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Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions

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Abstract

The marine red alga Pyropia tenera grows on intertidal rocks, where it undergoes dynamic environmental changes including temperature, desiccation, osmotic shock, and changes in light intensity. Therefore, Pyropia have developed a variety of strategies and mechanisms to overcome those environmental stressors. In an effort to identify the genes involved in the high-temperature tolerance of P. tenera, we generated 368,334 expression sequence tags (ESTs) using 454 sequencing technology and 3,331 ESTs using the Sanger method. Among the total ESTs, 222,024 reads were generated from gametophyte thalli under control condition and 149,641 reads were generated under high temperature condition. These ESTs were assembled into 17,870 contigs consisting of 336,016 reads, whereas 35,924 sequences remained as unassembled ESTs. Only 16.5 % of contigs shared significant similarity with an E value of ≤1E− 10 with UniProt sequence. The 95 different SSR motifs were discovered in 1,586 contigs. Trinucleotide repeat was absolutely predominant (90.2 %) SSR, and GGC was the most common motif. A comparison of the ESTs from gametophyte thalli under normal and heat stress conditions enabled us to identify the transcripts that were up or downregulated by high temperature. Most of transcripts produced under the high temperature condition belong to heat shock protein family and novel transcripts not matched to known genes in current public databases. These ESTs will provide valuable information to identify the DNA markers for the Pyropia species and the genes involved in the molecular mechanism of thermotolerance in red algae.

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Acknowledgments

This research was supported by a grant (RP-2011-BT-058) from National Fisheries Research and Development Institute, South Korea.

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Authors and Affiliations

  1. Department of Biology Education, Chonnam National University and KhumHo Research Institute, Gwangju, 500-757, South Korea

    San Choi, Sungoh Im, Namju Kim & Dong-Woog Choi

  2. Seaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-831, South Korea

    Mi Sook Hwang, Eun-Jeong Park & Yong-Gun Gong

  3. Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, South Korea

    Won-Joong Jeong

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  1. San Choi
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  2. Mi Sook Hwang
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  3. Sungoh Im
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  4. Namju Kim
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  6. Eun-Jeong Park
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Correspondence to Dong-Woog Choi.

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S. Choi and M.S. Hwang contributed equally to this paper.

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Choi, S., Hwang, M.S., Im, S. et al. Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions. J Appl Phycol 25, 1237–1246 (2013). https://doi.org/10.1007/s10811-012-9921-2

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