Whole genome sequencing of Thaumetopoea pityocampa revealed putative pesticide targets

Shahraki, Aida; Yu, Yanying; Gul, Zeynep Melis; Liang, Chunguang; Iyison, Necla Birgül

doi:10.1016/j.ygeno.2020.07.017

Cited by 5 publications

(7 citation statements)

References 26 publications

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“…The nucleotide sequences of AstR-C and AST-C were derived from the WGS data of the insect performed by our group (Thaumetopoea pityocampa ASH_NBICSL_2017, accession number of the assembled genome: WUAW00000000). The strategy to retrieve the sequences of AstR-C from the genome data is explained in Shahraki et al For AST-C, the same approach was applied. In brief, the protein sequences of Drosophila melanogaster and Helicoverpa armigera were used as queries to search for their orthologs in the new assembly contigs of T.…”

Section: Methodsmentioning

confidence: 99%

“…The nucleotide Sequence of T. pit AST-C was derived from the WGS data that are deposited in NCBI (Thaumetopoea pityocampa ASH_NBICSL_2017, accession number of the assembled genome: WUAW00000000). 12 The gene contained two introns that were removed and translated into the precursor protein. The obtained sequence was compared to the AST-C preprohormone of other species (Supporting Information Figure 1, panel A).…”

Section: Introductionmentioning

confidence: 99%

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Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents

Shahraki

Işbilir

Doğan

et al. 2021

J. Chem. Inf. Model.

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Insect neuropeptide receptors, including allatostatin receptor type C (AstR-C), a G protein-coupled receptor, are among the potential targets for designing next-generation pesticides that despite their importance in offering a new mode-of-action have been overlooked. Focusing on AstR-C of Thaumetopoea pityocampa, a common pest in Mediterranean countries, by employing resonance energy transfer-based methods, we showed Gαi/o coupling and β-arrestin recruitment of the receptor at sub-nanomolar and nanomolar ranges of the endogenous ligand, AST-C, respectively. Molecular docking and molecular dynamics simulation studies revealed the importance of extracellular loop 2 in AstRC/AST-C interaction, and a combination of in silico and in vitro approaches showed the substantial role of Q271 6.55 in G proteindependent activation of AstR-C possibly via contributing to the flexibility of the receptor's structure. The functional and structural insights obtained on T. pit AstR-C positively assist future efforts in developing environmentally friendly pest control agents that are needed urgently.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents

Shahraki

Işbilir

Doğan

et al. 2021

J. Chem. Inf. Model.

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“…Some of the well-known targets were selected, and their tissue expression was evaluated using qRT-PCR [87]. In a related study, we sequenced the genome of the pine processionary moth, Thaumetopoa pityocampa, a common pest in Mediterranean countries, and evaluated the expression of some GPCRs linked with critical physiological processes at RNA level [88]. Despite the extraordinary attractiveness of GPCRs as targets in developing next-generation pesticides, there is only one commercially available compound, Amitraz, that exert its function via a GPCR, Octopamine receptor [89] (http://www.irac-online.org).…”

Section: Next-generation Pesticidesmentioning

confidence: 99%

“…Some of the well‐known targets were selected, and their tissue expression was evaluated using qRT‐PCR [87]. In a related study, we sequenced the genome of the pine processionary moth, Thaumetopoa pityocampa , a common pest in Mediterranean countries, and evaluated the expression of some GPCRs linked with critical physiological processes at RNA level [88].…”

Section: Next‐generation Pesticidesmentioning

confidence: 99%

Are insect GPCRs ideal next‐generation pesticides: opportunities and challenges

et al. 2021

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The increasing human population, combined with low inefficiency and adverse effects of available pesticides, has magnified the urgent need of developing next-generation pesticides. Among the available approaches, strategies targeting invertebrate G protein-coupled receptors (GPCRs) are very promising as these receptors are the targets of endogenous neuropeptides/neuromodulators that upon binding to their receptors induce profound changes in insect physiology. Therefore, exploring GPCR regulators has great potential in the development of targeted next-generation pesticides. Despite the great potential of such alternative pesticides, so far there has been only one approved compound, Amitraz, which conveys its antipest activity via the GPCR Octopamine receptor. Here, we review the current status of pesticide development, hazards associated with conventional pesticide compounds, alternative strategies that involve next-generation of pesticides, structural features of GPCRs, and opportunities and challenges of targeting the members of this superfamily in invertebrates to develop anti-pest agents. In conclusion, we emphasize that the potential of GPCRs cannot be utilized in full without more genomic and transcriptomic data to improve our understanding of the complex network of peptidergic signaling pathways. We argue how vital it is to obtain three-dimensional (3D) structural data on physiologically important target GPCRs and encourage the readers to use the state of the art in silico methods such as virtual screening for the discovery of new pesticide compounds.

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“…With rapid advances in next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies, the cost of whole-genome sequencing has declined rapidly (Abdallah et al, 2019, Lin andHsu 2020). The whole-genome sequencing of many plants species has been achieved, laying a foundation for genetic research and molecular breeding and providing an opportunity to discover the genetic determinants of phenotypical traits (Lincoln 2012, Delsuc and Tilak 2015, Yano et al, 2016, Fontana et al, 2020, Kweon et al, 2020, Nouws et al, 2020, Regalado et al, 2020, Shahraki et al, 2020. For species without reference sequenced genomes, developing SSR molecular markers based on a genomic survey is considered as an efficient strategy (Zhou et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome survey sequencing of Ailanthus altissima and identification of simple sequence repeat (SSR) markers

Devi

Song

et al. 2022

Silvae Genetica

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Ailanthus altissima is a deciduous tree native to China and introduced to other parts of the world as an ornamental plant. It exhibits resistance to both abiotic and biotic stress factors and has various pharmacological effects and strong allelopathy, generating significant research interests. However, the genome sequence of this species has not been reported, limiting its research development. The purpose of the study was to determine the genome size and characteristics of A. altissima to conduct its genomic survey. Next-generation sequencing and K-mer analysis were employed to measure the genome size of A. altissima. Overall, a total of 61.93 Gb high-quality clean data were acquired, representing approximately 64.09× coverage of the A. altissima genome. The genomic characteristics of A. altissima include a genome size of 966.38 Mbp, a heterozygosis rate of 0.78 %, and a repeat rate of 41.22 %. A total of 735,179 genomic SSRs markers were identified based on genome survey sequences. Alignment analysis showed that A. altissima was closely related to Citrus sinensis and Leitneria florida-na. This study provides basic information for future whole-genomic sequencing of A. altissima. This will facilitate a knowledge of the population structure, genetic diversity, long distance-gene transfer, and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China, focusing on planted and natural forest stands.

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Whole genome sequencing of Thaumetopoea pityocampa revealed putative pesticide targets

Cited by 5 publications

References 26 publications

Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents

Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents

Are insect GPCRs ideal next‐generation pesticides: opportunities and challenges

Genome survey sequencing of Ailanthus altissima and identification of simple sequence repeat (SSR) markers

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