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

Hwang, Hee Ju; Patnaik, Bharat Bhusan; Kang, Se Won; Park, So Young; Chung, Jong Min; Sang, Miao; Park, Jie Eun; Min, Hye Rin; Seong, Jiyeon; Jo, Yong Hun; Noh, Mi Young; Lee, Jong Dae; Jung, Ki Yoon; Park, Hong Seog; Jeong, Heon Cheon; Lee, Yong Seok

doi:10.1111/1748-5967.12292

Cited by 6 publications

(4 citation statements)

References 52 publications

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“…2016a), the endangered diving beetle Cybister chinensis (Hwang et al . 2018), and the endangered dung beetle Copris tripartitus (Hwang et al . 2023) have been sequenced beyond the threatened butterflies listed in Figure 1.…”

Section: Tsi Of Korea For Conservation Management Of Butterfly Speciesmentioning

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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Section: Tsi Of Korea For Conservation Management Of Butterfly Speciesmentioning

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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“…Further, the transcriptome profile of the Asian giant hornet, Vespa mandarinia was able to screen new genes to understand the physiological attributes of the wasp enlisted as threatened species in Korea (Patnaik et al, 2016). Among the threatened molluscan species of Korea, the land snails such as Aegista chejuensis and Aegista quelpartensis , Koreanohadra kurodana , Satsuma myomphala (Kang et al, 2017) and Ellobium chinense (Kang et al, 2018) were prioritized for transcriptome sequencing. The detailed molecular components ascribed to innate immunity pathways were also screened from the transcriptome of a freshwater mussel, Cristaria plicata endangered in Korea (Patnaik et al, 2016) and an air-breathing land slug, Incilaria fruhstorferi (Patnaik et al, 2019).…”

Section: Journal Of Environmental Biologymentioning

confidence: 99%

“…De novo transcriptome of endangered triton shell, Charonia lampas sauliae identified transcripts that are channel proteins blocked by tetrodotoxin synthesized by symbiotic bacteria inhabiting the shells. Additionally, conotoxin superfamily peptides were discovered that could be synthesized for therapeutic interventions such as anti-cancer and pain-relief agents (Fassio et al, 2019;Yao et al, 2019;Hwang et al, 2021).The transcriptome of endangered diving beetle, Cybister japonicus and endangered dung beetle Copris tripartitus also enriched information on molecular resources including SSR discovery (Hwang et al, 2018;Hwang et al, 2023). With the large-scale availability of 'omics' resources, the threatened species initiative is taking proactive steps to complement local conservation efforts in the country.…”

Section: Journal Of Environmental Biologymentioning

confidence: 99%

The utility of transcriptomics in the conservation of sensitive and economically important species

Patnaik¹,

Lee²

2023

JEB

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The connection between the central dogma of biology [DNA --(Transcription)---› RNA –(Translation)--› Protein] and the 'omics' resources obtained from each molecule are now being exploited by conservation managers to protect biodiversity and ecosystems for sustainable development. Biodiversity doesn't necessarily mean the total number of species, it is more complex and includes genetic diversity within species and the diversity of habitats. Land-use changes, direct harvest, various forms of pollution, and climate change are the biggest threats to biodiversity, most of which are hardly documented at the molecular level to guide conservation actions and stop extinctions. Justifying the plasticity of species adaptability could ensure informed decisions on proposing suitable habitats for species translocations if the current distributional range is disturbed. The 'omics' resources (especially generated by high-throughput RNA and DNA sequencing approaches) have intervened on a larger scale recently to understand species physiology, evolutionary biology and ecology. This has supported enriched information on the evolution and evaluation of adaptive phenotypes in natural populations as well as the mechanism of physiological responses to various environmental perturbations (Alvarez et al., 2015; De Wit et al., 2015; Evans, 2015; Connon et al., 2018). Transcriptomics can unravel unparalleled mysteries in the context of conservation of sensitive and economically important species. Being smaller than genomes and tissue-specific, it reduces the amount of data generated and focuses on candidate gene expressions, understanding a species' response to environmental changes. It gives sufficient scope for studying the biology of a non-model species at the molecular level by de novo assembled transcript generation and annotation involving predicted gene function. Apart from the ontology and homology-based functional annotations, the transcriptomes can also be mined for the discovery of genetic markers such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) vital for assessments of genetic diversity and exploring species from newer habitats. Ultimately, such resources should be effectively integrated into management decisions and policies to contribute towards conservation. Utilization of transcriptome knowledge in conservation remains rare due to unfamiliarity of the interpretation of complex molecular data for managers. Hence, to overcome such a knowledge divide, the physiologists and the data scientists need to build partnerships with regulatory agencies and resource managers to translate transcriptomic evaluations to well-characterized molecular thresholds that can act as sensible markers to predict a species' adaptive plasticity in invoking compensatory mechanisms leading to recovery or non-recovery. Until and unless such conservative benchmarks are designed, the utility of the transcriptomes into management actions and policies seems debated. I have been associated with the Korean threatened species initiative for the past eight years as a researcher. The initiative has prioritized the Illumina HiSeq-based short-read platform for transcriptome generation and the Trinity suite for de novo assembly of clean reads. Further, a locally-curated database known as the PANM database (Protostome DB) has facilitated gene discovery in Red List molluscan and butterfly species of Korea that are threatened of extinction. Mostly, the transcriptomics pipeline adopted under this initiative has cataloged the functional resources in the context of immunity, growth and reproduction of species. Large-scale screening of SSR markers from transcriptome has highlighted the possibility of addressing species richness and diversity in disturbed natural habitats and the feasibility of finding species in newer habitats. This initiative has provided the first report to record ecologically-relevant traits from endangered lycaenid butterflies such as Protantigius superans and Spindasis takanosis and the nymphalid butterfly, Fabriciana nerippe (Patnaik et al., 2015; Hwang et al., 2016). Further, the transcriptome profile of the Asian giant hornet, Vespa mandarinia was able to screen new genes to understand the physiological attributes of the wasp enlisted as threatened species in Korea (Patnaik et al., 2016). Among the threatened molluscan species of Korea, the land snails such as Aegista chejuensis and Aegista quelpartensis (Kang et al., 2016), Koreanohadra kurodana (Kang et al., 2016), Satsuma myomphala (Kang et al., 2017) and Ellobium chinense (Kang et al., 2018) were prioritized for transcriptome sequencing. The detailed molecular components ascribed to innate immunity pathways were also screened from the transcriptome of a freshwater mussel, Cristaria plicata endangered in Korea (Patnaik et al., 2016) and an air-breathing land slug, Incilaria fruhstorferi (Patnaik et al., 2019). The discovery of the immunity components was useful in drafting a conceptual map of innate immune signaling in molluscs by addressing the putative involvement of the orthologs at different stages of pathway. Such resources are vital for functional genomics applications as they serve to understand the resistance or susceptibility of the host to microorganisms. De novo transcriptome of endangered triton shell, Charonia lampas sauliae identified transcripts that are channel proteins blocked by tetrodotoxin synthesized by symbiotic bacteria inhabiting the shells. Additionally, conotoxin superfamily peptides were discovered that could be synthesized for therapeutic interventions such as anti-cancer and pain-relief agents (Fassio et al., 2019; Yao et al., 2019; Hwang et al., 2021).The transcriptome of endangered diving beetle, Cybister japonicus and endangered dung beetle Copris tripartitus also enriched information on molecular resources including SSR discovery (Hwang et al., 2018; Hwang et al., 2023). With the large-scale availability of 'omics' resources, the threatened species initiative is taking proactive steps to complement local conservation efforts in the country. In India, there is a lack of similar consortium-based initiatives for understanding the local biodiversity of a region. This has restricted access to high-throughput molecular resources from the local biodiversity for meeting the challenges in health, agrifood and the environment. Hence, a consortium such as the National Biodiversity Genomics (NBG) consortium addressing the genome or transcriptome-guided discovery of molecular resources can act as a knowledge hub supporting environmental sustainability (Fig. 1). The consortium will be able to develop expertise in database development, bigdata analysis and bioinformatics, genetic diversity analysis and functional genomics resources. The consortium will also facilitate new opportunities in bigdata science, research-academia-industry partnerships for new product development, entrepreneurship, and outreach activities and invoke a forum for collaborations with International genomics consortiums. Such a consortium will keep the academics interested in the research supporting environmental sustainability with opportunities for workshops/ training, open-learning and modular courses, environmental education programs to encourage local action groups and conservation managers and create avenues for convergence research for resource utilization. Building 'omics' data infrastructure in a consortium to study the conservation of sensitive and economically-important species is needed in the country to invigorate attention on biodiversity conservation. In summary, such a consortium will build large-scale data resources, maximize the impact of national research infrastructure, build scientific capabilities, catalyze scientific collaborations and international linkages, and would accelerate research and translation into industry. I sincerely wish that the reference transcriptome characterization of native flora and fauna would be taken up in a consortium mode to unravel the unparalleled benefits of the resources in multi-dimensional research and development objectives. I am happy to share my research experience and expertise through this editorial on the 'Journal of Environmental Biology (JEB)' platform- a journal that I have been associated with for the last 15 years in different capacities as an author, reviewer, and editor. I appreciate the visions of Professor Dalela and the hardworking team over the years to make this journal a global environmental outlook tool for the benefit of society. Acknowledgment: This research was supported by Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Ministry of Education (2022R1A6C101B794), the National Research Foundation (NRF-2021R1A6A1A03039503 / NRF-2017R1D1A3B06034971) and Soonchunhyang University Research Fund.Further, the authors solicit the support received from the Agreement of Cooperation between Fakir Mohan University, Balasore, India and KNAR, Soonchunhyang University, Asan, Korea.

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“…There have been several chemical studies on species within the genus Cybister , including on C. tripunctatus which have been summarized in several excellent reviews on beetle defensive chemistry ( Schildknect, 1970 ; Dettner, 1987 , 2014 ). It does not appear that C. japonicus (= C. chinensis ) has been investigated for chemical composition, but it has recently been the subject genetic investigation using RNA seq technology ( Hwang et al ., 2018 ). Beetles in this genus contain a series of simple aromatic compounds as well as steroids, both used as glandular secretions (chemical constituents of C. tripunctatus , are shown in 43-49 in Fig.…”

Section: Beetles Used In Tcm By Familymentioning

confidence: 99%

Drug Discovery Insights from Medicinal Beetles in Traditional Chinese Medicine

Deyrup

Stagnitti

Perpetua

et al. 2021

Biomolecules & Therapeutics

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Traditional Chinese medicine (TCM) was the primary source of medical treatment for the people inhabiting East Asia for thousands of years. These ancient practices have incorporated a wide variety of materia medica including plants, animals and minerals. As modern sciences, including natural products chemistry, emerged, there became increasing efforts to explore the chemistry of this materia medica to find molecules responsible for their traditional use. Insects, including beetles have played an important role in TCM. In our survey of texts and review articles on TCM materia medica, we found 48 species of beetles from 34 genera in 14 different families that are used in TCM. This review covers the chemistry known from the beetles used in TCM, or in cases where a species used in these practices has not been chemically studied, we discuss the chemistry of closely related beetles. We also found several documented uses of beetles in Traditional Korean Medicine (TKM), and included them where appropriate. There are 129 chemical constituents of beetles discussed.

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

Cited by 6 publications

References 52 publications

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

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

The utility of transcriptomics in the conservation of sensitive and economically important species

Drug Discovery Insights from Medicinal Beetles in Traditional Chinese Medicine

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