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Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny

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Abstract

Sequence-based approaches, such as analyses of ribosome DNA (rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities. However, recent studies demonstrate both rDNA copy number variation and intra-individual (intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA (SSU rDNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that: (i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa; (ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template; (iii) compared with the most common version, other variant sequences differ in only 1–3 nucleotides, likely generated during macronuclear (somatic) amplification; (iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses; (v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall, these analyses indicate the need for careful consideration of SSU rDNA variation in analyses of the role of ciliates in ecosystems.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31772428), the National Science Foundation of the USA (1541511), Young Elite Scientists Sponsorship Program by CAST, and Fundamental Research Funds for the Central Universities (201841013 and 201762017). We thank Prof. Weibo Song, Ocean University of China (OUC), for the helpful suggestions in drafting this manuscript. Many thanks are also due to Wen Song, Chunyu Lian, Mingjian Liu, Borong Lu, Song Li, Rui Wang, Lun Wang and Yang Bai, graduate students in OUC, for their help in species identification.

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  1. Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China

    Yurui Wang, Chundi Wang, Yaohan Jiang, Feng Gao & Ying Yan

  2. Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China

    Yurui Wang, Chundi Wang, Yaohan Jiang, Feng Gao & Ying Yan

  3. Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA

    Laura A. Katz & Ying Yan

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  1. Yurui Wang
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Correspondence to Feng Gao or Ying Yan.

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Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny

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Wang, Y., Wang, C., Jiang, Y. et al. Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. Sci. China Life Sci. 62, 203–214 (2019). https://doi.org/10.1007/s11427-018-9422-5

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