Utility of divergent domains of 28S ribosomal RNA in species discrimination of paramphistomes (Trematoda: Digenea: Paramphistomoidea)

Abstract

Among the digenetic trematodes, paramphistomes are known to be the causative agent of "amphistomiasis" or the stomach fluke disease of domestic and wild animals, mainly ruminants. The use of 28S (divergent domains) and 18S rRNA for phylogenetic inference is significantly warranted for these flukes since it is as yet limited to merely the exploration of the second internal transcribed spacer (ITS2) region. The present study intended to explore the divergent domains (D1-D3) of 28S rRNA and simultaneously equate the phylogenetic information with 18S rRNA in paramphistomes. Divergence of the 28S rRNA domains was evident amongst the divergent (D) domains, where D1 domain emerged as the most variable and D2, the most robust domain, since the latter could provide a higher resolution of the species. D2 was the only domain that comprised compensatory mutations in the helices of its structural constraints; this domain is thus well suited for species distinction and may be considered a potential DNA barcode complementary to mitochondrial DNA. 28S (D1 + D2 + D3) rRNA provided a significant resolution of the taxa corroborating with the taxonomy of these flukes and thus proved to be more robust as a phylogenetic marker for lower levels than 18S rRNA. Phylogenetic inferences of paramphitomes are still scarcely explored; additional data from other taxa belonging to this family may estimate better the biodiversity of these flukes.

Molecular Characterization of Gastrothylax crumenifer (Platyhelminthes: Gastrothylacidae) from Goats in the Western Part of India by LSU of Nuclear Ribosomal DNA

“…The results of the present study confirmed that 28S ribosomal DNA region is a useful molecular marker for species identification and platyhelminthes phylogeny [ 29 , 30 , 31 , 32 ]. Phylogenetic analyses results based on 28S sequences revealed that G. crumenifer from Meerut is closely related with the G. crumenifer obtained from Shillong, and G. crumenifer from infected goats at Meerut region showed to be identical to other G. crumenifer corresponding sequences in GenBank, in accordance with previous studies [ 32 , 33 ]. It is also confirmed that there is a highly conserved character of the 28S gene among G. crumenifer isolates from different regions of India [ 32 , 33 ].…”

Phylogenetic relationships within Dicrocoeliidae (Platyhelminthes: Digenea) from birds from the Czech Republic using partial 28S rDNA sequences

“…The highly variable D1-D3 domains of 28S rDNA were shown to be suitable to identify species and determine phylogenetic relationships within Platyhelminthes (e.g., Shylla et al 2013;Razo-Mendivil et al 2014). Since the partial (D1-D3) 28S rRNA gene has been the molecular marker of choice in various studies, numerous sequences are available for comparative analysis within GenBank; also, universal primers to amplify the region across various diverse taxa within the Platyhelminthes are available.…”

Methods of Molecular Study

“…For studies of phylogenetic relationships among species from different genera to families, the highly conserved regions of rDNA are useful, such as the entire small subunit ribosomal RNA gene (ssrDNA; 18 S rDNA) and the partial (D1-D3) large subunit ribosomal RNA gene (lsrDNA; 28 S rDNA) sequences. 10,11 However, Shylla et al (2013) studied the species discrimination of the paramphistomes (Trematoda: Digenea) and recommended the use of the D1-D3 28 S rDNA for a significant resolution of the taxa corroborating with the taxonomy of the flukes. 4 Using only part of the 18 S rDNA gene can cause a gap in phylogenetic information because over half of its total length is very conserved regions.…”

“…These regions were used to estimate the phylogeny of 163 digenean taxa from 77 nominal families. 12 The data of these regions is suitable for inference of phylogenetic relationships among species, genera, and closely related families. 9 For the 28 S rDNA gene, the 5 0 end of this gene is known as the variable domain and has been used for studying the deep branches of the metazoans and some species of digeneans.…”

“…4 Using only part of the 18 S rDNA gene can cause a gap in phylogenetic information because over half of its total length is very conserved regions. 9,11,12 The internal transcribed spacer region of ribosomal DNA (ITS rDNA) has been used as the default marker for phylogenetic analysis. 10,11 However, Shylla et al (2013) studied the species discrimination of the paramphistomes (Trematoda: Digenea) and recommended the use of the D1-D3 28 S rDNA for a significant resolution of the taxa corroborating with the taxonomy of the flukes.…”