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United States Department of Agriculture

Agricultural Research Service

Research Project: AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS

Location: Genomics and Gene Discovery

Title: Sequencing and characterization of full-length sequence of 18S rRNA gene from the reniform nematode

Authors
item Nyaku, S -
item Kantety, R -
item Gu, Yong
item Venkateswara, S -
item Sharma, G -
item Lawrence, K -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 5, 2013
Publication Date: April 11, 2013
Citation: Nyaku, S.T., Kantety, R.V., Gu, Y.Q., Venkateswara, S.R., Sharma, G.V., Lawrence, K. 2013. Sequencing and characterization of full-length sequence of 18S rRNA gene from the reniform nematode. PLoS One. 8:e60891.

Interpretive Summary: The ribosomal DNA (rDNA) plays a pivotal role in protein synthesis in eukaryotes and changes in this gene can profoundly affect ecological interaction, and host range, trophic production and thus the overall growth and resource requirement. Therefore, the ramification of rRNA variation affects far beyond cell biology alone. The ribosomal DNA (rDNA) region is made up of hundreds of copies of tandemly repeated transcription units within the genomes of organisms. It consists of 18S, 5.8S, and 28S genes as well as internal and external transcribed spacers (ITS and ETS). Other molecular mechanisms such as gene conversions and unequal crossing-over also participate in keeping the copies of the repeats identical. The 18S rDNA is pivotal in phylogenetic analysis including its length and copy numbers provide significant amount of genetic information and various regions of this gene evolve at different rates. In this study, we characterized sequences of 28 rDNA from reniform nematode to elucidate its sequence variation. In addition, we identified the presence of transcription binding sites within the sequences. This work enabled comparisons in the secondary structures in the variable regions identified within the sequence, providing new insights into the sequence conservation of rDNA genes.

Technical 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. Variation within this gene is rare but it has been observed in few metazoan species. For the first time, we have identified two sequence variants within the full coding region of 18S rRNA gene from single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). Specific variable base sites (94 or 5.4%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rRNA variants of RN, in 15 (30.6%) and 34 (69.4%) of the 49 RN clones, for RN_VAR1 and RN_VAR2 respectively. Four and three transcription binding factor sites were identified for RN_VAR1 and RN_VAR2, respectively. Gene conversion was observed in RN_VAR1 (SSU1B3, SSU1B2, and SSU1B10) sequences. Neighbor-joining trees generated showed RN_VAR1 being very similar to R. reniformis, while RN_VAR2 sequence was similar to nematodes in the super-family Hoplolaimidae. Reniform variant 2 (RN_VAR2) was more highly expressed than RN_VAR1 within the RN 18S rRNA gene. This is the first report of the identification of two major variants of the full 18S rRNA gene in the same RN. This report documents the variant identification and attempts to explain the rationale for the simultaneous co-existence in these two variants for this gene with critical functionality in a single reniform nematode.

Last Modified: 8/22/2014
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