Gossypium barbadense (AD2) Hai7124 genome ZJU Assembly v1.1 & Annotation a1
About the assembly
We adopted a hierarchical approach to perform the chromosome-scale assembly. The 800 Gb high-quality data (>330× genome coverage) generated from a series of PCR-free libraries, mate paired-end read (MP) libraries and 10× GemCode library were assembled using the software package DenovoMAGIC3 (NRGene, Nes Ziona, Israel). Initially, the assembly of G. barbadense cv. Hai7124 that captured 2.23 Gb was generated. Thereafter, the initial scaffolds were further corrected and merged using optical mapping data (BioNano Genomics). Finally, we used three-dimensional proximity information obtained by Hi-C and our updated ultra-dense genetic map with 6,165,057 single-nucleotide polymorphisms (SNPs) to check, order and orient these super-scaffolds. A total of 115 erroneously assembled loci were detected and corrected.
Additional information about this analysis:
The chromosomes (pseudomolecules) and scaffolds for G. barbadense 'Hai7124' genome. These files belong to the ZJU assembly v1.1
The predicted gene model, their alignments and proteins for G. barbadense 'Hai7124' genome. These files belong to the ZJU assembly v1.1 & annotation a1
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.
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. arboreum 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.
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.
Functional annotation files for the Gossypium barbadense ZJU Genome v1.1 are available for download below. The Gossypium barbadense ZJU 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).
Homology of the Gossypium barbadense ZJU 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 (TAIR10), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.