Study : De novo sequencing and characterization of inflorescence transcriptome of the rice bean (Vigna umbellata) for gene discovery and SSR marker development
Identification
Name
De novo sequencing and characterization of inflorescence transcriptome of the rice bean (Vigna umbellata) for gene discovery and SSR marker development
Identifier
dXJuOkVWQS9zdHVkeS9QUkpOQTM5MTgzNw==
Source
Description
Rice bean (Vigna umbellata) is a warm season annual legume crop mainly grown in East Asia. Only limited genomic resources are available for this legume species. In this study, approximately 48.3 million high quality cDNA sequence reads were obtained from young inflorescence of rice bean using RNA-seq and assembled into 38,501 unigenes with an average length of 1,165 bp. Of these unigenes, 33,636 (87.4 %) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 22,409 (58.2 %) could be classified into gene ontology categories, 25,880 (67.2 %) into Swiss-Prot categories and 20,486 (53.2 %) into KOG database categories. A total of 12,367 (32.1 %) were mapped onto 127 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 4,266 EST-SSRs were identified as potential molecular markers. AG/CT (28.8 %), AAG/CTT (14.1 %), ATG/ATC (7.8 %) and ACC/GGT (6.8 %) are the four major repeat motifs. Our comprehensive database complemented the existing resources and the large number EST-SSR in this study will better facilitates future researches for the construction of high-resolution genetic linkage maps, comparative mapping and molecular breeding in rice bean improvement.
Data files