Dear Cotton Researchers,
The CottonGen team is pleased to announce the availability of the draft G. raimondii (D genome) presented in the Wang et al., 2012 Nature Genetics publication, graciously provided by Drs. Shuxun Yu, Jun Wang and Yu-Xian Zhu to CottonGen. The assembly includes their pseudomolecules, predicted genes, non-coding RNA and repeats. In addition, the CottonGen team has aligned to the genome several commonly used resources such as CottonGen RFLP, SSR, and SNP markers, NCBI cotton dbSNP, CottonGen unigenes, PlantGDB unigenes, Josh Udall's 454-derived transcript contigs, NCBI cotton dbEST, NCBI cotton mRNA and protein sequences from various plant genomes. Additionally, the gene models have been annotated with Gene Ontology (GO), InterPro (IPR) domains and KEGG pathways and orthologs. The assembly and all ancillary annotations and alignments are available for exploration with GBrowse on the CottonGen website and are available for sequence comparison on our BLAST servers. All files are available for download on the CottonGen G. raimondii genome page or from our FTP repository.
In the near future we will be adding a page for each gene providing all functional and structural details. Another announcement will be sent when these additional resources are available.
Here are some quick links:
Draft G. raimondii genome page http://www.cottongen.org/species/Gossypium_raimondii/bgi-cgp_genome_v1.0
GBrowse Viewer: http://www.cottongen.org/gb/gbrowse/CGP_Dgenome/
FTP downloads: ftp://ftp.bioinfo.wsu.edu/species/Gossypium_raimondii/CGP-BGI_G.raimondii_Dgenome/
NCBI BLAST (returns results to screen): http://www.cottongen.org/tools/blast
Batch BLAST (returns results parsed in an excel file): http://www.cottongen.org/tools/batch_blast
The CottonGen team