Transcriptome sequencing and SNP detection in Phoebe chekiangensis

Bing He; Yingang Li; Zhouxian Ni; Li-An Xu

doi:10.7717/peerj.3193

Transcriptome sequencing and SNP detection in Phoebe chekiangensis

PeerJ. 2017 May 10:5:e3193. doi: 10.7717/peerj.3193. eCollection 2017.

Authors

Bing He^#¹, Yingang Li^#^{1

2}, Zhouxian Ni¹, Li-An Xu¹

Affiliations

¹ Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
² Zhejiang Academy of Forestry, Zhejiang Academy of Forestry, Hangzhou, China.

^# Contributed equally.

Abstract

Background: Phoebe chekiangensis is a rare tree species that is only distributed in south-eastern China. Although this species is famous for its excellent wood properties, it has not been extensively studied at the molecular level.

Results: Here, the transcriptome of P. chekiangensis was sequenced using next-generation sequencing technology, and 75,647 transcripts with 48,011 unigenes were assembled and annotated. In addition, 162,938 putative single nucleotide polymorphisms (SNPs) were predicted and 25 were further validated using the Sanger method.

Conclusion: The currently available SNP prediction software packages showed low levels of correspondence when compared. The transcriptome and SNPs will contribute to the exploration of P. chekiangensis genetic resources and the understanding of its molecular mechanisms.

Keywords: Next-generation sequencing; Phoebe chekiangensis; SNP prediction; Sanger method; Software comparison.

Grants and funding

This work was financially supported by the Major Science and Technology Project (No. 2010C12009), Zhejiang Province, China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.