.0 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 2021-09) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.
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 arboreum HAU v2.0 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.
Wang M, Li J, Qi Z, Long Y, Pei L, Huang X, Grover CE, Du X, Xia C, Wang P, Liu Z, You J, Tian X, Ma Y, Wang R, Chen X, He X, Fang DD, Sun Y, Tu L, Jin S, Zhu L, Wendel JF, Zhang X. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat Genet. 2022 Dec;54(12):1959-1971. doi: 10.1038/s41588-022-01237-2. Epub 2022 Dec 6. PMID: 36474047.
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. arboreum genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.