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Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Cindy Martens (UGent) , Klaas Vandepoele (UGent) and Yves Van de Peer (UGent)
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Abstract
The chromalveolates form a highly diverse and fascinating assemblage of organisms, ranging from obligatory parasites such as Plasmodium to free-living ciliates and algae such as kelps, diatoms, and dinoflagellates. Many of the species in this monophyletic grouping are of major medical, ecological, and economical importance. Nevertheless, their genome evolution is much less well studied than that of higher plants, animals, or fungi. In the current study, we have analyzed and compared 12 chromalveolate species for which whole-sequence information is available and provide a detailed picture on gene loss and gene gain in the different lineages. As expected, many gene loss and gain events can be directly correlated with the lifestyle and specific adaptations of the organisms studied. For instance, in the obligate intracellular Apicomplexa we observed massive loss of genes that play a role in general basic processes such as amino acid, carbohydrate, and lipid metabolism, reflecting the transition of a free-living to an obligate intracellular lifestyle. In contrast, many gene families show species-specific expansions, such as those in the plant pathogen oomycete Phytophthora that are involved in degrading the plant cell wall polysaccharides to facilitate the pathogen invasion process. In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer.
Keywords
PLASMODIUM-FALCIPARUM, THEILERIA-PARVA, PHYLOGENETIC ANALYSIS, PHYTOPHTHORA-RAMORUM, RIBOSOMAL-RNA, PROTEIN, GENES, EUKARYOTES, SEQUENCES, CLASSIFICATION

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MLA
Martens, Cindy, et al. “Whole-Genome Analysis Reveals Molecular Innovations and Evolutionary Transitions in Chromalveolate Species.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 105, no. 9, 2008, pp. 3427–32, doi:10.1073/pnas.0712248105.
APA
Martens, C., Vandepoele, K., & Van de Peer, Y. (2008). Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(9), 3427–3432. https://doi.org/10.1073/pnas.0712248105
Chicago author-date
Martens, Cindy, Klaas Vandepoele, and Yves Van de Peer. 2008. “Whole-Genome Analysis Reveals Molecular Innovations and Evolutionary Transitions in Chromalveolate Species.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 105 (9): 3427–32. https://doi.org/10.1073/pnas.0712248105.
Chicago author-date (all authors)
Martens, Cindy, Klaas Vandepoele, and Yves Van de Peer. 2008. “Whole-Genome Analysis Reveals Molecular Innovations and Evolutionary Transitions in Chromalveolate Species.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 105 (9): 3427–3432. doi:10.1073/pnas.0712248105.
Vancouver
1.
Martens C, Vandepoele K, Van de Peer Y. Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2008;105(9):3427–32.
IEEE
[1]
C. Martens, K. Vandepoele, and Y. Van de Peer, “Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species,” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 105, no. 9, pp. 3427–3432, 2008.
@article{439527,
  abstract     = {{The chromalveolates form a highly diverse and fascinating assemblage of organisms, ranging from obligatory parasites such as Plasmodium to free-living ciliates and algae such as kelps, diatoms, and dinoflagellates. Many of the species in this monophyletic grouping are of major medical, ecological, and economical importance. Nevertheless, their genome evolution is much less well studied than that of higher plants, animals, or fungi. In the current study, we have analyzed and compared 12 chromalveolate species for which whole-sequence information is available and provide a detailed picture on gene loss and gene gain in the different lineages. As expected, many gene loss and gain events can be directly correlated with the lifestyle and specific adaptations of the organisms studied. For instance, in the obligate intracellular Apicomplexa we observed massive loss of genes that play a role in general basic processes such as amino acid, carbohydrate, and lipid metabolism, reflecting the transition of a free-living to an obligate intracellular lifestyle. In contrast, many gene families show species-specific expansions, such as those in the plant pathogen oomycete Phytophthora that are involved in degrading the plant cell wall polysaccharides to facilitate the pathogen invasion process. In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer.}},
  author       = {{Martens, Cindy and Vandepoele, Klaas and Van de Peer, Yves}},
  issn         = {{0027-8424}},
  journal      = {{PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}},
  keywords     = {{PLASMODIUM-FALCIPARUM,THEILERIA-PARVA,PHYLOGENETIC ANALYSIS,PHYTOPHTHORA-RAMORUM,RIBOSOMAL-RNA,PROTEIN,GENES,EUKARYOTES,SEQUENCES,CLASSIFICATION}},
  language     = {{eng}},
  number       = {{9}},
  pages        = {{3427--3432}},
  title        = {{Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species}},
  url          = {{http://doi.org/10.1073/pnas.0712248105}},
  volume       = {{105}},
  year         = {{2008}},
}

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