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

Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D. Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Pröschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean Michel Claverie, Igor V. GrigorievJames L. Van Etten

Research output: Contribution to journalArticle

153 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberR39
JournalGenome biology
Volume13
Issue number5
DOIs
StatePublished - May 25 2012

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Coccomyxa
microalga
Synteny
chromosome
Chlorophyta
genome
Genome
chromosomes
protein
Orthophosphate Dikinase Pyruvate
Chromosomes
Chromosomes, Human, Pair 20
Cold Climate
cellulose synthase
microorganisms
Chlorella
Chlamydomonas reinhardtii
Polar Regions
Retroelements
Proteins

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. / Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane; Kuo, Alan; Brueggeman, Andrew; Dunigan, David D.; Gurnon, James; Ladunga, Istvan; Lindquist, Erika; Lucas, Susan; Pangilinan, Jasmyn; Pröschold, Thomas; Salamov, Asaf; Schmutz, Jeremy; Weeks, Donald; Yamada, Takashi; Lomsadze, Alexandre; Borodovsky, Mark; Claverie, Jean Michel; Grigoriev, Igor V.; Van Etten, James L.

In: Genome biology, Vol. 13, No. 5, R39, 25.05.2012.

Research output: Contribution to journalArticle

Blanc, G, Agarkova, I, Grimwood, J, Kuo, A, Brueggeman, A, Dunigan, DD, Gurnon, J, Ladunga, I, Lindquist, E, Lucas, S, Pangilinan, J, Pröschold, T, Salamov, A, Schmutz, J, Weeks, D, Yamada, T, Lomsadze, A, Borodovsky, M, Claverie, JM, Grigoriev, IV & Van Etten, JL 2012, 'The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation', Genome biology, vol. 13, no. 5, R39. https://doi.org/10.1186/gb-2012-13-5-r39
Blanc, Guillaume ; Agarkova, Irina ; Grimwood, Jane ; Kuo, Alan ; Brueggeman, Andrew ; Dunigan, David D. ; Gurnon, James ; Ladunga, Istvan ; Lindquist, Erika ; Lucas, Susan ; Pangilinan, Jasmyn ; Pröschold, Thomas ; Salamov, Asaf ; Schmutz, Jeremy ; Weeks, Donald ; Yamada, Takashi ; Lomsadze, Alexandre ; Borodovsky, Mark ; Claverie, Jean Michel ; Grigoriev, Igor V. ; Van Etten, James L. / The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. In: Genome biology. 2012 ; Vol. 13, No. 5.
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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.",
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AU - Blanc, Guillaume

AU - Agarkova, Irina

AU - Grimwood, Jane

AU - Kuo, Alan

AU - Brueggeman, Andrew

AU - Dunigan, David D.

AU - Gurnon, James

AU - Ladunga, Istvan

AU - Lindquist, Erika

AU - Lucas, Susan

AU - Pangilinan, Jasmyn

AU - Pröschold, Thomas

AU - Salamov, Asaf

AU - Schmutz, Jeremy

AU - Weeks, Donald

AU - Yamada, Takashi

AU - Lomsadze, Alexandre

AU - Borodovsky, Mark

AU - Claverie, Jean Michel

AU - Grigoriev, Igor V.

AU - Van Etten, James L.

PY - 2012/5/25

Y1 - 2012/5/25

N2 - 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.

AB - 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.

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