A review on the molecular characterization of digenean parasites using molecular markers with special reference to ITS region

Abstract

SummaryThe rDNA region of eukaryotes has the immense potential to resolve the evolutionary and phylogeny problems using molecular markers. As evident from the present review, ITS region data is considered for interpretation of inter and intra-specifi c variations of 136 studies of 33 families including 78 genus and 114 species affecting individuals worldwide. Along with ITS-1 and ITS-2 region in 29 studies 18S region, in 38 studies 28S region and in 43 studies mitochondrial genes (COI and NDI) were also analyzed. Three new genera (Allobilharzia gen. nov., Caulanus gen. nov., and Latuterus gen. nov.) and 49 new species were discovered. Only 47 studies expressed variations at intra-specifi c and inter-specifi c level in complete ITS region, ITS-1 and ITS-2 rDNA sequences due to differences in nucleotide positions. According to the fi ndings ITS region is more reliable and precise marker for demarcation and identifi cation of species in combination of other DNA markers. Major studies were involved around the parasites of families Fasciolidae, Schistosomatidae, Opisthorchidae, Paragonimidae and Paramphistomidae, Clinostomidae, Diplostomidae, Haploporidae, among others infecting humans, farm animals, birds, fi shes, reptiles and amphibians on the clinical basis. In future, molecular and bioinformatics aspects based on genetic variations will lead to explore the untouched areas of trematodes.

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

“…Ideally, the genetic marker should have an optimal evolution rate to provide sufficient informative sites for phylogenetic analysis and molecular identification. The marker should also show high interspecific variation between closely related species, which can be assessed through genetic distances to ascertain whether the marker has ‘sufficient’ sequence variation between organisms [ 1 , 9 , 10 , 40 , 41 ]. In this study, we used the average genetic distances for determining sequence variation between the taxa studied.…”

“…The highly conserved sequences make the nuclear rRNA genes a potentially helpful source of genetic markers for resolving higher taxonomic levels for organisms [ 1 , 6 , 10 ]. Within nDNA, the internal transcribed spacer (ITS) regions possess a higher degree of sequence variation than the nuclear rRNA genes because of a faster nucleotide substitution rate [ 6 , 8 , 10 , 11 ]. Although multiple types of genetic markers are suitable for molecular systematics and identification purposes, the varying properties of the genetic markers complicate the choice for their respective applications.…”

“…For the purposes of molecular identification, the nuclear ITS regions have been utilized successfully for species differentiation because of their high degree of sequence variation. Numerous studies have demonstrated the applicability of species-specific ITS primers to identify helminths for diagnostic purposes [ 10 , 24 , 25 ]. MtDNA genes have also been used to discriminate between species and populations [ 26 – 28 ].…”

The ribosomal transcription units of Haplorchis pumilio and H. taichui and the use of 28S rDNA sequences for phylogenetic identification of common heterophyids in Vietnam

“…This is particularly so when phylogenetically divergent species are being compared and suggest that this region is not suitable for deep-level phylogenies [17]. At the level of genus and species, however, alignments of ITS sequences have proved valuable for phylogenetic studies and molecular taxonomy [17, 41, 42]. …”

Application of different molecular markers in biotechnology

“…ITS is a degraded region during maturation in ribosomal transcript. (Choudhary et al, 2015) ITS due to more variation properties than ribosomal sequences have been commonly used for molecular markers to figure out phylogenetic analysis and/or identification of bacteria, plant and animal strains and/or species (Lee et al, 2017;Rocha et al, 2019;Ali et al, 2019;Fazeli-Nasab et al, 2020). Pourahmad et al (2019) performed sequence analysis of the mycobacterial 16S-23S ITS region to determine aquatic mycobacteria species, reporting effectiveness of this marker.…”