De novo transcriptome sequencing of triton shell Charonia lampas sauliae: Identification of genes related to neurotoxins and discovery of genetic markers

Hwang, Hee Ju; Patnaik, Bharat Bhusan; Chung, Jong Min; Sang, Miao; Park, Jie Eun; Kang, Se Won; Park, So Young; Jo, Yong Hun; Park, Hong Seog; Baliarsingh, Snigdha; Han, Yeon Soo; Lee, Yong Seok

doi:10.1016/j.margen.2021.100862

Cited by 7 publications

(4 citation statements)

References 55 publications

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“…Over the past 15 years, RNA-seq has replaced Sanger sequencing of EST libraries, enabling comprehensive characterization of toxin repertoires in several venomous organisms [ 4 , 10 , 49–52 ]. However, with increasing accessibility to transcriptomic data, the bottleneck has shifted from sequencing to data analysis.…”

Section: Discussionmentioning

confidence: 99%

DeTox: a pipeline for the detection of toxins in venomous organisms

Ringeval,

Farhat,

Fedosov

et al. 2024

Briefings in Bioinformatics

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Venomous organisms have independently evolved the ability to produce toxins 101 times during their evolutionary history, resulting in over 200 000 venomous species. Collectively, these species produce millions of toxins, making them a valuable resource for bioprospecting and understanding the evolutionary mechanisms underlying genetic diversification. RNA-seq is the preferred method for characterizing toxin repertoires, but the analysis of the resulting data remains challenging. While early approaches relied on similarity-based mapping to known toxin databases, recent studies have highlighted the importance of structural features for toxin detection. The few existing pipelines lack an integration between these complementary approaches, and tend to be difficult to run for non-experienced users. To address these issues, we developed DeTox, a comprehensive and user-friendly tool for toxin research. It combines fast execution, parallelization and customization of parameters. DeTox was tested on published transcriptomes from gastropod mollusks, cnidarians and snakes, retrieving most putative toxins from the original articles and identifying additional peptides as potential toxins to be confirmed through manual annotation and eventually proteomic analysis. By integrating a structure-based search with similarity-based approaches, DeTox allows the comprehensive characterization of toxin repertoire in poorly-known taxa. The effect of the taxonomic bias in existing databases is minimized in DeTox, as mirrored in the detection of unique and divergent toxins that would have been overlooked by similarity-based methods. DeTox streamlines toxin annotation, providing a valuable tool for efficient identification of venom components that will enhance venom research in neglected taxa.

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Section: Discussionmentioning

confidence: 99%

DeTox: a pipeline for the detection of toxins in venomous organisms

Ringeval,

Farhat,

Fedosov

et al. 2024

Briefings in Bioinformatics

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“…The annotation profile of the PANM-DB was also utilized to screen the putative candidate transcripts of H. flava female ticks in relation to adaptation. The PANM-DB has been consistently used to retrieve valuable transcripts related to adaptation in protostome species, including butterflies, moths, gastropods and other molluscs [ 6 , 48 – 51 ]. The assembled transcripts of larva and nymph stages of the H. flava transcriptome showed a match of 48.6% to the near-reported species, with Ixodes scapularis the most represented species [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers

Sang,

Patnaik,

Park

et al. 2023

Parasites Vectors

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Background Ticks are ectoparasites capable of directly damaging their hosts and transmitting vector-borne diseases. The ixodid tick Haemaphysalis flava has a broad distribution that extends from East to South Asia. This tick is a reservoir of severe fever with thrombocytopenia syndrome virus (SFTSV) that causes severe hemorrhagic disease, with cases reported from China, Japan and South Korea. Recently, the distribution of H. flava in South Korea was found to overlap with the occurrence of SFTSV. Methods This study was undertaken to discover the molecular resources of H. flava female ticks using the Illumina HiSeq 4000 system, the Trinity de novo sequence assembler and annotation against public databases. The locally curated Protostome database (PANM-DB) was used to screen the putative adaptation-related transcripts classified to gene families, such as angiotensin-converting enzyme, aquaporin, adenylate cyclase, AMP-activated protein kinase, glutamate receptors, heat shock proteins, molecular chaperones, insulin receptor, mitogen-activated protein kinase and solute carrier family proteins. Also, the repeats and simple sequence repeats (SSRs) were screened from the unigenes using RepeatMasker (v4.0.6) and MISA (v1.0) software tools, followed by the designing of SSRs flanking primers using BatchPrimer 3 (v1.0) software. Results The transcriptome produced a total of 69,822 unigenes, of which 46,175 annotated to the homologous proteins in the PANM-DB. The unigenes were also mapped to the EuKaryotic Orthologous Groups (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) specializations. Promiscuous presence of protein kinase, zinc finger (C2H2-type), reverse transcriptase, and RNA recognition motif domains was observed in the unigenes. A total of 3480 SSRs were screened, of which 1907 and 1274 were found as tri- and dinucleotide repeats, respectively. A list of primer sequences flanking the SSR motifs was detailed for validation of polymorphism in H. flava and the related tick species. Conclusions The reference transcriptome information on H. flava female ticks will be useful for an enriched understanding of tick biology, its competency to act as a vector and the study of species diversity related to disease transmission. Graphical abstract

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“…2019; Hwang et al . 2021). This is also true for other arthropod species, including insects (Seong et al .…”

Section: Characteristics Of Butterfly Transcriptome Under Tsi Of Koreamentioning

confidence: 99%

Transcriptome‐derived molecular resources for the conservation of threatened butterflies in Korea

Patnaik,

Park,

Sang

et al. 2023

Entomological Research

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Butterflies are expedient biodiversity indicators of a healthy environment. As virtuous pollinators, they provide environmental and economic benefits to the agricultural and natural ecosystem. The global loss of the butterfly community, especially in tropical regions, is causing irreparable damage to the ecological landscape. This decline in population is due to habitat degradation, forest succession, loss of symbiotic relations, economic loss due to flooding, forest development plans, low grassland area, global warming, and reforestation. Moreover, the limited information on the molecular resources of butterflies impedes informed conservation planning. The Threatened Species Initiative (TSI) of Korea has started to utilize the benefits of transcriptome‐guided discovery of molecular resources of a few butterfly species, and a few others are in the pipeline. The cataloging of new genes and genetic markers provides the possibility to promote selective utilization of fitness traits for adaptation of the species to the wild and a newer habitat. In this review, we assessed the versatility of whole‐transcriptome information of the Korean threatened butterfly species, such as the lycaenid Protantigius superans and Spindasis takanosis, the Nymphalid butterfly, Fabriciana nerippe, and the Papilionid species Parnassius bremeri. The schema employed under TSI, including the sequencing and downstream bioinformatics pipeline, could act as a reference for research outside of Korean butterflies. While the molecular resources are available to be exploited, their utilization for conservation is still in its infancy. It is important to synthesize these studies together to catalyze further conservation work applying genomics approaches.

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De novo transcriptome sequencing of triton shell Charonia lampas sauliae: Identification of genes related to neurotoxins and discovery of genetic markers

Cited by 7 publications

References 55 publications

DeTox: a pipeline for the detection of toxins in venomous organisms

DeTox: a pipeline for the detection of toxins in venomous organisms

Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers

Transcriptome‐derived molecular resources for the conservation of threatened butterflies in Korea

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