Molecular Genetics and Genomics

, Volume 291, Issue 5, pp 1999–2014 | Cite as

Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers

  • Se Won Kang
  • Bharat Bhusan Patnaik
  • Hee-Ju Hwang
  • So Young Park
  • Jong Min Chung
  • Dae Kwon Song
  • Hongray Howrelia Patnaik
  • Jae Bong Lee
  • Changmu Kim
  • Soonok Kim
  • Hong Seog Park
  • Yeon Soo Han
  • Jun Sang Lee
  • Yong Seok Lee
Original Article

Abstract

The Korean endemic land snail Koreanohadra kurodana (Gastropoda: Bradybaenidae) found in humid areas of broadleaf forests and shrubs have been considered vulnerable as the number of individuals are declining in recent years. The species is poorly characterized at the genomic level that limits the understanding of functions at the molecular and genetics level. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset of visceral mass tissue of K. kurodana by the Illumina paired-end sequencing technology. Over 234 million quality reads were assembled to a total of 315,924 contigs and 191,071 unigenes, with an average and N50 length of 585.6 and 715 bp and 678 and 927 bp, respectively. Overall, 36.32 % of the unigenes found matches to known protein/nucleotide sequences in the public databases. The direction of the unigenes to functional categories was determined using COG, GO, KEGG, and InterProScan protein domain search. The GO analysis search resulted in 22,967 unigenes (12.02 %) being categorized into 40 functional groups. The KEGG annotation revealed that metabolism pathway genes were enriched. The most prominent protein motifs include the zinc finger, ribonuclease H, reverse transcriptase, and ankyrin repeat domains. The simple sequence repeats (SSRs) identified from >1 kb length of unigenes show a dominancy of dinucleotide repeat motifs followed with tri- and tetranucleotide motifs. A number of unigenes were putatively assessed to belong to adaptation and defense mechanisms including heat shock proteins 70, Toll-like receptor 4, AMP-activated protein kinase, aquaporin-2, etc. Our data provide a rich source for the identification and functional characterization of new genes and candidate polymorphic SSR markers in K. kurodana. The availability of transcriptome information (http://bioinfo.sch.ac.kr/submission/) would promote the utilization of the resources for phylogenetics study and genetic diversity assessment.

Keywords

Koreanohadra kurodana Transcriptomics De novo assembly Functional annotation Simple sequence repeats 

Supplementary material

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Supplementary material 1 (DOCX 12 kb)
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Supplementary material 2 (XLSX 14 kb)
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Supplementary material 3 (XLSX 279 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Se Won Kang
    • 1
  • Bharat Bhusan Patnaik
    • 1
    • 2
  • Hee-Ju Hwang
    • 1
  • So Young Park
    • 1
  • Jong Min Chung
    • 1
  • Dae Kwon Song
    • 1
  • Hongray Howrelia Patnaik
    • 1
  • Jae Bong Lee
    • 3
  • Changmu Kim
    • 4
  • Soonok Kim
    • 4
  • Hong Seog Park
    • 5
  • Yeon Soo Han
    • 6
  • Jun Sang Lee
    • 7
  • Yong Seok Lee
    • 1
  1. 1.Department of Life Science and Biotechnology, College of Natural SciencesSoonchunhyang UniversityAsanKorea
  2. 2.Trident School of Biotech SciencesTrident Academy of Creative Technology (TACT)BhubaneswarIndia
  3. 3.Korea Zoonosis Research Institute (KOZRI)Chonbuk National UniversityIksanKorea
  4. 4.National Institute of Biological ResourcesIncheonKorea
  5. 5.Research Institute, GnC BIO Co., LTD.DaejeonKorea
  6. 6.College of Agriculture and Life ScienceChonnam National UniversityGwangjuKorea
  7. 7.Institute of Environmental ResearchKangwon National UniversityChuncheon-siKorea

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