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

Abstract

Background Molecular 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. Methods To 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. Results The 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. Conclusions This 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.

Genetic and morphological identification of filarial worm from Iberian hare in Portugal

“…As refered before, no sequences are presently available for Micipsella genus regarding genes myoHC , hsp70 and rbp1 and 18S rDNA . Furthermore, given the lower resolution at lower taxonomic levels of nuclear 18S rDNA compared with mitochondrial 12S rDNA 49 , the 18S rDNA sequence of the specimens being described showed 99.15% similarity both with Rumenfilaria andersoni (KP760163) (Spendidofilariinae) and Filarioid sp. (EF081340) (Filarioidea).…”

“…The mitochondrial 12S rDNA is a genetic marker useful to study the molecular systematics of nematodes and to reveal intra-phyla relationships 49 . It is often concatenad to other mitochondrial genes such as coxI 13 and 16S DNA 49 , to potentiate the discriminatory power of the nucleotide variability.…”

Molecular Characterization of Paramphistomum cervi in Buffaloes

“…Thus PCR can detect the minute amount of DNA for identifying the genetic fingerprints of Paramphistome [18,35]. Several valuable genetic markers including mtDNA and 18S rRNA, have been used effectively to identify trematode species [3]. The 18S rRNA sequences are mostly utilized for Paramphistomum species identification [17,36].…”

“…The purified sequence was BLAST in NCBI to scan for similar sequences deposited from different regions for the same gene fragment. The scanned Paramphistomum species sequences were downloaded and aligned in the BioEdit Sequence Alignment Editor v 7.0.5 2 and a phylogenetic tree was constructed using maximum likelihood method keeping 1000 bootstrap replicates for branch support in MEGA v X software 3 . A distantly related trematode species Taenia solium (Accession: Q260091) was taken as an outgroup to examine the reliability of the phylogenetic tree.…”

Applying taxonomic boundaries for species identification (ABIapp): A convenient and accurate application for species delimitation of parasitic helminths

“…PCR was performed in a final volume of 30 µl, containing 15 µl of 2X i-TaqTM mastermix (iNtRON Biotechnology, Gyeonggi, South Korea), 10 µM to 50 µM of each primer and template DNA. The thermocycling conditions followed those detailed in the respective publications describing the primers [28][29][30][31][32][33]. Amplicons were visualized on 1% agarose gel stained with RedSafe® (Thomas Scientific, New Jersey, USA), and successful amplicons were purified using the Geneaid PCR purification kit (Geneaid Biotech Ltd., Taipei, Taiwan).…”