title: Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery.
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. longicaudatuswas 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 onT. longicaudatusmakes it difficult to obtain valuable genetic information for marker-aided selection programs. In this study, whole-transcriptome sequencing ofT. longicaudatusgenerated 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 N50length 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 ofT. longicaudatus, and it provides valuable insights for genetic research and molecular-assisted breeding of this important species.
authors.affiliation: Genomic Informatics Center, Hankyong National University, 327 Chungang-no, Anseong-si, Gyeonggi-do 17579, Korea. s-jiyeon@hanmail.net.
authors.forename: Jiyeon
authors.initials: J
authors.lastname: Seong
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do 31538, Korea. bioksw@naver.com.
authors.forename: Se Won
authors.initials: SW
authors.lastname: Kang
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do 31538, Korea. drbharatbhusan4@gmail.com.|Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha 751024, India. drbharatbhusan4@gmail.com.
authors.forename: Bharat Bhusan
authors.initials: BB
authors.lastname: Patnaik
authors.affiliation: Biodiversity Conservation & Change Research Division, Nakdonggang National Institute of Biological Resources, 137 Donam 2-gil, Sangju, Gyeongsangbuk-do 37242, Korea. cindysory@naver.com.
authors.forename: So Young
authors.initials: SY
authors.lastname: Park
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do 31538, Korea. hwamux@naver.com.
authors.forename: Hee Ju
authors.initials: HJ
authors.lastname: Hwang
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do 31538, Korea. jong6922@daum.net.
authors.forename: Jong Min
authors.initials: JM
authors.lastname: Chung
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do 31538, Korea. elegangce@naver.com.
authors.forename: Dae Kwon
authors.initials: DK
authors.lastname: Song
authors.affiliation: Department of Applied Biology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea. annemi@chonnam.ac.kr.
authors.forename: Mi Young
authors.initials: MY
authors.lastname: Noh
authors.affiliation: Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Korea. biopark@kribb.re.kr.
authors.forename: Seung-Hwan
authors.initials: SH
authors.lastname: Park
authors.affiliation: Genomic Informatics Center, Hankyong National University, 327 Chungang-no, Anseong-si, Gyeonggi-do 17579, Korea. jeon5894@gmail.com.
authors.forename: Gwang Joo
authors.initials: GJ
authors.lastname: Jeon
authors.affiliation: Genomic Informatics Center, Hankyong National University, 327 Chungang-no, Anseong-si, Gyeonggi-do 17579, Korea. kebinkhs@empal.com.
authors.forename: Hong Sik
authors.initials: HS
authors.lastname: Kong
authors.affiliation: National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea. sokim90@korea.kr.
authors.forename: Soonok
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Biology Education, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Korea. uwhwang@knu.ac.kr.
authors.forename: Ui Wook
authors.initials: UW
authors.lastname: Hwang
authors.affiliation: Research Institute, GnC BIO Co., LTD., 36 Banseokro, Yuseong-gu, Daejeon 34069, Korea. 5022daniel@gmail.com.
authors.forename: Hong Seog
authors.initials: HS
authors.lastname: Park
authors.affiliation: College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea. hanys@chonnam.ac.kr.
authors.forename: Yeon Soo
authors.initials: YS
authors.lastname: Han
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do 31538, Korea. yslee@sch.ac.kr.
authors.forename: Yong Seok
authors.initials: YS
authors.lastname: Lee
keywords: Illumina sequencing; SSRs (simple sequence repeats); Triops longicaudatus; tadpole shrimp; transcriptome