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Characterization of 18S-ITS1-5.8S rDNA in eleven species in Soleidae: implications for phylogenetic analysis

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Abstract

For several decades, both concerted evolution and non-concerted evolution of rRNA genes have been discovered in a wide variety of species. To explore the evolutionary patterns and to evaluate the variability at the intra-individual and interspecific levels in Soleidae, a total of 233 complete 18S-ITS1-5.8S rDNA sequences from 11 representative species were generated. The results indicated that six species had little variation, suggesting a concerted evolutionary pattern. However, in the other five species, much variation was observed. Two or three types of 18S and ITS1-5.8S, or even the entire 18S-ITS1-5.8S rDNA sequence, were identified, suggesting a non-concerted evolutionary pattern. According to the pseudogene identification criteria, Type B and C in the five species that underwent non-concerted evolution were postulated as pseudogenes. The phylogenetic analysis based on these rDNA sequences showed that some of the pseudogenes diverged from the corresponding species or even clustered with other species, and the potential causes for this are discussed. Further analyses of the pseudogenes revealed that they could also provide particular evolutionary information, suggesting that pseudogenes should be taken into consideration rather than being discarded arbitrarily. Moreover, the results provided molecular support for the inclusion of Pseudaesopia japonica in the genus Pseudaesopia, and not in Zebrias or other genera.

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (31272273) and Scientific Research Foundation for the Introduction of Talent of Zhejiang Ocean University.

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Authors and Affiliations

  1. National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China

    Li Gong

  2. National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022, China

    Li Gong

  3. Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China

    Wei Shi, Min Yang & Xiaoyu Kong

  4. South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510000, China

    Wei Shi, Min Yang & Xiaoyu Kong

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  1. Li Gong
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  4. Xiaoyu Kong
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Correspondence to Xiaoyu Kong.

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Gong, L., Shi, W., Yang, M. et al. Characterization of 18S-ITS1-5.8S rDNA in eleven species in Soleidae: implications for phylogenetic analysis. Hydrobiologia 819, 161–175 (2018). https://doi.org/10.1007/s10750-018-3634-8

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  • DOI: https://doi.org/10.1007/s10750-018-3634-8

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