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.

Transcriptome analysis of air-breathing land slug, Incilaria fruhstorferi reveals functional insights into growth, immunity, and reproduction

“…The most classical C2H2 Znfs are known to have versatile functions, including DNA (DNA-binding domains of transcription factors), RNA, and protein contacts [37]. Our results support transcriptome studies in the land snail, Satsuma myomphala [11] and the pearl bivalve, C. plicata [12], wherein the C2H2 Znfs were found to be the most conserved domain with representations of immunoglobulin-like fold domain. Protein kinase-like domain attributes critical phosphorylation functions to the intracellular protein kinases related to signal extrapolation during key metabolic, cellular, or immune processes.…”

“…The unigenes were further explored for the functional annotation and microsatellite identification. The average length of unigenes obtained in this study was higher compared to the transcriptome assembly of other molluscs, including Cristaria plicata (737.1) [12], Satsuma myomphala (571.7 bp) [11], Aegista chejuensis / Aegista quelpartensis (735.4/705.6) [18] and Pinctada maxima (407 bp) [34].…”

“…By and large, the transcriptome projects involving molluscs have included commercially exploited species and/or endangered species. This includes the critically endangered land snail, Satsuma myomphala [11]; Korea endangered freshwater pearl bivalve, Cristaria plicata [12], Australian mollusc, Dicathais orbita [13], Sydney rock oyster, Saccostrea glomerata [14], and the freshwater snail, Oncomelania hupensis [15], among others. The above studies identified genes with major impacts on ecologically relevant traits.…”

De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

“…Reasons for the non-annotated sequences could be, lack of conserved protein domains in short sequences, or in some cases the transcriptome have non-coding genes, UTRs, random transcriptional noise or incomplete spliced introns which are non-homologues to the sequences available in the public databases. This may also be one of the possible reasons that genes have not shown expression at the time of RNA extraction or those genes are expressed at very low levels 46 .…”

RNA Sequencing, De novo assembly, functional annotation and SSR analysis of the endangered diving beetle Cybister chinensis (= Cybister japonicus) using the Illumina platform

“…Majority of non-redundant unigenes was >2001 bp. and arthropods alike (Park et al 2016;Seong et al 2016;Kang et al 2016a). While all the earlier reports utilized version 1.0 of the database , the present study utilized the latest version released with updated sequences (Kang et al 2016b).…”