Transcriptome sequencing and SNP detection in Phoebe chekiangensis

Transcriptome sequencing and SNP detection in Phoebe chekiangensis

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 usi...

Full description

Bibliographic Details
Main Authors: Bing He, Yingang Li, Zhouxian Ni, Li-an Xu
Format: Article
Language:English
Published: PeerJ Inc. 2017-05-01
Series:PeerJ
Subjects:
Phoebe chekiangensis
SNP prediction
Next-generation sequencing
Sanger method
Software comparison
Online Access:https://peerj.com/articles/3193.pdf
id doaj-df14ff1e77364301988826318c73fd95
record_format Article
spelling doaj-df14ff1e77364301988826318c73fd952020-11-24T23:53:20ZengPeerJ Inc.PeerJ2167-83592017-05-015e319310.7717/peerj.3193Transcriptome sequencing and SNP detection in Phoebe chekiangensisBing He0Yingang Li1Zhouxian Ni2Li-an Xu3Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, ChinaCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, ChinaCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, ChinaCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, ChinaBackground 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.https://peerj.com/articles/3193.pdfPhoebe chekiangensisSNP predictionNext-generation sequencingSanger methodSoftware comparison
collection DOAJ
language English
format Article
sources DOAJ
author Bing He
Yingang Li
Zhouxian Ni
Li-an Xu
spellingShingle Bing He
Yingang Li
Zhouxian Ni
Li-an Xu
Transcriptome sequencing and SNP detection in Phoebe chekiangensis
PeerJ
Phoebe chekiangensis
SNP prediction
Next-generation sequencing
Sanger method
Software comparison
author_facet Bing He
Yingang Li
Zhouxian Ni
Li-an Xu
author_sort Bing He
title Transcriptome sequencing and SNP detection in Phoebe chekiangensis
title_short Transcriptome sequencing and SNP detection in Phoebe chekiangensis
title_full Transcriptome sequencing and SNP detection in Phoebe chekiangensis
title_fullStr Transcriptome sequencing and SNP detection in Phoebe chekiangensis
title_full_unstemmed Transcriptome sequencing and SNP detection in Phoebe chekiangensis
title_sort transcriptome sequencing and snp detection in phoebe chekiangensis
publisher PeerJ Inc.
series PeerJ
issn 2167-8359
publishDate 2017-05-01
description 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.
topic Phoebe chekiangensis
SNP prediction
Next-generation sequencing
Sanger method
Software comparison
url https://peerj.com/articles/3193.pdf
work_keys_str_mv AT binghe transcriptomesequencingandsnpdetectioninphoebechekiangensis
AT yingangli transcriptomesequencingandsnpdetectioninphoebechekiangensis
AT zhouxianni transcriptomesequencingandsnpdetectioninphoebechekiangensis
AT lianxu transcriptomesequencingandsnpdetectioninphoebechekiangensis
_version_ 1725470297047433216

Similar Items