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Combined Analysis of the Chloroplast Genome andTranscriptome of the Antarctic Vascular PlantDeschampsia antarctica Desv

Cited 37 time in wos
Cited 35 time in scopus
Title
Combined Analysis of the Chloroplast Genome andTranscriptome of the Antarctic Vascular PlantDeschampsia antarctica Desv
Authors
Lee, Jong Eun
Lee, Hyoungseok
Park, Hyun
Shin, Seung Chul
Kang, Yoonjee
Keywords
Antarctic Sejong stationDeschampsia antarcticachloroplastgenome
Issue Date
2014
Citation
Lee, Jong Eun, et al. 2014. "Combined Analysis of the Chloroplast Genome andTranscriptome of the Antarctic Vascular PlantDeschampsia antarctica Desv". PLOS ONE, 9(3): 92501-NaN.
Abstract
Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been researched as an important ecological marker and as an extremophile plant for studies on stress tolerance. Despite its importance, little genomic information is available for D. antarctica. Here, we report the complete chloroplast genome, transcriptome profiles of the coding/noncoding genes, and the posttranscriptional processing by RNA editing in the chloroplast system. The complete chloroplast genome of D. antarctica is 135,362 bp in length with a typical quadripartite structure, including the large (LSC: 79,881 bp) and small (SSC: 12,519 bp) single-copy regions, separated by a pair of identical inverted repeats (IR: 21,481 bp). It contains 114 unique genes, including 81 unique protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Sequence divergence analysis with other plastomes from the BEP clade of the grass family suggests a sister relationship between D. antarctica, Festuca arundinacea and Lolium perenne of the Poeae tribe, based on the whole plastome. In addition, we conducted high-resolution mapping of the chloroplast-derived transcripts. Thus, we created an expression profile for 81 protein-coding genes and identified ndhC, psbJ, rps19, psaJ, and psbA as the most highly expressed chloroplast genes. Small RNA-seq analysis identified 27 small noncoding RNAs of chloroplast origin that were preferentially located near the 5′- or 3′-ends of genes. We also found >30 RNA-editing sites in the D. antarctica chloroplast genome, with a dominance of C-to-U conversions. We assembled and characterized the complete chloroplast genome sequence of D. antarctica and investigated the features of the plastid transcriptome. These data may contribute to a better understanding of the evolution of D. antarctica within the Poaceae family for use in molecular phylogenetic studies and may also help researchers understand the characteristics of the chloroplast transcriptome.
URI
https://repository.kopri.re.kr/handle/201206/7254
DOI
http://dx.doi.org/10.1371/journal.pone.0092501
Type
Article
Indexed
SCIE
Appears in Collections  
2013-2013, Study of Non-coding RNAs under Environmental Stress in Deschampsia antarctica (13-13) / Lee, Jong Eun (PE13120)
2014-2016, Antarctic Organisms: Cold-Adaptation Mechanism and Its Application (14-16) / Park; Hyun (PE14070; PE15070; PE16070)
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