Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1
About the Assembly
Single-molecule real-time sequencing technology (PacBio RSII) was applied to assemble de novo the genome sequence of G. barbadense accession 3–79, generated 210.98 Gb of genome sequence with an estimated depth of coverage of at least 80× for the genome. Illumina paired-end data was used to correct low-quality nucleotides and insertions/deletions (InDels) from the PacBio sequencing. These polished contigs were processed for a hybrid assembly by using high-resolution optical mapping (BioNano Genomics Irys) data from the same accessions. To construct chromosome-scale scaffolds, we used high-throughput chromosome conformation capture (Hi-C) data from each accession to categorize and order these assemblies obtained by optical mapping.
Wang et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature genetics. 2018 Dec 03
Additional information about this analysis:
The Gossypium barbadense HAU Genome v2.0 assembly files are available in FASTA and GFF3 formats.
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 HAU Genome v2.0 are available for download below. The Gossypium barbadenseTexas 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).
The Gossypium hirsutum HAU genome v2.0 gene prediction files are available in FASTA and GFF3 formats.
Homology of the Gossypium barbadenseHAU 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-9 was used for the NCBI nr (Release 2018-05) and 1e-6 for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2018-04), and UniProtKB/TrEMBL (Release 2018-04) 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 G. barbadense HAU v2.0 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.
Protein alignments available below were performed by the CottonGen Team of the Main Bioinformatics Lab at WSU. The alignment tool 'exonerate' was used to map protein sequences onto the G. barbadense HAU v2.0 genome. Only alignments with a percent identity of 90% were retained.
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 genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.