Gossypium arboreum (A2) SXY1 genome CRI-Updated v1_a1
About the assembly
A new assembly of the Gossypium arboreum genome (cultivated diploid cotton Shixiya1) was reported by the Cotton Research Institute of Chinese Academy of Agricultural Sciences (CRI-CAAS). The reassembled vesrion is on the basis of PacBio long-reads and Hi-C technologies, and the population structure and genomic divergence trends of 243 diploid cotton accessions was analyzed. A number of candidate loci that may facilitate the genetic improvement of cotton lint production were identified.
142.54 Gb of raw PacBio reads (approximately 77.6-fold genome coverage) was generated by using SMRT sequencing technology and these reads were assembled into 8,223 contigs, producing a 1,710 Mb G. arboreum genome with a contig N50 of 1,100 kb; the longest contig in the new assembly was 12.37 Mb.
Du et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature genetics. 2018 May 07.
The chromosomes (pseudomolecules) and scaffolds for G. aboreum genome. These files belong to the CRI Updated Assembly v1.0
The predicted gene model, their alignments and proteins for G. aboreum genome. These files belong to the CRI Updated Assembly 1.0 & Annotation 1.0
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.
Homology of the Gossypium arboreum CRI 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 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.
Functional annotation files for the Gossypium arboreum CRI Genome v1.0 are available for download below. The Gossypium arboreumCRI 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).
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. arboreum genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
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. arboreum CRI v1.0 genome. Only alignments with a percent identity of 90% were retained.