Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics
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.
KeywordsEllobium chinense Transcriptome Illumina sequencing Simple sequence repeats
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.
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.
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/).
- Bouchet P, Rocroi JP (2005) Classification and nomenclature of gastropod families. Malacologia Int J Malacol 47:1–2Google Scholar
- Coscia MR, Giacomelli S, Oreste U (2011) Toll-like receptors: an overview from invertebrates to vertebrates. Invertebr Survival J 8:210–226Google Scholar
- Dayrat B, Conrad M, Balayan S, White TR, Albrecht C, Golding R, Gomes SR, Harasewych MG, de Frias Martins AM (2011) Phylogenetic relationships and evolution of the pulmonate gastropods (Mollusca): new insights from increased taxon sampling. Mol Phylogenet Evol doi:10.1016/j.ympev.2011.02.014 PubMedGoogle Scholar
- Fiedler TJ, Hudder A, Mckay SJ, Shivkumar S, Capo TR, Schmmale MC, Walsh PJ (2010) The transcriptome of the early life history stages of the Californian Sea Hare Aplysia californica. Comp Biochem Physiol Part D 5:165–170Google Scholar
- Heyland A, Vue Z, Voolstra CR, Medina M, Moroz LL (2010) Developmental transcriptome of Aplysia californica. J Exptl Zool B 316B:13–134Google Scholar
- Kang SW, Patnaik BB, Hwang HJ, Park SY, Wang TH, Park EB, Chung JM, Song DK, Patnaik HH, Lee JB et al (2016) De novo transcriptome generation and annotation of two Korean endemic land snails, Aegista chejuensis and Aegista quelpartensis, using Illumina paired-end sequencing technology”. Int J Mol Sci 17:379CrossRefPubMedPubMedCentralGoogle Scholar
- Patnaik BB, Hwang HJ, Kang SW, Park SY, Wang TH, Park EB, Chung JM, Song DK, Kim C, Kim S et al (2015) Transcriptome characterization of non-model endangered lycaenids, Protantigius superans and Spindasis takanosis, using Illumina HiSeq 2500 sequencing. Intl J Mol Res 16:29948–29970Google Scholar
- Patnaik BB, Wang TH, Kang SW, Hwang HJ, Park SY, Park EB, Chung JM, Song DK, Kim C, Kim S et al (2016) Sequencing, de novo assembly, and annotation of the transcriptome of the endangered freshwater pearl bivalve, Cristaria plicata, provides novel insights into functional genes and marker discovery. PLoS ONE 11:e0148622CrossRefPubMedPubMedCentralGoogle Scholar
- Wang L, Wang L, Huang M, Zhang H, Song L (2011) The immune role of C-type lectins in molluscs. Invertebr Surviv J 8:241–246Google Scholar
- Wang H, Nettleton D, Ying K (2014) Copy number variation detection using next generation sequencing read counts. BMC Bioinform 15:109Google Scholar
- Zhou J, Li C, Li Y, Su X, Li T (2013) cDNA cloning and mRNA expression of heat shock protein 70 gene in blood clam Tegillarca granosa against heavy metals challenge. Afr J Biotechnol 12:2341–2352Google Scholar