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

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).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.Algae consist of an extremely diverse, polyphyletic group of eukaryotic photosynthetic organisms. To characterize the genetic and metabolic diversity of chlorophytes (eukaryotic green algae) and to better understand how this diversity reflects adaptation to different habitats, we sequenced the trebouxiophyceaen Coccomyxa subellipsoidea C-169 NIES 2166. C-169 is a small elongated non-motile unicellular green alga (cell size of approximately 3 to 9 μm; Figure S1A in Additional file 1) isolated in the polar summer of 1959/60 at Marble Point, Antarctica, from dried algal peat [1]. The Antarctic is a particularly harsh environment, with extremely low temperatures (as low as -88°C), frequent and rapid fluctuations from freezing to thawing temperatures, severe wi