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samedi 23 février 2013
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The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation
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.
Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses.
Background
Giant viruses in the genus Chlorovirus (family Phycodnaviridae) infect eukaryotic
green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was
sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses
in public databases. Presented here are the draft genome sequences of 35
additional chloroviruses (287 – 348 Kb / 319 – 381 predicted protein encoding genes)
collected across the globe; they infect one of three different green
algal species.
These new data allowed us to analyze the genomic landscape of 41 chloroviruses,
which revealed some remarkable features about these viruses.
Results
Genome colinearity, nucleotide conservation and phylogenetic
affinity were limited to chloroviruses infecting the same host, confirming the
validity of the three previously known subgenera. Clues for the existence of a
fourth new subgenus indicate that the boundaries of chlorovirus diversity are
not completely determined. Comparison of the chlorovirus phylogeny with that of
the algal hosts indicates that chloroviruses have changed hosts in their
evolutionary history. Reconstruction of the ancestral genome suggests that the
last common chlorovirus ancestor had a slightly more diverse protein repertoire
than modern chloroviruses. However, more than half of the defined chlorovirus
gene families have a potential recent origin (after Chlorovirus divergence), among
which a portion shows compositional evidence for horizontal gene transfer. Only
a few of the putative acquired proteins had close homologs in databases raising
the question of the true donor organism(s). Phylogenomic analysis identified
only seven proteins whose genes were potentially exchanged between the algal host
and the chloroviruses.
The present evaluation of the genomic evolution pattern suggests that chloroviruses differ from that described in the related Poxviridae and Mimiviridae. Our study shows that the fixation of algal host genes has been anecdotal in the evolutionary history of chloroviruses. We finally discuss the incongruence between compositional evidence of horizontal gene transfer and lack of close relative sequences in the databases, which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.
Conclusion
The present evaluation of the genomic evolution pattern suggests that chloroviruses differ from that described in the related Poxviridae and Mimiviridae. Our study shows that the fixation of algal host genes has been anecdotal in the evolutionary history of chloroviruses. We finally discuss the incongruence between compositional evidence of horizontal gene transfer and lack of close relative sequences in the databases, which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.
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