Transcriptome Sequencing and Analysis of Wild Pear (Pyrus hopeiensis) Using the Illumina Platform

Abstract

Pears are cultivated worldwide as an economically valuable fruit of the Rosaceae. Because of the lack of genomic resources, few molecular biology studies have 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 hopeiensis is an endangered and valuable horticultural plant species, and its transcriptome was sequenced in this study. Overall, 25,877,477 high-quality reads and 48,278 unigenes were generated with the Illumina platform from four different tissue samples. A total of 27,005 (55.94 %) unigenes were successfully annotated. Of these, 26,941 and 19,248 unigenes were annotated in the National Center for Biotechnology Information non-redundant (Nr) protein database and the Swiss-Prot protein database, respectively. In addition, 18,590 and 7505 unigenes were assigned to Gene Ontology and Cluster of Orthologous Groups classifications, respectively, and a total of 5104 unigenes were mapped to 123 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 4301 simple sequence repeat markers were identified in P. hopeiensis, which will be used in future research of the genetic diversity of Pyrus. Finally, the results indicated that lignin biosynthesis, secondary metabolism and suberin/cutin/wax biosynthesis were involved in the russet pericarp formation process of P. hopeiensis. Detailed examination of these pathways revealed 54 candidate genes were predicted based on the KEGG pathways, which encoded 10 key enzymes involved in lignin biosynthesis; moreover, 33 additional regulatory genes for pigmentation of wild pear russet pericarp were also summarized. In summary, this effective RNA-Seq study provides comprehensive genetic and genomic insight into the endangered P. hopeiensis species, which will improve future studies on the molecular mechanism of the appearance and quality of this fruit.