DNA barcoding in autotrophic euglenids: evaluation of COI and 18s rDNA.
Autotrophic euglenids (Euglenophyceae) are a common and abundant group of microbial eukaryotes in freshwater habitats. They have a limited number of features, which can be observed using light microscopy, thus species identification is often problematic. Establishing a barcode for this group is therefore an important step toward the molecular identification of autotrophic euglenids. Based on the literature, we selected verified species and used a plethora of available methods to validate two molecular markers: COI and 18S rDNA (the whole sequence and three fragments separately) as potential DNA barcodes. Analyses of the COI gene were performed based on the data set of 43 sequences (42 obtained in this study) representing 24 species and the COI gene was discarded as a DNA barcode mainly due to a lack of universal primer sites. For 18S rDNA analyses we used a data set containing 263 sequences belonging to 86 taxonomically verified species. We demonstrated that the whole 18S rDNA is too long to be a useful marker, but from the three shorter analyzed variable regions we recommend variable regions V2V3 and V4 of 18S rDNA as autotrophic euglenid barcodes due to their high efficiency (above 95% and 90%, respectively).
Department of Molecular Phylogenetics and Evolution, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
Maja
M
Łukomska-Kowalczyk
Department of Molecular Phylogenetics and Evolution, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
Anna
A
Karnkowska
Department of Molecular Phylogenetics and Evolution, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
Małgorzata
M
Krupska
Department of Molecular Phylogenetics and Evolution, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
Rafał
R
Milanowski
Department of Molecular Phylogenetics and Evolution, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
Bożena
B
Zakryś
D058893:DNA Barcoding, Taxonomic; D016054:DNA, Protozoan / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D016822:Euglenida / Q000145:classification* / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA
D016054:DNA, Protozoan; D015800:Protozoan Proteins; D012337:RNA, Ribosomal, 18S; D003576:Electron Transport Complex IV
18S rDNA; COI; DNA barcoding; Euglenophyceae; autotrophic euglenids