Characterization of the Two Intra-Individual Sequence Variants in the 18S rRNA Gene in the Plant Parasitic Nematode, Rotylenchulus reniformis

Abstract

The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene.

Morphological and molecular characterisation of one new and several known species of the reniform nematode, Rotylenchulus Linford & Oliveira, 1940 (Hoplolaimidae: Rotylenchulinae), and a phylogeny of the genus

“…To the best of our knowledge, R. reniformis is the only organism among the phylum Nematoda for which this phenomenon has been described so far. These rRNA types showed substantial differences in sequences from each other: the 18S rRNA -5.5% (Nyaku et al, 2013b), the D2-D3 of 28S rRNA up to 15.6%, the ITS rRNA up to 24.5% (this study). In our study we also found two distinct ITS rRNA types for R. macrosomoides sp.…”

“…Reconstruction of secondary structure models for two types of the D2 of 28S rRNA for R. reniformis and mutation mapping showed that both models have similar conservative folding and most point mutations were compensatory, confirming that both gene rRNA types are functional. Nyaku et al (2013b) also revealed that both 18S rRNA types were expressed in nematode tissues as their sequences were present in ESTs. Fig.…”

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

“…The presence of indels within rRNA gene sequences may also cause problems during OTU clustering if gaps are not appropriately treated (Flynn et al 2015;THIS ISSUE). Considering the nature of rRNA genes (McTaggart and Crease, 2005;McTaggart and Crease 2009;Nyaku et al 2013), the issues raised here are likely to affect any study that applies these markers, regardless of the particular HTS technology employed. Given the conceptual and practical difficulty in translating OTUs to species, we argue that alternative approaches should also be considered when attempting to describe community composition.…”

A Rapid Diagnostic for Detection ofAphelenchoides besseyiandA. fujianensisBased on Real-Time PCR

“…Intra-individual variability of ribosomal cistrons is rare compared with the ITS but has been observed in some metazoans (Carranza et al 1996;McTaggart and Crease 2009), including nematodes (Bik et al 2013;Nyaku et al 2013). In the flatworm Dugesia mediterranea, two variants of the SSU region were found coexisting in the same individual.…”

“…the SSU region were identified (Nyaku et al 2013), and these authors considered this as a result of a recombination event during unequal crossing over between sister chromatids or rDNA between the chromosomes X and Y, carrying coevolution of these sequences in these chromosomes. Thus, the presence of variant sequences with high affinity to A. fujianensis coexisting in specimens of A. besseyi could be evidence of a recent hybridization event, or even that these sibling species recently diverged from a common parental lineage.…”