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Borodovsky, Mark

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Author: Agarkova, Irina ×

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    The genome of the polar eukaryotic microalga coccomyxa subellipsoidea reveals traits of cold adaptation
    (Georgia Institute of Technology, 2012) 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.
    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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    The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex
    (Georgia Institute of Technology, 2010-09) Blanc, Guillaume ; Duncan, Garry ; Agarkova, Irina ; Borodovsky, Mark ; Gurnon, James ; Kuo, Ala ; Lindquist, Erika ; Lucas, Susan ; Pangilinan, Jasmyn ; Polle, Juergen ; Salamov, Asaf ; Terry, Astrid ; Yamada, Takashi ; Dunigan, David D. ; Grigoriev, Igor V. ; Claverie, Jean-Michel ; Van Etten, James L.
    Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.