title: NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene)-A new "Holy Grail" phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)?
abstract: Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.
authors.affiliation: Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland; Department of Zoology, University of Sao Paulo, 05508-090 Sao Paulo, Brazil.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Blandenier
authors.affiliation: Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland. Electronic address: enrique.lara@unine.ch.
authors.forename: Enrique
authors.initials: E
authors.lastname: Lara
authors.affiliation: Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland; Botanical Garden of Neuchâtel, Chemin du Perthuis-du-Sault 58, 2000 Neuchâtel, Switzerland.
authors.forename: Edward A D
authors.initials: EA
authors.lastname: Mitchell
authors.affiliation: Department of Zoology, University of Sao Paulo, 05508-090 Sao Paulo, Brazil.
authors.forename: Daniel M C
authors.initials: DM
authors.lastname: Alcantara
authors.affiliation: Julianaweg 10, 1241VW Kortenhoef, Netherlands.
authors.forename: Ferry J
authors.initials: FJ
authors.lastname: Siemensma
authors.affiliation: Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin St., 1113 Sofia, Bulgaria.
authors.forename: Milcho
authors.initials: M
authors.lastname: Todorov
authors.affiliation: Department of Zoology, University of Sao Paulo, 05508-090 Sao Paulo, Brazil. Electronic address: dlahr@ib.usp.br.
authors.forename: Daniel J G
authors.initials: DJ
authors.lastname: Lahr
mesh_terms: D056894:Amoebozoa / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000592:standards*; D017125:Genes, Protozoan / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D009245:NADH Dehydrogenase / Q000235:genetics*; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D005819:Genetic Markers; D009245:NADH Dehydrogenase
keywords: Arcella; Environmental DNA survey; Intergenic region; Mitochondrion; Molecular barcoding