Open Access Research

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

Guillaume Blanc1*, Irina Agarkova2, Jane Grimwood3, Alan Kuo3, Andrew Brueggeman4, David D Dunigan2, James Gurnon2, Istvan Ladunga4, Erika Lindquist3, Susan Lucas3, Jasmyn Pangilinan3, Thomas Pröschold5, Asaf Salamov3, Jeremy Schmutz3, Donald Weeks4, Takashi Yamada6, Alexandre Lomsadze7, Mark Borodovsky7, Jean-Michel Claverie1, Igor V Grigoriev3 and James L Van Etten2

Author affiliations

1 Structural and Genomic Information Laboratory, UMR7256 CNRS, Aix-Marseille University, Mediterranean Institute of Microbiology (FR3479), Marseille, FR-13385, France

2 Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska - Lincoln, Lincoln, NE 68583-0722, USA

3 DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

4 Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA

5 Department of Applied Ecology, University of Rostock, Department Applied Ecology, Albert-Einstein-Str. 3, D-18059 Rostock, Germany

6 Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan

7 Georgia Tech Center for Bioinformatics and Computational Genomics, Joint Georgia Tech and Emory Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA 30332, USA

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Citation and License

Genome Biology 2012, 13:R39  doi:10.1186/gb-2012-13-5-r39

Published: 25 May 2012

Abstract

Background

Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced.

Results

The 48.8 Mb genome contained in 20 chromosomes exhibits significant synteny conservation with the chromosomes of its relatives Chlorella variabilis and Chlamydomonas reinhardtii. The order of the genes is highly reshuffled within synteny blocks, suggesting that intra-chromosomal rearrangements were more prevalent than inter-chromosomal rearrangements. Remarkably, Zepp retrotransposons occur in clusters of nested elements with strictly one cluster per chromosome probably residing at the centromere. Several protein families overrepresented in C. subellipsoidae include proteins involved in lipid metabolism, transporters, cellulose synthases and short alcohol dehydrogenases. Conversely, C-169 lacks proteins that exist in all other sequenced chlorophytes, including components of the glycosyl phosphatidyl inositol anchoring system, pyruvate phosphate dikinase and the photosystem 1 reaction center subunit N (PsaN).

Conclusions

We suggest that some of these gene losses and gains could have contributed to adaptation to low temperatures. Comparison of these genomic features with the adaptive strategies of psychrophilic microbes suggests that prokaryotes and eukaryotes followed comparable evolutionary routes to adapt to cold environments.