Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers
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.
KeywordsKoreanohadra kurodana Transcriptomics De novo assembly Functional annotation Simple sequence repeats
This work was supported by the grant entitled “The Genetic and Genomic Evaluation of Indigenous Biological Resources” funded by the National Institute of Biological Resources (NIBR201503202) and Soonchunhyang University Research Fund.
Compliance with ethical standards
All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.
Conflict of interest
The authors declare that they have no conflict of interest.
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarkis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29CrossRefPubMedPubMedCentralGoogle Scholar
- Castellanos-Martinez S, Arteta D, Catarino S, Gestal C (2014) De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNASeq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana. PLoS One 9:e107873CrossRefPubMedPubMedCentralGoogle Scholar
- Chen DN, Zhang GQ (2004) Fauna Sinica (Mollusca: Gastropoda: Stylommatophora: Bradybaenidae). Science Press, Beijing, pp 140–142Google Scholar
- Chen X, Yang Q, Li H, Li H, Hong Y, Pan L, Chen N, Zhu F, Chi X, Zhu W, Chen M, Liu H, Yang Z, Zhang E, Wang T, Zhong N, Wang M, Liu H, Wen S, Li X, Zhou G, Li S, Wu H, Varshney R, Liang X, Yu S (2015) Transcriptome-wide sequencing provides insights into geocarpy in peanut (Arachis hypogea L.). Plant Biotechnol. doi: 10.1111/pbi.12487 Google Scholar
- Coppe A, Pujolar JM, Maes GE, Larsen PF, Hansen MM, Bernatchez L, Zane L, Bortoluzzi S (2010) Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of critically endangered European eel. BMC Genom 11:635CrossRefGoogle Scholar
- Firmino AAP, Fonseca FC, de Macedo LLP, Coelho RR, de Souza Jr JDA, Togawa RC, Silva-Junior OB, Pappas-Jr GJ, Mattar da Silva MC, Engler G, Grossi-de-Sa MF (2013) Transcriptome analysis in cotton ball weevil (Anthonomus grandis) and RNA interference in insect pests. PLoS One 8:e85079CrossRefPubMedPubMedCentralGoogle Scholar
- Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNAseq data without a reference genome. Nat Biotechnol 29:644–652CrossRefPubMedPubMedCentralGoogle Scholar
- Hirano T, Kameda Y, Chiba S (2014) Phylogeny of the land snails bradybaena and phaeohelix (Pulmonata: Bradybaenidae) in Japan. J Mollusc Studies, pp 1–7Google Scholar
- Huang C-W, Lee Y-C, Lin S-M, Wu W-L (2014) Taxonomic revision of Aegista subchinensis (Mollendorf, 1884) (Stylommatophora, Bradybaenidae) and a description of new species of Aegista from eastern Taiwan based on multilocus phylogeny and comparative morphology. Zookeys 445:31–55CrossRefPubMedGoogle Scholar
- Hwang H-J, Patnaik BB, Kang SW, Park SY, Wang TH, Park EB, Chung JM, Song DK, Patnaik HH, Kim C, Kim S, Lee JB, Jeong HC, Park HS, Han YS, Lee YS (2016) RNA sequencing, de novo assembly and functional annotation of a Nymphalid butterfly, Fabriciana nerippe Felder, 1862. Entomol Res. doi: 10.1111/1748-5967.12164 Google Scholar
- Kuznik-Kowalska E, Lewandowska M, Pokroyszko BM, Prockow M (2013) Reproduction, growth and circadian activity of the snail Bradybaena fruticum (O.F. Muller, 1774) (Gastropoda: Pulmonata: Bradybaenidae) in the laboratory. Cent Eur J Biol 8:693–700Google Scholar
- Kwon OK, Park KM, Lee JS (1993) Colored shells of Korea. Academic Publishing Co., SeoulGoogle Scholar
- Lee JS, Kwon OK (1993) Chromosomal studies of eight species of Bradybaenidae in Korea. Korean J Malacol 9:30–43Google Scholar
- Min DK, Lee JS, Koh DB, Je JK (2004) Molluscs in Korea. Hangeul Publishing Company, Min Molluscan Research Institute, Korea, p 566Google Scholar
- Moroz LL, Edwards JR, Puthanveettil SV, Kohn AB, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, Jezzini S, Lovell P, Iannucculli W, Chen M, Nguyen T, Sheng H, Shaw R, Kalachikov S, Panchin YV, Farmerie W, Russo JJ, Ju J, Kandel ER (2006) Neuronal transcriptome of Aplysia: neuronal compartments and circuitary. Cell 127:1453–1467CrossRefPubMedPubMedCentralGoogle Scholar
- Noseworthy RG, Lim N-R, Choi K-S (2007) A catalogue of the mollusks of the Jeju Island, South Korea. Korean J Malacol 23:65–104Google Scholar
- Pallavicini A, Canapa A, Barucca M, Alfoldi J, Biscotti MA, Buonocore F, De Moro G, Di Palma F, Fausto AM, Forconi M, Gerdol M, Makapedua DM, Turner-Meier J, Olmo E, Scapigliati G (2013) Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis. BMC Genom 14:538CrossRefGoogle Scholar
- Patnaik BB, Hwang H-J, Kang SW, Park SY, Wang TH, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JB, Jeong HC, Park HS, Han YS, Lee YS (2015) Transcriptome characterization for non-model endangered lycaenids, Protantigius superans and Spindasis takanosis, using Illumina HiSeq 2500 sequencing. Int J Mol Sci 16:29948–29970CrossRefPubMedPubMedCentralGoogle Scholar
- Patnaik BB, Park SY, Kang SW, Hwang H-J, Wang TH, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JB, Jeong HC, Park HS, Han YS, Lee YS (2016a) Transcriptome profile of the Asian Giant Hornet (Vespa mandarinia) using Illumina HiSeq 4000 sequencing: De novo assembly, functional annotation, and discovery of SSR markers. Int J Genomics, Article ID 4169587. doi: 10.1155/2016/4169587
- Patnaik BB, Wang TH, Kang SW, Hwang H-J, Park SY, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JS, Han YS, Park HS, Lee YS (2016b) Sequencing, de novo assembly, and annotation of the transcriptome of the endangered fresh water pearl bivalve Cristaria plicata provides novel insights into functional genes and marker discovery. PLoS One 11:e0148622Google Scholar
- Schileyko AA (2004) Treatise on recent terrestrial pulmonate molluscs. Pt. 12. Bradybaenidae, Monodeniidae, Xanthonychidae, Epiphragmophoridae, Helminthoglyptidae, Elonidae, Humboldtianidae, Sphincterochilidae, Cochlicellidae. Ruthenica Suppl 2:1627–1763Google Scholar
- Storey KB, Storey JM (2010) Metabolic regulation and gene expression during aestivation. In: Navas CA, Carvalho JE (eds) Aestivation: molecular and physiological aspects, progress in molecular and subcellular biology, vol 49. Springer, Berlin. doi: 10.1007/978-3-642-02421-4_2
- Sysoev A, Schileyko A (2009) Land snails and slugs of Russia and adjacent countries. Pensoft, SofiaGoogle Scholar
- Wang L, Yang C, Song L (2013) The molluscan HSP70s and their expression in hemocytes. ISJ 10:77–83Google Scholar
- Wu S-P, Hwang C-C, Huang H-M, Chang H-W, Lin Y-S, Lee P-F (2007) Land molluscan fauna of the Dongsha Island with twenty two recorded species. Taiwania 52:145–151Google Scholar