Gossypium hirsutum (AD1) 'HPF17' genome ZJU_v1
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Overview
HPF17 is one Hainan Island cotton (HIC) belonging to a wild Gossypium hirsutum (Heterotypic Synonym: Gossypium purpurascens Poir.) and was collected from Yacheng, Sanya, Hainan Province, China. Hainan Island Native Cotton (HIC) has long been grown extensively on Hainan Island, China. We assembled a high-quality genome of one HIC plant, HPF17. The genome size of HPF17 was estimated to be ~2,055 Mb based on K-mer analysis. We produced 130.65 Gb (~57 x genome equivalent) of high-quality PacBio circular consensus sequencing (CCS) reads and assembled the genome using hifiasm. The initial assembly generated 3,394 contigs with an N50 value of 13.20 Mb. Subsequently, we categorized and ordered the contigs to produce chromosome-scale scaffolds using approximately 50-fold coverage of valid unique interacting paired-end data generated through high-throughput chromosome conformation capture (Hi-C) (Table S12). The final assembly included 2,558,691,823 bases and 3,343 scaffolds, resulting in a scaffold N50 value of 88.21 Mb. A total of 2,267,310,418 (88.61 %) bases from the contigs were anchored and oriented onto pseudochromosomes. Table S12
Publication: Cheng et al., Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton. Assembly
The chromosomes (pseudomolecules) for Gossypium hirsutum 'HPF17' genome. These files belong to the Gossypium hirsutum (AD1) 'HPF17' genome ZJU_v1.
Functional Analysis
Functional annotation files for the Gossypium hirsutum HPF17 Genome v1.0 are available for download below. The Gossypium hirsutum HPF17 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 hirsutum'(AD1) 'HPF17' genome. These files belong to the Gossypium hirsutum (AD1) 'HPF17' genome ZJU_v1
Homology
Homology of the Gossypium hirsutum HPF17 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 hirsutum HPF17 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
Publication Cheng Y, Huang C, Hu Y, Jin S, Zhang X, Si Z, Zhao T, Chen J, Fang L, Dai F, Yang W, Wang P, Mei G, Guan X, Zhang T. Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton. Journal of advanced research. 2023 Mar 24. 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 HPF17 genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
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