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Open Access Highly Accessed Research article

Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd)

Min Xie1, Ying Huang1, Yanping Zhang1, Xin Wang1, Hua Yang2, Oliver Yu2, Wenhao Dai3 and Congbing Fang12*

Author Affiliations

1 School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui, P R China

2 Key Laboratory of Tea Biochemistry & Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei 230036, Anhui, P R China

3 Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA

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BMC Genomics 2013, 14:823  doi:10.1186/1471-2164-14-823

Published: 23 November 2013

Abstract

Background

Pear (Pyrus spp) is an important fruit species worldwide; however, its genetics and genomic information is limited. Combining the Solexa/Illumina RNA-seq high-throughput sequencing approach (RNA-seq) with Digital Gene Expression (DGE) analysis would be a powerful tool for transcriptomic study. This paper reports the transcriptome profiling analysis of Chinese white pear (P. bretschneideri) using RNA-seq and DGE to better understand the molecular mechanisms in fruit development and maturation of Chinese white pear.

Results

De novo transcriptome assembly and gene expression analysis of Chinese white pear were performed in an unprecedented depth (5.47 gigabase pairs) using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system. Approximately, 60.77 million reads were sequenced, trimmed, and assembled into 90,227 unigenes. These unigenes comprised 17,619 contigs and 72,608 singletons with an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR, and COGs at NCBI, Pfam, InterPro, and KEGG) found that 61,636 unigenes can be annotated with gene descriptions, conserved protein domains, or gene ontology terms. By BLASTing all 61,636 unigenes in KEGG, a total of 31,215 unigenes were annotated into 121 known metabolic or signaling pathways in which a few primary, intermediate, and secondary metabolic pathways are directly related to pear fruit quality. DGE libraries were constructed for each of the five fruit developmental stages. Variations in gene expression among all developmental stages of pear fruit were significantly different in a large amount of unigenes.

Conclusion

Extensive transcriptome and DGE profiling data at five fruit developmental stages of Chinese white pear have been obtained from a deep sequencing, which provides comprehensive gene expression information at the transcriptional level. This could facilitate understanding of the molecular mechanisms in fruit development and maturation. Such a database can also be used as a public information platform for research on molecular biology and functional genomics in pear and other related species.