Castor bean, (Ricinus communis L., Euphorbiaceae) is an important non-edible oilseed crop. Its seed oil contains a high ricinoleic acid concentration (~90%), an unusual hydroxylated fatty acid, and is a vital industrial raw material. castor bean have been widely used by humans since prehistoric times, dating to ~24,000 years before present. Considering the high economic value and the easy growth in unfavorable environments, castor bean has been extensively cultivated in tropical and subtropical countries. The draft genome of castor bean inbred cultivar Hale has been released in 2010. The assembly covered the genome ∼4.6×, spanning 350 Mb, which contains 25,800 scaffolds and identifes 31,237 gene models. If only the 3,500 scaffolds larger than 2 kb are considered, the assembly spans 325 Mb with an N50 of 0.56 Mb.
In this project, we de novo assembled a chromosome-level genome assembly (~336 Mb) of the wild progenitor of castor bean (Ethiopia) with contig N50 of 11.59 Mb and scaffold N50 of 32.06 Mb. We annotated 25,814 protein-coding genes, 40,954 transcripts and 3,180 noncoding RNAs in the wild castor bean genome. Recently, we are developing a high-resolution transcriptome map, defining the gene structure of castor bean by using the single-molecule long-read sequencing. Besides, we are profiling the epigentic features including DNA nethylation and histone modification in castor bean seeds. Integrating these data is crucial for further functional genomics research on castor bean. Here, we constructed the Ricinus communis DataBase (RcDB) , which is freely accessible to the castor bean research community. The RcDB mainly focused on castor bean genome sequence and corresponding gene annotations, and had several distinctive features:
a) RcDB is an integrated knowledge database, which include not only basic gene information, but also gene functional annotation, gene expression profiles and gene network information;
b) RcDB provides a user-friendly interface and a convenient search option, allowing efficient recovery of sequence, gene expression matrix, gene network and other information;
c) RcDB also provides the tools which focus on more specific purposes, such as online BLAST service, GBrowse genome browser and Tools -- a tool suite for genome sequence retrieving, gene ID conversion and gene network construction.
We believe RcDB will provide a valuable resource and also an important platform for the fundamental and applied research on the distinctive oilseed plant castor bean and other related plants.