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Open Access Highly Accessed Research article

Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq

Guoqin Liu12, Wanshun Li3, Penghua Zheng1, Tong Xu3, Lijuan Chen3, Dongfeng Liu1, Sayed Hussain1 and Yuanwen Teng1*

Author affiliations

1 Department of Horticulture, The State Agricultural Ministry’s Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou, 310058,, Zhejiang Province, China

2 College of Agriculture, Guizhou University, Guiyang, 550025,, Guizhou Province, China

3 BGI-tech, Shenzhen, 518083,, Guangdong Province, China

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Citation and License

BMC Genomics 2012, 13:700  doi:10.1186/1471-2164-13-700

Published: 12 December 2012

Abstract

Background

Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic information for pear is currently unavailable, transcriptome and digital gene expression data for this species would be valuable resources to better understand the molecular and biological mechanisms regulating its bud dormancy.

Results

We performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of ‘Suli’ pear (Pyrus pyrifolia white pear group) using the Illumina RNA-seq system. RNA-Seq generated approximately 100 M high-quality reads that were assembled into 69,393 unigenes (mean length = 853 bp), including 14,531 clusters and 34,194 singletons. A total of 51,448 (74.1%) unigenes were annotated using public protein databases with a cut-off E-value above 10-5. We mainly compared gene expression levels at four time-points during bud dormancy. Between Nov. 15 and Dec. 15, Dec. 15 and Jan. 15, and Jan. 15 and Feb. 15, 1,978, 1,024, and 3,468 genes were differentially expressed, respectively. Hierarchical clustering analysis arranged 190 significantly differentially-expressed genes into seven groups. Seven genes were randomly selected to confirm their expression levels using quantitative real-time PCR.

Conclusions

The new transcriptomes offer comprehensive sequence and DGE profiling data for a dynamic view of transcriptomic variation during bud dormancy in pear. These data provided a basis for future studies of metabolism during bud dormancy in non-model but economically-important perennial species.

Keywords:
‘Suli’ pear (Pyrus pyrifolia white pear group); Transcriptome; Bud dormancy; RNA-Seq