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.
Highlights
The ribosomal DNA plays a pivotal role in protein synthesis in eukaryotes and changes in these genes can profoundly affect ecological interactions, host range, trophic production, and the overall growth and resource requirement of the organism [1]
Two types of 18S ribosomal DNA (rDNA) sequences were observed from Multiple sequence alignment (MSA), these were labeled as reniform nematode variant 1 (RN_VAR1) and reniform variant 2 (RN_VAR2) referred to as the first and second variants of the 18S rDNA sequence of the reniform nematode (RN), respectively
Ribosomal DNA codes for RNA molecules and these are separated by intergenic spacers that control transcription of the rRNA genes
Summary
The ribosomal DNA (rDNA) plays a pivotal role in protein synthesis in eukaryotes and changes in these genes can profoundly affect ecological interactions, host range, trophic production, and the overall growth and resource requirement of the organism [1]. The rDNA region is composed of numerous copies of tandemly repeated transcription units within the genome. It consists of the 18S, 5.8S, and 28S genes as well as internal and external transcribed spacers (ITS and ETS) [2]. Concerted evolution is implicated in the conservative nature of the repeats [3,4], through molecular mechanisms such as gene conversion [4,5] and unequal crossing-over [6]. Intra and inter variations within the 18S rRNA gene sequences of species have been observed in genomes of some organisms [7,8,9] often attributed to frequent recombination events involving unequal crossovers and gene conversions producing rDNA units having similar sequences [9]
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