Gossypium barbadense (AD2) 'Gb_M210936' genome HAU_v1
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Overview
To fill the vacancy of genome resource between wild cotton and annual sea-island cotton, a perennial sea-island cotton accession, Lianhemumian (联核木棉), from Denggao village, Lujiang town, Longyang District, Baoshan City, Yunnan, China (the germplasm bank number is M210936 in Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China, and it is named as Gb_M210936) was sequenced through single-molecule real-time HiFi on the PacBio platform, and was assembled using HiFiasm. Illumina reads and HiFi reads were aligned to the assembled genome by BWA (v0.7.17) and minimap2 (v2.23), respectively, to evaluate alignment and coverage. Table S2. Alignment rate and coverage rate of sequencing reads
Assembly
The chromosomes (pseudomolecules) for Gossypium barbadense 'M210946' genome. These files belong to the Gossypium barbadense (AD2) 'Gb_M210936' genome HAU_v1.
Functional Analysis
Functional annotation files for the Gossypium barbadense Gb_M210936 Genome v1.0 are available for download below. The Gossypium barbadense Gb_M210936 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 barbadense 'M210946' genome. These files belong to the Gossypium barbadense (AD2) 'Gb_M210936' genome HAU_v1
Homology
Homology of the Gossypium barbadense Gb_M210936 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 barbadense Gb_M210936 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. barbadense Gb_M210936 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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