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Distribution, Function and Polymorphism Characteristics of Microsatellites in Pyropia yezoensis Transcriptome

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Abstract

The distribution, putative function and polymorphism characteristics of simple sequence repeats (SSRs) in P. yezoensis transcriptome were analyzed in this study. In tota., 307. SSRs were detected among 2681 unigenes. Trinucleotide types were dominant, constituting 91.87% of all the microsatellites. The most abundant SSR was CCG (71.03%) and the second abundant one was AGC (234, 7.61%). A total of 111 (3.61%) dinucleotide types were found and the most abundant one was AC (51, 1.66%) which was followed by CG (34, 1.11%). SSRs identified showed a GC bases preference; GC bases constituted 89.73% of all the SSR bases. SSRs occurrence number decreased as repetitions increased. Annotation results exhibited that the majority of SSRs-containing unigenes have the functions of ‘metabolic process’, ‘binding’ and ‘catalytic activity’ and existed as the forms of ‘cell’, ‘cell component’ and ‘organelle’. The dominant amino acids that SSRs coded were Ala (28.59%), Arg (26.02%), Gly (14.35%) and Pro (13.65%). Amplification results showed that 3 out 23 SSRs from transcriptome (13.04%) and 8 out 77 SSRs from genome (10.39%) were polymorphic.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Nos. 31372517, 31672641), the Scientific and Technological Innovation Project Financially Supported by Qingdao National Laboratory for Marine Science and Technology (No. 2015ASKJ02), the Project of National Infrastructure of Fishery Germplasm Resources (No. 2016DKA30470), Fundamental Research Funds for the Central Universities (Nos. 201762016, 201562018, 201564009), and the Program for Chinese Outstanding Talents in Agriculture Scientific Research.

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Authors and Affiliations

  1. Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China

    Yang Liu, Xue Pan, Kuipeng Xu & Yunxiang Mao

  2. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China

    Yunxiang Mao

  3. College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China

    Yang Liu, Xue Pan, Kuipeng Xu & Yunxiang Mao

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  1. Yang Liu
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Correspondence to Yunxiang Mao.

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Liu, Y., Pan, X., Xu, K. et al. Distribution, Function and Polymorphism Characteristics of Microsatellites in Pyropia yezoensis Transcriptome. J. Ocean Univ. China 18, 693–700 (2019). https://doi.org/10.1007/s11802-019-3817-6

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  • DOI: https://doi.org/10.1007/s11802-019-3817-6

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