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A paradox: rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata (Protista, Ciliophora)

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Abstract

Some of the most extreme genome wide rearrangements are found in ciliates, which are unique in possessing both germline micronucleus and somatic macronucleus in every cell/organism. A series of DNA rearrangement events, including DNA elimination, chromosomal fragmentation, gene unscrambling and alternative processing, happen during macronuclear development. To assess the molecular evolution of macronuclear and germline-limited sequences in different cryptic species of Chilodonella uncinata, we characterized the actin, α-tubulin and β-tubulin genes in the micronucleus and macronucleus genomes of USA-SC2 strain and compared them with other strains (i.e. cryptic species). Three main results are: (i) rearrangement patterns between germline and soma are conserved for each gene among the cryptic species of C. uncinata; (ii) in contrast, the germline-limited regions are highly divergent in sequence and length among the cryptic species; (iii) pointer shifting is frequent among the cryptic species. We speculate that pointer sequences may serve as the buffer between the conserved macronuclear destined sequences and rapidly-evolving internal eliminated sequences. The data combined with previous studies demonstrate the plasticity of gene rearrangement among different groups of ciliates and add to the growing data for the role of genome rearrangements in species differentiation.

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Acknowledgements

We are grateful to Professor Weibo Song (OUC) for his kind help in preparing the draft and illustrations. This work was supported by the Natural Science Foundation of China (31772428), Young Elite Scientists Sponsorship Program by CAST (2017QNRC001), Fundamental Research Funds for the Central Universities (201841013) to Feng Gao, and the AREA award from the National Institutes of Health (1R15GM113177–01) to Laura A. Katz.

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Authors and Affiliations

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

    Tengteng Zhang, Chundi Wang & Feng Gao

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

    Tengteng Zhang, Chundi Wang & Feng Gao

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

    Laura A. Katz

  4. Program in Organismic and Evolutionary Biology, UMass-Amherst, Amherst, MA, 01003, USA

    Laura A. Katz

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  1. Tengteng Zhang
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  4. Feng Gao
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Correspondence to Feng Gao.

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Zhang, T., Wang, C., Katz, L.A. et al. A paradox: rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata (Protista, Ciliophora). Sci. China Life Sci. 61, 1071–1078 (2018). https://doi.org/10.1007/s11427-018-9333-1

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