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Global transcriptome analysis of Sabina chinensis (Cupressaceae), a valuable reforestation conifer
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2016 (English)In: Molecular breeding, ISSN 1380-3743, E-ISSN 1572-9788, Vol. 36, no 7, 99Article in journal (Refereed) Published
Abstract [en]

Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species' unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (similar to 9.0 bp) were obtained, and 116,814 unigenes (>= 200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.

Place, publisher, year, edition, pages
2016. Vol. 36, no 7, 99
Keyword [en]
Sabina chinensis, De novo assembly, RNA-Seq, Gene discovery, EST-SSR
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Ecology
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URN: urn:nbn:se:umu:diva-130133DOI: 10.1007/s11032-016-0526-3ISI: 000380238300017OAI: oai:DiVA.org:umu-130133DiVA: diva2:1064215
Available from: 2017-01-12 Created: 2017-01-12 Last updated: 2017-03-31Bibliographically approved

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Zhao, WeiWang, Xiao-Ru
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Department of Ecology and Environmental Sciences
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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
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