Gossypium herbaceum (A1) 'ZhongCao1' genome HAU_v1
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Overview
About the assembly Seven new assembly and annotation of seven diploid cotton genomes were reported in Wang, et al. Net. Genet. 2022 Dec. They are: Two of G. herbaceum (A1) genomes (a wild form 'A1a' and an A1 cultivar 'ZhongCao1’), each one of G. anomalum (B1), G. sturtianum (C1), G. stocksii (E1), G. longicalyx (F1) and G. bickii (G1). The seven genomes were assembled by integration of Nanopore long reads (126–161×), Illumina short reads (52–79×) and high-throughput chromosome conformation capture (Hi-C) data. Table 1 is the summary of detailed information in 7 genome assemblies. Table 1. Summary of detailed information in 7 genome assemblies.
Publication Wang M et al., Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat Genet, 2022 Dec;54(12):1959-1971
Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium herbaceum '(A1)' genome. This file belongs to the HAU G. herbaceum Assembly v1.0
Functional Analysis
Functional annotation files for the Gossypium herbaceum HAU Genome v1.0 are available for download below. The Gossypium herbaceum HAU 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 Gossypium herbaceum'(D5)' genome. These files belong to the HAU G. herbaceum Assembly v1.0
Homology
Homology of the Gossypium herbaceum HAU 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 2023-07), and UniProtKB/TrEMBL (Release 2023-07) 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 herbaceum HAU 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.
Publication
Wang M et al., Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat Genet, 2022 Dec;54(12):1959-1971 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. herbaceum genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
Links
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