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Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress

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Abstract

Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been studied as an extremophile that has successfully adapted to marginal land with the harshest environment for terrestrial plants. However, limited genetic research has focused on this species due to the lack of genomic resources. Here, we present the first de novo assembly of its transcriptome by massive parallel sequencing and its expression profile using D. antarctica grown under various stress conditions. Total sequence reads generated by pyrosequencing were assembled into 60,765 unigenes (28,177 contigs and 32,588 singletons). A total of 29,173 unique protein-coding genes were identified based on sequence similarities to known proteins. The combined results from all three stress conditions indicated differential expression of 3,110 genes. Quantitative reverse transcription polymerase chain reaction showed that several well-known stress-responsive genes encoding late embryogenesis abundant protein, dehydrin 1, and ice recrystallization inhibition protein were induced dramatically and that genes encoding U-box-domain-containing protein, electron transfer flavoprotein-ubiquinone, and F-box-containing protein were induced by abiotic stressors in a manner conserved with other plant species. We identified more than 2,000 simple sequence repeats that can be developed as functional molecular markers. This dataset is the most comprehensive transcriptome resource currently available for D. antarctica and is therefore expected to be an important foundation for future genetic studies of grasses and extremophiles.

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Abbreviations

AOX:

Alternative oxidase

DEG:

Differentially expressed gene

DHN:

Dehydrin

EC:

Enzyme commission

EST:

Expressed sequence tags

GC:

Guanine–cytosine

GI:

GIGANTEA

GO:

Gene ontology

IRIP:

Ice recrystallization inhibition protein

IVD:

Isovaleryl Co-A dehydrogenase

KEGG:

Kyoto Encyclopedia of Genes and Genomes

LEA:

Late embryogenesis abundant protein

PEPC:

Phosphoenolpyruvate carboxylase

ProDH:

Proline dehydrogenase

qPCR:

Quantitative reverse transcription polymerase chain reaction

SSR:

Simple sequence repeat

TIM:

Inner membrane translocase subunit

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Acknowledgments

This work was supported by Functional Genomics on Polar Organisms grant (PE12020) funded by Korea Polar Research Institute (KOPRI).

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Authors and Affiliations

  1. Division of Life Sciences, Korea Polar Research Institute, 12 Gaetbeol-ro, Yeonsu-gu, Incheon, 406-840, Korea

    Jungeun Lee, Eun Kyeung Noh, Seung Chul Shin, Hyun Park & Hyoungseok Lee

  2. Bio&Health Team, Future IT R&D Laboratory, LGE Advanced Research Institute, 38 Baumoe-ro, Seocho-gu, Seoul, 137-724, Korea

    Hyung-Seok Choi

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  1. Jungeun Lee
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  2. Eun Kyeung Noh
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Correspondence to Hyoungseok Lee.

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Lee, J., Noh, E.K., Choi, HS. et al. Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress. Planta 237, 823–836 (2013). https://doi.org/10.1007/s00425-012-1797-5

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