Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

Naowarat Saralamba,Kittipong Chaisiri,Abigail Hui En Chan,Serge Morand,Urusa Thaenkham

doi:10.1186/s13071-020-04242-8

Abstract

BackgroundMolecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics.MethodsTo study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms.ResultsThe phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers.ConclusionsThis study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

Highlights

Molecular advances have accelerated our understanding of nematode systematics and taxonomy
Evaluation of potential genetic markers for molecular systematics of nematodes DNA sequences from the National Center for Biotechnology Information (NCBI) database were obtained for nuclear ribosomal regions internal transcribed spacer 1 (ITS1) and internal transcribed spacer 2 (ITS2), 18S and 28S ribosomal RNA (rRNA) genes, and mitochondrial genes of cox1 and 12S and 16S rRNA
The potential of mitochondrial 12S and 16S rRNA genes for DNA barcoding of nematodes cannot be disregarded, as we have shown the capability of these two genetic markers to discriminate between species

Summary

Introduction

Molecular advances have accelerated our understanding of nematode systematics and taxonomy. Commonly known as roundworms, comprise the second largest phylum in Animalia, which has more than 40,000 extant species [1]. They are a highly diverse group of organisms, and of the extant species, approximately a third of them are found in vertebrates, with a significant proportion causing diseases in humans and animals worldwide [2]. A substantial proportion of the world’s population is at risk of acquiring diseases caused by nematodes. Animal parasitic nematodes cause substantial economic losses by infecting livestock [3]

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