title: The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.
abstract: 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.
authors.affiliation: Centre National de la Recherche Scientifique, Laboratoire Information Génomique et Structurale UPR2589, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, 13009 Marseille, France. guillaume.blanc@igs.cnrs-mrs.fr
authors.forename: Guillaume
authors.initials: G
authors.lastname: Blanc
authors.forename: Garry
authors.initials: G
authors.lastname: Duncan
authors.forename: Irina
authors.initials: I
authors.lastname: Agarkova
authors.forename: Mark
authors.initials: M
authors.lastname: Borodovsky
authors.forename: James
authors.initials: J
authors.lastname: Gurnon
authors.forename: Alan
authors.initials: A
authors.lastname: Kuo
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Jasmyn
authors.initials: J
authors.lastname: Pangilinan
authors.forename: Juergen
authors.initials: J
authors.lastname: Polle
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Astrid
authors.initials: A
authors.lastname: Terry
authors.forename: Takashi
authors.initials: T
authors.lastname: Yamada
authors.forename: David D
authors.initials: DD
authors.lastname: Dunigan
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Claverie
authors.forename: James L
authors.initials: JL
authors.lastname: Van Etten
mesh_terms: D001482:Base Composition; D002473:Cell Wall / Q000378:metabolism; D002708:Chlorella / Q000235:genetics* / Q000821:virology; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D005407:Flagella / Q000235:genetics; D018745:Genome, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D010937:Plant Growth Regulators / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D012098:Reproduction; D017422:Sequence Analysis, DNA; D013559:Symbiosis
chemical_list: D018744:DNA, Plant; D010937:Plant Growth Regulators