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Pyrosequencing analysis of the antarctic hairgrass Deschampsia antarctica under various abiotic stresses

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Title
Pyrosequencing analysis of the antarctic hairgrass Deschampsia antarctica under various abiotic stresses
Other Titles
Pyrosequencing analysis of the antarctic hairgrass Deschampsia antarctica under various abiotic stresses
Authors
Park, Mira
Lee, Yoo Kyung
Kim, Ji Hyun
Lee, Hyoungseok
Kim, Il-Chan
Yim, Joung Han
Choi, Hyung-Seok
Keywords
Deschampsia antarctica; antarctic; pyrosequencing
Issue Date
2010
Citation
Park, Mira, et al. 2010. Pyrosequencing analysis of the antarctic hairgrass Deschampsia antarctica under various abiotic stresses. 극지연구소. 극지연구소. 2010.05.27~.
Abstract
Deschampsia antarctica is the only monocot that thrives in the Antarctic region. Despite it is an invaluable species to study mechanisms of molecular adaptation to extreme environments, little transcriptome information is available. In order to get a broad view of genetic responses to various abiotic stresses, we synthesized and sequenced cDNA fragments from RNAs of plant samples under low temperature, high salt, and PEG treatment. Using massively parallel pyrosequencing, we obtained 370,169 D. antarctica expressed sequence tags (ESTs) at an average size of 212 bp per read. A majority of sequences (337,581 reads) could be assembled into 28,177 contigs with an average size of 425 bp, and 32,588 singletons, resulting in a total of 60,765 unigenes. In silico analysis using 28,177 contigs revealed that 585, 586, and 774 contigs were specifically up-regulated, and 36, 379, and 217 contigs were specifically down-regulated by low temperature, high salt, and PEG treatment, respectively. D. antarctica 44K microarray was designed and prepared to investigate differential expression profile under cold stresses. Analysis of microarray to compare plants grown at 25ºC and 4ºC have shown that 137 genes significantly were induced by cold and 115 genes were repressed. Also, comparative analysis of expression pattern between D. antarctica and barley under cold was conducted to find genes working specifically in D. antarctica. Results have shown about 300 genes having significantly different expression pattern between two monocot species.
URI
http://repository.kopri.re.kr/handle/201206/8049
Conference Name
극지연구소
Conference Place
극지연구소
Conference Date
2010.05.27~
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