Transcriptome Sequencing and Analysis of Wild Pear (Pyrus trilocularis) using the Illumina Platform

Abstract

Pears are cultivated worldwide as an economically valuable fruit of family Rosaceae. Because of the lack of genomic resources, few molecular biology studies have been focused on wild pear which are less abundant than partially cultivated pear species. However, high-throughput transcriptome sequencing technologies enabled the advent of genomic studies requiring shorter time and minimal costs, allowing efficient wild pear research. Pyrus trilocularis is an endangered and valuable horticultural plant species, and its transcriptome was sequenced in this study. Overall, 21860128 high-quality reads and 42879 unigenes were generated with the Illumina platform from 4 different tissue samples. A total of 26059 (60.77%) unigenes were successfully annotated. Of these, 26029 and 18467 unigenes were annotated in the NCBI Nr protein database and the Swiss-Prot database, respectively. In addition, 18872 and 7199 unigenes were assigned to GO and COG classifications, respectively, and a total of 4993 unigenes were mapped to 129 KEGG pathways. Furthermore, 3864 SSR markers were identified in P. trilocularis, which will be used in future research of the genetic diversity of Pyrus. Finally, 100 candidate genes were predicted on the basis of KEGG pathways, which may encode key enzymes involved in plant hormone signal transduction. In summary, this effective RNA-Seq study provides comprehensive genetic and genomic insight into the endangered P. trilocularis species, which may improve future studies on the molecular mechanism of the pear tree resistance.