Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths

Abigail Hui En Chan (1) , Abigail Hui En Chan (1) , Kittipong Chaisiri (1) , Sompob Saralamba (1) , Serge Morand (2, 3, 4) , Urusa Thaenkham (1)

1 Faculty of Tropical Medicine - Department of Clinical Tropical Medicine [Bangkok, Thailand]
2 UMR ASTRE - Animal, Santé, Territoires, Risques et Ecosystèmes
3 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
4 KU - Kasetsart University [Bangkok, Thailand]

Background: Genetic markers are employed widely in molecular studies, and their utility depends on the degree of sequence variation, which dictates the type of application for which they are suited. Consequently, the suitability of a genetic marker for any specific application is complicated by its properties and usage across studies. To provide a yardstick for future users, in this study we assess the suitability of genetic markers for molecular systematics and species identification in helminths and provide an estimate of the cutoff genetic distances per taxonomic level. Methods: We assessed four classes of genetic markers, namely nuclear ribosomal internal transcribed spacers, nuclear rRNA, mitochondrial rRNA and mitochondrial protein-coding genes, based on certain properties that are important for species identification and molecular systematics. For molecular identification, these properties are interspecies sequence variation; length of reference sequences; easy alignment of sequences; and easy to design universal primers. For molecular systematics, the properties are: average genetic distance from order/suborder to species level; the number of monophyletic clades at the order/suborder level; length of reference sequences; easy alignment of sequences; easy to design universal primers; and absence of nucleotide substitution saturation. Estimation of the cutoff genetic distances was performed using the 'K-means' clustering algorithm. Results: The nuclear rRNA genes exhibited the lowest sequence variation, whereas the mitochondrial genes exhibited relatively higher variation across the three groups of helminths. Also, the nuclear and mitochondrial rRNA genes were the best possible genetic markers for helminth molecular systematics, whereas the mitochondrial proteincoding and rRNA genes were suitable for molecular identification. We also revealed that a general gauge of genetic distances might not be adequate, using evidence from the wide range of genetic distances among nematodes.

Mots clés: Genetic marker; Molecular systematics; Molecular identification; Helminth; K-means

Domaines: Sciences du Vivant [q-bio]

Abigail Hui En Chan, Abigail Hui En Chan, Kittipong Chaisiri, Sompob Saralamba, Serge Morand, et al.. Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths. Parasites & Vectors, 2021, 14 (1), ⟨10.1186/s13071-021-04737-y⟩. ⟨hal-03313140⟩