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

  • 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
Research Article

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.

Keywords

Ellobium chinense Transcriptome Illumina sequencing Simple sequence repeats 

Notes

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.

Author 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.

Compliance with ethical standards

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/).

Supplementary material

13258_2017_620_MOESM1_ESM.docx (14 kb)
Supplementary material 1 (DOCX 14 KB)

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Copyright information

© The Genetics Society of Korea and Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Se Won Kang
    • 2
  • Bharat Bhusan Patnaik
    • 3
  • So Young Park
    • 4
  • Hee-Ju Hwang
    • 1
  • Jong Min Chung
    • 1
  • Min Kyu Sang
    • 1
  • Hye Rin Min
    • 1
  • Jie Eun Park
    • 1
  • Jiyeon Seong
    • 5
  • Yong Hun Jo
    • 6
  • Mi Young Noh
    • 6
  • Jong Dae Lee
    • 7
  • Ki Yoon Jung
    • 1
  • Hong Seog Park
    • 8
  • Yeon Soo Han
    • 6
  • Jun Sang Lee
    • 9
  • Yong Seok Lee
    • 1
  1. 1.Department of Life Science and Biotechnology, College of Natural SciencesSoonchunhyang UniversityAsanSouth Korea
  2. 2.Biological Resources CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)Jungeup-siSouth Korea
  3. 3.Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT)Chandaka Industrial EstateBhubaneswarIndia
  4. 4.Nakdonggang National Institute of Biological ResourcesBiodiversity Conservation and Climate Change DivisionSangju-siSouth Korea
  5. 5.Genomic Informatics CenterHankyong National UniversityAnseong-siSouth Korea
  6. 6.Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life SciencesChonnam National UniversityGwangjuSouth Korea
  7. 7.Department of Environmental Health Science, College of Natural SciencesSoonchunhyang UniversityAsanSouth Korea
  8. 8.Research InstituteGnC BIO Co., LTD.Yuseong-guSouth Korea
  9. 9.Institute of Environmental ResearchKangwon National UniversityChuncheon-siSouth Korea

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