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Int. J. Mol. Sci. 2016, 17(3), 379; doi:10.3390/ijms17030379

De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology

1
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, 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
National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea
5
Research Institute, GnC BIO Co., LTD. 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Korea
6
Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do 243341, Korea
7
College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Kotb Abdelmohsen
Received: 7 January 2016 / Revised: 5 March 2016 / Accepted: 9 March 2016 / Published: 15 March 2016
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
View Full-Text   |   Download PDF [4068 KB, uploaded 15 March 2016]   |  

Abstract

Aegista chejuensis and Aegista quelpartensis (Family-Bradybaenidae) are endemic to Korea, and are considered vulnerable due to declines in their population. The limited genetic resources for these species restricts the ability to prioritize conservation efforts. We sequenced the transcriptomes of these species using Illumina paired-end technology. Approximately 257 and 240 million reads were obtained and assembled into 198,531 and 230,497 unigenes for A. chejuensis and A. quelpartensis, respectively. The average and N50 unigene lengths were 735.4 and 1073 bp, respectively, for A. chejuensis, and 705.6 and 1001 bp, respectively, for A. quelpartensis. In total, 68,484 (34.5%) and 77,745 (33.73%) unigenes for A. chejuensis and A. quelpartensis, respectively, were annotated to databases. Gene Ontology terms were assigned to 23,778 (11.98%) and 26,396 (11.45) unigenes, for A. chejuensis and A. quelpartensis, respectively, while 5050 and 5838 unigenes were mapped to 117 and 124 pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, we identified and annotated 9542 and 10,395 putative simple sequence repeats (SSRs) in unigenes from A. chejuensis and A. quelpartensis, respectively. We designed a list of PCR primers flanking the putative SSR regions. These microsatellites may be utilized for future phylogenetics and conservation initiatives. View Full-Text
Keywords: Bradybaenidae; land snails; transcriptome; de novo assembly; simple sequence repeats Bradybaenidae; land snails; transcriptome; de novo assembly; simple sequence repeats
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Kang, S.W.; Patnaik, B.B.; Hwang, H.-J.; Park, S.Y.; Wang, T.H.; Park, E.B.; Chung, J.M.; Song, D.K.; Patnaik, H.H.; Lee, J.B.; Kim, C.; Kim, S.; Park, H.S.; Lee, J.S.; Han, Y.S.; Lee, Y.S. De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology. Int. J. Mol. Sci. 2016, 17, 379.

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