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Pyrosequence Analysis of Expressed Sequence Tags for the Antarctic Hairgrass Deschampsia antarctica under Various Abiotic Stresses

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Title
Pyrosequence Analysis of Expressed Sequence Tags for the Antarctic Hairgrass Deschampsia antarctica under Various Abiotic Stresses
Other Titles
파이로시퀑싱을 이용하여 다양한 비생물 스트레스 하에서 발현하는 남극좀새풀 유전체 분석
Authors
Kim, Il-Chan
Lee, Yoo Kyung
Yim, Joung Han
Park, Mira
Kim, Ji Hyun
Choi, Hyung-Seok
Lee, Hyoungseok
Keywords
Deschampsia antarctica; Expressed sequence tag; pyrosequencing; stress
Issue Date
2009
Citation
Kim, Il-Chan, et al. 2009. Pyrosequence Analysis of Expressed Sequence Tags for the Antarctic Hairgrass Deschampsia antarctica under Various Abiotic Stresses. SCAR. SCAR. 2009.08.21~.
Abstract
Deschampsia antarctica is the only monocot that thrives in the Antarctic region. Despite it is an invaluable resource for the identification of genes associated with tolerance to various environmental pressures, 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 one control and three 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. Finally, we could have a total of 60,765 unigenes containing 28,177 singletons. Using similarity searches against several public databases, we constructed a functional classification of the ESTs into categories such as genes related to responses to stimuli, as well as photosynthesis and metabolism. 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. Real-time PCR analysis of various stress responsive genes revealed different patterns of regulation in the different environments, suggesting that these genes are involved in responses to specific environmental factors.
URI
http://repository.kopri.re.kr/handle/201206/7927
Conference Name
SCAR
Conference Place
SCAR
Conference Date
2009.08.21~
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