Identification of novel EST-SSR markers from the de novo transcriptome sequence and application in persimmon (Diospyros L.)

摘要

Persimmon (Diospyros L.) is one of the most important commercially cultivated fruit crops in the world. However, the research on the molecular biology of persimmon is very less due to the lack of genomic and transcriptome data. In this study, the persimmon transcriptomes were sequenced from a new species of Diospyros L. (Deyangshi). Illumina sequencing generated 44,522,166 high-quality clean reads that were assembled into 48,012 unigenes with an average length of 835 bp. A total of 27,586 unigenes (57.7% of all unigenes) were annotated, and 14,275 unigenes were classified into 24 function classification using Clusters of Orthologous Groups of proteins (COG) database, 71,073 unigenes were assigned to 45 functional groups using Gene Ontology (GO) database, 7,186 annotated sequences were assigned to 124 specific metabolic pathways by Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Furthermore, 8,741 simple sequence repeats (SSRs) were identified from 7,074 unigenes. 100 pairs of primers were selected to evaluate the validity and universality in twenty genotypes of persimmon, and 89 pairs generated clear and abundant bands. This is the first report to develop SSR markers for persimmon by transcriptome information. These data could be used as an important resource for studying the genetics and molecular biology for persimmon in future work.