title: Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae.
abstract: Morphological identification of naked lobose amoebae has always been a problem, hence the development of reliable molecular tools for species distinction is a priority for amoebae systematics. Previous studies based on SSU rDNA sequences provided a backbone for the phylogeny of Amoebozoa but were of little help for the species distinctions in this group. On one hand, the SSU rDNA sequences were rather conserved between closely related species; on the other hand, the intra-strain polymorphism of the SSU gene obscured species identification. In the present study, a 3' fragment of the SSU, a complete ITS1-5.8S-ITS2 block and a 5' fragment of COI gene were cloned and sequenced for six Vannella morphospecies, of which V. simplex was represented by six different isolates. SSU rDNA and ITS were found to be inappropriate for species differentiation, while distinctive and homogenous COI sequences were obtained for each well-defined morphospecies. Moreover, a number of distinct COI genotypes have been identified among V. simplex isolates. This suggests that COI may be a good candidate for DNA barcoding of amoebae, but further studies are necessary to confirm the accurateness of the COI gene as a barcode in other gymnamoebae, and to understand the taxonomic meaning of COI variations.
authors.affiliation: Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, Tikhoretsky ave. 4, 194064 St. Petersburg, Russia. nosema@mail.ru
authors.forename: Elena
authors.initials: E
authors.lastname: Nassonova
authors.forename: Alexey
authors.initials: A
authors.lastname: Smirnov
authors.forename: Jose
authors.initials: J
authors.lastname: Fahrni
authors.forename: Jan
authors.initials: J
authors.lastname: Pawlowski
mesh_terms: D056894:Amoebozoa / Q000145:classification* / Q000235:genetics*; D000818:Animals; D016000:Cluster Analysis; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D020459:Genes, rRNA; D024101:Mitochondrial Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D021122:Protein Subunits / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics; D016053:RNA, Protozoan / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D016054:DNA, Protozoan; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D024101:Mitochondrial Proteins; D021122:Protein Subunits; D015800:Protozoan Proteins; D016053:RNA, Protozoan; D012337:RNA, Ribosomal, 18S; D003576:Electron Transport Complex IV