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Genes 2016, 7(12), 114; doi:10.3390/genes7120114

Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery

1
Genomic Informatics Center, Hankyong National University, 327 Chungang-no, Anseong-si, Gyeonggi-do 17579, Korea
2
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do 31538, Korea
3
Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha 751024, India
4
Biodiversity Conservation & Change Research Division, Nakdonggang National Institute of Biological Resources, 137 Donam 2-gil, Sangju, Gyeongsangbuk-do 37242, Korea
5
Department of Applied Biology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea
6
Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Korea
7
National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea
8
Department of Biology Education, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Korea
9
Research Institute, GnC BIO Co., LTD., 36 Banseokro, Yuseong-gu, Daejeon 34069, Korea
10
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: Paolo Cinelli
Received: 12 September 2016 / Revised: 19 November 2016 / Accepted: 24 November 2016 / Published: 2 December 2016
(This article belongs to the Section Molecular Genetics)
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Abstract

The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs. In this study, whole-transcriptome sequencing of T. longicaudatus generated 39.74 GB of clean data and a total of 269,822 contigs using the Illumina HiSeq 2500 platform. After clustering, a total of 208,813 unigenes with an N50 length of 1089 bp were generated. A total of 95,105 unigenes were successfully annotated against Protostome (PANM), Unigene, Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX with a cut-off of 1E−5. A total of 57,731 unigenes were assigned to GO terms, and 7247 unigenes were mapped to 129 KEGG pathways. Furthermore, 1595 simple sequence repeats (SSRs) were detected from the unigenes with 1387 potential SSR markers. This is the first report of high-throughput transcriptome analysis of T. longicaudatus, and it provides valuable insights for genetic research and molecular-assisted breeding of this important species. View Full-Text
Keywords: Triops longicaudatus; tadpole shrimp; transcriptome; Illumina sequencing; SSRs (simple sequence repeats) Triops longicaudatus; tadpole shrimp; transcriptome; Illumina sequencing; SSRs (simple sequence repeats)
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Seong, J.; Kang, S.W.; Patnaik, B.B.; Park, S.Y.; Hwang, H.J.; Chung, J.M.; Song, D.K.; Noh, M.Y.; Park, S.-H.; Jeon, G.J.; Kong, H.S.; Kim, S.; Hwang, U.W.; Park, H.S.; Han, Y.S.; Lee, Y.S. Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery. Genes 2016, 7, 114.

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