Sequencing and de novo assembly of visceral mass transcriptome of the critically endangered land snail Satsuma myomphala: Annotation and SSR discovery

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Title
Sequencing and de novo assembly of visceral mass transcriptome of the critically endangered land snail Satsuma myomphala: Annotation and SSR discovery
Author(s)
Se Won Kang; B B Patnaik; H J Hwang; S Y Park; J M Chung; D K Song; H H Patnaik; J B Lee; C Kim; S Kim; Y S Park; H S Park; Seung Hwan Park; Y S Han; J S Lee; Y S Lee
Bibliographic Citation
Comparative Biochemistry and Physiology D-Genomics & Proteomics, vol. 21, pp. 77-89
Publication Year
2017
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 >?1?kb 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.
Keyword
De novo annotationFunctional annotationIllumina sequencingSatsuma myomphalaSimple sequence repeatsTranscriptome
ISSN
1744-117X
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.cbd.2016.10.004
Type
Article
Appears in Collections:
Jeonbuk Branch Institute > Biological Resource Center > 1. Journal Articles
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