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Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain

Ryohei Ueno^1,

¹ Laboratory of Marine Biochemistry, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo 108-8477, Japan
² Lehrstuhl für Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, Erlangen 91058, Germany
³ Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan

Correspondence
Shugo Watabe
awatabe{at}mail.ecc.u-tokyo.ac.jp

Informational genes such as those encoding rRNAs are related to transcription and translation, and are thus considered to be rarely subject to lateral gene transfer (LGT) between different organisms, compared to operational genes having metabolic functions. However, several lines of evidence have suggested or confirmed the occurrence of LGT of DNA segments encoding evolutionarily variable regions of rRNA genes between different organisms. In the present paper, we show, for the first time to our knowledge, that variable regions of the 18S rRNA gene are segmentally replaced by multiple copies of different sequences in a single strain of the green microalga Prototheca wickerhamii, resulting in at least 17 genotypes, nine of which were actually transcribed. Recombination between different 18S rRNA genes occurred in seven out of eight variable regions (V1–V5 and V7–V9) of eukaryotic small subunit (SSU) rRNAs. While no recombination was observed in V1, one to three different recombination loci were demonstrated for the other regions. Such segmental replacement was also implicated for helix H37, which is defined as V6 of prokaryotic SSU rRNAs. Our observations provide direct evidence for redundant recombination of an informational gene, which encodes a component of mature ribosomes, in a single strain of one organism.

Present address: Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.

The GenBank/EMBL/DDBJ accession numbers for the SSU rRNA sequences of Prototheca wickerhamii identified in this work are AB251576–AB251599.

Two supplementary figures showing the primers used for mPCR and RT-PCR, and secondary structure models for mosaic 18S rRNA helices, are available with the online version of this paper.