Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temp
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Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions San Choi & Mi Sook Hwang & Sungoh Im & Namju Kim & Won-Joong Jeong & Eun-Jeong Park & Yong-Gun Gong & Dong-Woog Choi Received: 20 October 2011 / Revised and accepted: 1 October 2012 / Published online: 21 October 2012 # Springer Science+Business Media Dordrecht 2012
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. Keywords Pyropia tenera . Rhodophyta . ESTs . Heat temperature response (HTR) gene . Transcriptome
Introduction Electronic supplementary material The online version of this article (doi:10.1007/s10811-012-9921-2) contains supplementary material, which is available to authorized users. S. Choi and M.S. Hwang contributed equally to this paper. S. Choi : S. Im : N. Kim : D.-W. Choi (*) Department of Biology Education, Chonnam National University and KhumHo Research Institute, Gwangju 500-757, South Korea e-mail: [email protected] M. S. Hwang : E.-J. Park : Y.-G. Gong Seaweed Research Center, National Fisheries Research and Development Institute, Mokpo 530-831, South Korea W.-J. Jeong Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, South Korea
Pyropia tenera (Kjellman) Kikuchi, Miyata, Hwang & Choi has been used as an edible red alga and cultured in East Asia (Hwang et al. 2005; Miura 1988). Under natural conditions, most Pyropia grow in the in
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