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Biochemistry (Moscow)

, Volume 72, Issue 12, pp 1313–1323 | Cite as

Do we need many genes for phylogenetic inference?

  • V. V. Aleshin
  • A. V. Konstantinova
  • K. V. Mikhailov
  • M. A. Nikitin
  • N. B. Petrov
Article

Abstract

Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales + Spizellomycetales + Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis), and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha + Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize reconstruction artifacts.

Key words

molecular evolution homoplasy origin of multicellular organisms secondary structure of SSU rRNA Tylenchida 

Abbreviations

eEF1A

eukaryotic elongation factor 1A

EFL

elongation factor-like (a paralog of elongation factor 1A)

FUBI

ubiquitin-like peptide fused with S30 ribosomal protein of animals and other Holozoa

Hsp

heat shock protein, chaperon

RpL

ribosomal protein of large ribosomal subunit

RpS

ribosomal protein of small ribosomal subunit

tef

gene of elongation factor 1A

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Copyright information

© Pleiades Publishing, Ltd. 2007

Authors and Affiliations

  • V. V. Aleshin
    • 1
  • A. V. Konstantinova
    • 1
  • K. V. Mikhailov
    • 2
  • M. A. Nikitin
    • 2
  • N. B. Petrov
    • 1
  1. 1.Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
  2. 2.Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia

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