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Genes 2016, 7(7), 35; doi:10.3390/genes7070035

Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery

1
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunghyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea
2
Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha 751024, India
3
Korea Zoonosis Research Institute (KOZRI), Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do 54528, Korea
4
College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea
5
National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon 22689, Korea
6
Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Korea
7
Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do 243341, Korea
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Paolo Cinelli
Received: 28 April 2016 / Revised: 5 July 2016 / Accepted: 6 July 2016 / Published: 22 July 2016
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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Abstract

An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this species. In the present study, the transcriptomic sequencing and de novo assembly of C. retropictus generated a total of 241,696,750 high-quality reads. These assembled to 282,838 unigenes with mean and N50 lengths of 736.9 and 1201 base pairs, respectively. Of these, 125,616 unigenes were subjected to annotation analysis with known proteins in Protostome DB, COG, GO, and KEGG protein databases (BLASTX; E ≤ 0.00001) and with known nucleotides in the Unigene database (BLASTN; E ≤ 0.00001). The GO analysis indicated that cellular process, cell, and catalytic activity are the predominant GO terms in the biological process, cellular component, and molecular function categories, respectively. In addition, 2093 unigenes were distributed in 107 different KEGG pathways. Furthermore, 49,280 simple sequence repeats were identified in the unigenes (>1 kilobase sequences). This is the first report on the identification of transcriptomic and microsatellite resources for C. retropictus, which opens up the possibility of exploring traits related to the adaptation and acclimatization of this species. View Full-Text
Keywords: Clithon retropictus; transcriptome; de novo assembly; functional annotation; simple sequence repeats Clithon retropictus; transcriptome; de novo assembly; functional annotation; simple sequence repeats
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MDPI and ACS Style

Park, S.Y.; Patnaik, B.B.; Kang, S.W.; Hwang, H.-J.; Chung, J.M.; Song, D.K.; Sang, M.K.; Patnaik, H.H.; Lee, J.B.; Noh, M.Y.; Kim, C.; Kim, S.; Park, H.S.; Lee, J.S.; Han, Y.S.; Lee, Y.S. Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery. Genes 2016, 7, 35.

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