Chinese Science Bulletin

, Volume 56, Issue 20, pp 2119–2130

Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology

  • Hui Yang
  • YunXiang Mao
  • FanNa Kong
  • GuanPin Yang
  • Fei Ma
  • Li Wang
Open AccessArticle Marine Biology

DOI: 10.1007/s11434-011-4546-4

Cite this article as:
Yang, H., Mao, Y., Kong, F. et al. Chin. Sci. Bull. (2011) 56: 2119. doi:10.1007/s11434-011-4546-4

Abstract

With high-throughput Solexa sequencing technology, we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated, which were assembled into 31538 unigenes. Blast analysis showed that 56.7% unigenes were novel, which represented the specific genes of Porphyra and/or rhodophytes. Several hundreds of unigenes related to stress tolerance were discovered, including genes related to desiccation-(211) and high light-tolerance (31), flavonoid biosynthesis (10), reactive oxygen scavenging (48) and other stress-tolerance processes (208), which indicated there existed complex and diversity modes of stress tolerance in this species. A complete set of essential genes involved in the C3-(57) and C4-(44) carbon fixation pathway (except pyruvate phosphate dikinase) were discovered, which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra. Moreover, by statistically analyzing the types, proportions and frequencies of the interspersed repeats (TEs) and simple sequence repeats (SSRs), we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs, promoting our understanding of structural characteristics of the transcriptome. This study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research.

Keywords

Porphyra yezoensisred algaetranscriptomeSolexa sequencing technologyexpressed sequence tagsfunctional analysistransposable elementsmicrosatellites
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© The Author(s) 2011

Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited.

Authors and Affiliations

  • Hui Yang
    • 1
  • YunXiang Mao
    • 1
  • FanNa Kong
    • 1
  • GuanPin Yang
    • 1
  • Fei Ma
    • 1
  • Li Wang
    • 1
  1. 1.College of Marine Life SciencesOcean University of ChinaQingdaoChina