Gossypium barbadense (AD2) 3-79 genome HGS v1.1_a1
About the assembly
The WGS assembly of Gossypium barbadense v1.1 was isolated from '3-79' (isolate=1400233.01) with 90.05x of the genome coverage. The data was submitted by HGS (HudsonAlpha Genome Sequencing Center) and stored under NCBI BioProject PRJNA516411.
The chromosomes (pseudomolecules) for Gossypium barbadense 3-79 genome. These files belong to the HGS Assembly v1.1
The predicted gene model, their alignments and proteins for G. barbadense 3-79 genome. These files belong to the HGS-AD2 Assembly v1.1
All annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar. Each data type page will provide a description of the available files and links do download. Alternatively, you can use the FTP repository for bulk download.
Functional annotation files for the Gossypium barbadense HGS Genome v1.1 are available for download below. The Gossypium barbadense HGS Genome 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).
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. australe genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 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 barbadense genome 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.
Homology of the Gossypium barbadense HGS Genome v1.1 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 2018-05) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.