Transcriptome profiling analysis of pear (Pyrus bretschneideri Rehd.) reveals insight into the gene expression during fruit development and maturation

Background: Pear is one of the most important fruit species. However, pear genomic information is currently unavailable. The Solexa/ Illumina RNA-seq and digital gene expression (DGE) are high-throughput sequencing approaches and are newly developed powerful tools for transcriptomic studies. This study reports the transcriptome profiling analysis of Pyrus bretschneideri Rehd. using RNA-seq and DGE for better understanding the molecular mechanisms of biological aspects, especially pear fruit development and maturation. Results: Using high-throughput Illumina RNA-seq combined with a tag-based DGE system, De novo transcriptome assembly and gene expression analysis of P. bretschneideri Rehd. were performed at an unprecedented depth (5.47 gigabase pairs). Approximate 60.77 million reads were obtained, trimmed, and assembled into 90,227 unigenes, with an average length of 508 bp and an N50 of 635 bp, which consisted of 17,619 contig clusters and 72,608 singletons. Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 61,636 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. 34.60% of unigenes (31,215) were annotated against KEGG in 121 known metabolic or signalling pathways. DGE libraries of five different developmental fruit stages were constructed to analyze the DGE profiling, the gene expression variations between two transition fruit stages were compared. Thousands of genes showed significantly different expression levels based on the various comparisons. Conclusion: The extensive transcriptome and DGE profiling data have obtained from the deep sequencing of pear plant, which can serve as an important public information platform for gene expression, genomics, and functional genomic studies in P. bretschneideri, and provide comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms in fruit development and maturation.