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...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-05-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3193.pdf |
| _version_ | 1797420087965122560 |
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| author | Bing He Yingang Li Zhouxian Ni Li-an Xu |
| author_facet | Bing He Yingang Li Zhouxian Ni Li-an Xu |
| author_sort | Bing He |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T06:57:35Z |
| format | Article |
| id | doaj.art-df14ff1e77364301988826318c73fd95 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:57:35Z |
| publishDate | 2017-05-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-df14ff1e77364301988826318c73fd952023-12-03T10:02:49ZengPeerJ 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 |
| 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 |
| title | 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_short | Transcriptome sequencing and SNP detection in Phoebe chekiangensis |
| title_sort | transcriptome sequencing and snp detection in phoebe chekiangensis |
| topic | Phoebe chekiangensis SNP prediction Next-generation sequencing Sanger method Software comparison |
| url | https://peerj.com/articles/3193.pdf |
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