Gossypium raimondii (D5) 'D5-3' genome BGI-CGP-draft_v1
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Overview
About the Assembly The Gossypium raimondii acc 'D5-3' diploid genome is considered the contributor of the D subgenome of economical important tetraploid cotton (Gossypium hirsutum and Gossypium barbadense). Paired-end reads obtained FROM chado.the Illumina HiSeq 2000 platform were obtained FROM chado.various libraries with different insert sizes. The assembly was performed using SoapDenovo to generate contigs and SSPACE was used to scaffold the contigs using the paired-end reads.
The work was performed by researchers FROM chado.the Cotton Research Institute of the Chinese Academy of Agricultural Sciences, the Beijing Genomics Institute (BGI) at Shenzhen, Peking University, USDA-ARS, and the University of Copenhagen
Acknowledgements
CottonGen acknowledges with thanks the provision of the draft cotton D genome by Drs. Shuxun Yu, Jun Wang and Yu-Xian Zhu as presented in the Wang et al., 2012 Nature Genetics publication. Assembly
The pseudomolecules (putative chromosomes & scaffolds) for the G. raimondii assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Wang et al., 2012.
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. raimondii 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 CottonGen Team of 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. raimondii assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Wang et al., 2012.
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.
Non-coding DNA
Non-coding DNA: Non coding RNA for the G. raimondii assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Wang et al., 2012. The available files are in GFF3 format.
Protein Homology
Homology of the Gossypium raimondiiCGP-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
Repeats
Repeats for the G. raimondii assembly were identified for the original genome assembly. Details can be found in the Nature Genetics paper by Wang et al., 2012. The available files are in GFF3 format.
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. raimondii 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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