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Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics

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Abstract

Ellobium chinense (Pfeiffer, 1854) is a brackish pulmonate species that inhabits the bases of mangrove trees and is most commonly found in salt grass meadows. Threats to mangrove ecosystems due to habitat degradation and overexploitation have threatened the species with extinction. In South Korea, E. chinense has been assessed as vulnerable, but there are limited data on its population structure and distribution. The nucleotide and protein sequences for this species are not available in databases, which limits the understanding of adaptation-related traits. We sequenced an E. chinense cDNA library using the Illumina platform, and the subsequent bioinformatics analysis yielded 227,032 unigenes. Of these unigenes, 69,088 were annotated to matched protein and nucleotide sequences in databases, for an annotation rate of 30.42%. Among the predominant gene ontology terms, cellular and metabolic processes (under the biological process category), membrane and cell (under the cellular component category), and binding and catalytic activity (under the molecular function category) were noteworthy. In addition, 4850 unigenes were distributed to 15 Kyoto Encyclopaedia of Genes and Genomes based enrichment categories. Among the candidate genes related to adaptation, angiotensin I converting enzyme, adenylate cyclase activating polypeptide, and AMP-activated protein kinase were the most prominent. A total of 15,952 simple sequence repeats (SSRs) were identified in sequences of > 1 kb in length. The di- and trinucleotide repeat motifs were the most common. Among the repeat motif types, AG/CT, AC/GT, and AAC/GTT dominated. Our study provides the first comprehensive genomics dataset for E. chinense, which favors conservation programs for the restoration of the species and provides sufficient evidence for genetic variability among the wild populations.

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Acknowledgements

This work was supported by the grant “The Genetic and Genomic Evaluation of Indigenous Biological Resources” funded by the National Institute of Biological Resources (NIBR201503202) and the Soonchunhyang University Research Fund.

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Author notes

  1. Se Won Kang and Bharat Bhusan Patnaik have contributed equally to this work.

Authors and Affiliations

  1. Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea

    Hee-Ju Hwang, Jong Min Chung, Min Kyu Sang, Hye Rin Min, Jie Eun Park, Ki Yoon Jung & Yong Seok Lee

  2. Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181, Ipsin-gil, Jungeup-si, Jeollabuk-do, 56212, South Korea

    Se Won Kang

  3. Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha, 751024, India

    Bharat Bhusan Patnaik

  4. Nakdonggang National Institute of Biological Resources, Biodiversity Conservation and Climate Change Division, 137, Donam-2-gil, Sangju-si, Gyeongsangbuk-do, 37242, South Korea

    So Young Park

  5. Genomic Informatics Center, Hankyong National University, 327 Chungang-ro, Anseong-si, Kyonggi-do, 17579, South Korea

    Jiyeon Seong

  6. Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea

    Yong Hun Jo, Mi Young Noh & Yeon Soo Han

  7. Department of Environmental Health Science, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea

    Jong Dae Lee

  8. Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea

    Hong Seog Park

  9. Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 243341, South Korea

    Jun Sang Lee

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  1. Se Won Kang
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Contributions

SWK, BBP, HJH, YSH and YSL designed the experiments. MKS, HRM, JEP, SYP, YHJ, MYN, JMC, JDL and JS performed the experiments. BBP, HJH, KYJ, JS and SWK analyzed the data. BBP, HJH, KYJ, MYN, and SWK wrote the paper. HSP, JSL, and YSH contributed reagents/materials/analysis tools. YSL supervised the entire study.

Corresponding author

Correspondence to Yong Seok Lee.

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Conflict of interest

All authors ‘Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee-Ju Hwang, Jong Min Chung, Min Kyu Sang, Hye Rin Min, Jie Eun Park, Jiyeon Seong, Yong Hun Jo, Mi Young Noh, Jong Dae Lee, Ki Yoon Jung, Hong Seog Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee’ declare that they do not have conflict of interest.

Ethical approval

The handling of E. chinense was conducted in accordance with the International Guiding Principles for Biomedical Research involving animals (1985 http://www.ncbi.nlm.nih.gov/books/NBK25438/).

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Kang, S.W., Patnaik, B.B., Park, S.Y. et al. Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics. Genes Genom 40, 333–347 (2018). https://doi.org/10.1007/s13258-017-0620-x

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