Gossypium arboreum (A2) 'SXY1' genome CGP-BGI_v2_a1
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Overview
About the Assembly The Gossypium arboreum diploid genome is a putative contributor of the A subgenome of tetraploid cotton species. A highly homozygous single-seed descendant, derived from 18 successive generations of self-fertilization, of the cultivated diploid cotton Shixiya1 (SXY1) was used for DNA sequencing. Paired-end reads obtained from the Illumina HiSeq 2000 platform were obtained from various libraries of different insert sizes. The assembly was performed using SoapDenovo to generate contigs and scaffolds.
The work was performed by researchers from the Cotton Research Institute (CRI) of the Chinese Academy of Agricultural Sciences, the Beijing Genomics Institute (BGI) at Shenzhen, Peking University, Agricultural University of Hebei, USDA-ARS, the University of Copenhagen, King Adbulaziz University, Macau University of Science and Technology, and University of Hong Kong. The predicted genes and proteins for the G. arboreum assembly were identified in the original genome assembly, all other annotation was performed by CottonGen.
Assembly
The pseudomolecules (putative chromosomes & scaffolds) for the G. arboreum assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Li et al., 2014.
Downloads
All assembly and annotation files are available for download by selecting the desired data type in the left-hand side bar. Each data type page will provide a description of the available files and links to download. Functional Annotation
G. arboreum proteins were analyzed using InterProScan and the KEGG Automated Annotation Server (KAAS) in order to assign InterPro domains, Gene Ontology (GO) terms, KEGG pathways and KEGG orthologs. This work was performed by the Main Bioinformatics Lab at Washington State University. Term assignments to genes are available in compressed text files and KEGG hier files and maps are available for browsing with the KeggHier tool.
Genes
The predicted genes and proteins for the G. arboreum assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Li et al., 2014.
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 G. 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 and CMap are linked to JBrowse.
Protein Homology
Homology of the Gossypium.arboreum BGI_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 (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.
Publication
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. arboreum genome assembly. Alignments with an alignment length of 97% and 98% identify were preserved. The available files are in GFF3 format.
Links
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