title: Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd).
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui, P R China. fcb_ah@ahau.edu.cn.
authors.forename: Min
authors.initials: M
authors.lastname: Xie
authors.forename: Ying
authors.initials: Y
authors.lastname: Huang
authors.forename: Yanping
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.forename: Hua
authors.initials: H
authors.lastname: Yang
authors.forename: Oliver
authors.initials: O
authors.lastname: Yu
authors.forename: Wenhao
authors.initials: W
authors.lastname: Dai
authors.forename: Congbing
authors.initials: C
authors.lastname: Fang
mesh_terms: D002874:Chromosome Mapping; D017124:Conserved Sequence; D005638:Fruit / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D031989:Pyrus / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D010940:Plant Proteins