title: Sequencing and de novo assembly of visceral mass transcriptome of the critically endangered land snail Satsuma myomphala: Annotation and SSR discovery.
abstract: Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis. We identified 103,774 unigenes of which 37,959, 12,890, and 17,699 were annotated in the PANM (Protostome DB), Unigene, and COG (Clusters of Orthologous Groups) databases, respectively. In addition, 14,451 unigenes were predicted under Gene Ontology functional categories, with 4581 assigned to a single category. Furthermore, 3369 sequences with 646 having Enzyme Commission (EC) numbers were mapped to 122 pathways in the Kyoto Encyclopedia of Genes and Genomes Pathway database. The prominent protein domains included the Zinc finger (C2H2-like), Reverse Transcriptase, Thioredoxin-like fold, and RNA recognition motif domain. Many unigenes with homology to immunity, defense, and reproduction-related genes were screened in the transcriptome. We also detected 3120 putative simple sequence repeats (SSRs) encompassing dinucleotide to hexanucleotide repeat motifs from >1kb unigene sequences. A list of PCR primers of SSR loci have been identified to study the genetic polymorphisms. The transcriptome data represents a valuable resource for further investigations on the species genome structure and biology. The unigenes information and microsatellites would provide an indispensable tool for conservation of the species in natural and adaptive environments.
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea.
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, Chungcheongnam-do 31538, Republic of Korea; Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar, Odisha, 751024, India.
authors.forename: Bharat Bhusan
authors.initials: BB
authors.lastname: Patnaik
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea.
authors.forename: Hee-Ju
authors.initials: HJ
authors.lastname: Hwang
authors.affiliation: Biodiversity Conservation & Change Research Division, Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea.
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, Chungcheongnam-do 31538, Republic of Korea.
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, Chungcheongnam-do 31538, Republic of Korea.
authors.forename: Dae Kwon
authors.initials: DK
authors.lastname: Song
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea.
authors.forename: Hongray Howrelia
authors.initials: HH
authors.lastname: Patnaik
authors.affiliation: Korea Zoonosis Research Institute (KOZRI), Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do 54528, Republic of Korea.
authors.forename: Jae Bong
authors.initials: JB
authors.lastname: Lee
authors.affiliation: National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Republic of Korea.
authors.forename: Changmu
authors.initials: C
authors.lastname: Kim
authors.affiliation: National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Republic of Korea.
authors.forename: Soonok
authors.initials: S
authors.lastname: Kim
authors.affiliation: Research Institute, GnC BIO Co., Ltd., 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Republic of Korea.
authors.forename: Hong Seog
authors.initials: HS
authors.lastname: Park
authors.affiliation: Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil (Shinjeong0dong), Jungeup-si, Jeollabuk-do,56212, Republic of Korea.
authors.forename: Seung-Hwan
authors.initials: SH
authors.lastname: Park
authors.affiliation: Department of Nursing, College of Medicine, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea.
authors.forename: Young-Su
authors.initials: YS
authors.lastname: Park
authors.affiliation: College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
authors.forename: Yeon Soo
authors.initials: YS
authors.lastname: Han
authors.affiliation: Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon-do-si 243341, Republic of Korea.
authors.forename: Jun Sang
authors.initials: JS
authors.lastname: Lee
authors.affiliation: Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea. Electronic address: yslee@sch.ac.kr.
authors.forename: Yong Seok
authors.initials: YS
authors.lastname: Lee
mesh_terms: D000818:Animals; D019295:Computational Biology; D056727:Endangered Species; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D012908:Snails / Q000235:genetics* / Q000254:growth & development; D059467:Transcriptome / Q000235:genetics*; D014781:Viscera / Q000378:metabolism*
keywords: De novo annotation; Functional annotation; Illumina sequencing; Satsuma myomphala; Simple sequence repeats; Transcriptome