Transcriptome profiling reveals sex‐specific gene expressions in pupal and adult stages of the mosquito <i>Culex pipiens</i>

Martynova, T. V.; Kamanda, P.; Sim, Cheolho

doi:10.1111/imb.12735

Cited by 3 publications

(1 citation statement)

References 33 publications

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“…albopictus, and Cx. pipiens have followed with similarly impactful results (Caragata et al, 2017;Chung et al, 2020;Gamez et al, 2020;Martynova et al, 2022).…”

Section: Technological Advancements In Genomics and Transcriptomics P...mentioning

confidence: 90%

Intrinsic factors driving mosquito vector competence and viral evolution: a review

Lewis,

Gallichotte,

Randall

et al. 2023

Front. Cell. Infect. Microbiol.

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Mosquitoes are responsible for the transmission of numerous viruses of global health significance. The term “vector competence” describes the intrinsic ability of an arthropod vector to transmit an infectious agent. Prior to transmission, the mosquito itself presents a complex and hostile environment through which a virus must transit to ensure propagation and transmission to the next host. Viruses imbibed in an infectious blood meal must pass in and out of the mosquito midgut, traffic through the body cavity or hemocoel, invade the salivary glands, and be expelled with the saliva when the vector takes a subsequent blood meal. Viruses encounter physical, cellular, microbial, and immunological barriers, which are influenced by the genetic background of the mosquito vector as well as environmental conditions. Collectively, these factors place significant selective pressure on the virus that impact its evolution and transmission. Here, we provide an overview of the current state of the field in understanding the mosquito-specific factors that underpin vector competence and how each of these mechanisms may influence virus evolution.

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“…albopictus, and Cx. pipiens have followed with similarly impactful results (Caragata et al, 2017;Chung et al, 2020;Gamez et al, 2020;Martynova et al, 2022).…”

Section: Technological Advancements In Genomics and Transcriptomics P...mentioning

confidence: 90%

Intrinsic factors driving mosquito vector competence and viral evolution: a review

Lewis,

Gallichotte,

Randall

et al. 2023

Front. Cell. Infect. Microbiol.

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RNA-Seq-Pop: Exploiting the sequence in RNA-Seq - a Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae

Nagi

Oruni

Weetman

et al. 2022

Preprint

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We provide a reproducible and scalable Snakemake workflow, called RNA-Seq-Pop, which provides end-to-end analysis of RNA-Seq data sets. The workflow allows the user to perform quality control, differential expression analyses, call genomic variants and generate a range of commonly-used summary statistics. Additional options include the calculation of allele frequencies of variants of interest, summaries of genetic variation and population structure (in measures such as nucleotide diversity, Wattersons theta, PCA), and genome wide selection scans (Fst, PBS), together with clear visualisations. We demonstrate the utility of the workflow by investigating pyrethroid-resistance in selected strains of the major malaria mosquito, Anopheles gambiae. The workflow provides additional modules specifically for An. gambiae, including estimating recent ancestry and determining the karyotype of common chromosomal inversions. Results: The Busia lab-colony used for selections was collected in Busia, Uganda, in November 2018. We performed a comparative analysis of three groups: a parental G24 Busia strain; its deltamethrin-selected G28 offspring; and the susceptible reference strain Kisumu. Measures of genetic diversity reveal patterns consistent with that of laboratory colonisation and selection, with the parental Busia strain exhibiting the highest nucleotide diversity of 1.04x10-3, followed by the selected Busia offspring (7.1x10-4), and finally, Kisumu (6.2x10-4). Differential expression and variant analyses reveal that the selected Busia colony exhibits a number of distinct mechanisms of pyrethroid resistance, including the Vgsc-995S target-site mutation, upregulation of SAP genes, P450s, and a cluster of carboxylesterases. During deltamethrin selections, the 2La chromosomal inversion rose in frequency (from 33% to 86%), suggesting a link with pyrethroid resistance, which was previously observed in field samples from the same region. RNA-Seq-Pop analysis also reveals that the most widely-used insecticide-susceptible An. gambiae strain, Kisumu, appears to be a hybrid strain of An. gambiae and its sibling species An. coluzzii, which should be taken into consideration in future research. RNA-Seq-Pop is designed for ease of use, does not require programming skills and integrates the package manager Conda to ensure that all dependencies are automatically installed for the user. We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in An. gambiae and other taxa.

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RNA‐Seq‐Pop: Exploiting the sequence in RNA sequencing—A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae

Nagi

Oruni

Weetman

et al. 2023

Molecular Ecology Resources

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We provide a reproducible and scalable Snakemake workflow, called RNA-Seq-Pop, which provides end-to-end analysis of RNA sequencing data sets. The workflow allows the user to perform quality control, perform differential expression analyses and call genomic variants. Additional options include the calculation of allele frequencies of variants of interest, summaries of genetic variation and population structure, and genome-wide selection scans, together with clear visualizations. RNA-Seq-Pop is applicable to any organism, and we demonstrate the utility of the workflow by investigating pyrethroid resistance in selected strains of the major malaria mosquito, Anopheles gambiae. The workflow provides additional modules specifically for An. gambiae, including estimating recent ancestry and determining the karyotype of common chromosomal inversions. The Busia laboratory colony used for selections was collected in Busia, Uganda, in November 2018. We performed a comparative analysis of three groups: a parental G24 Busia strain; its deltamethrin-selected G28 offspring; and the susceptible reference strain Kisumu. Measures of genetic diversity reveal patterns consistent with that of laboratory colonization and selection, with the parental Busia strain exhibiting the highest nucleotide diversity, followed by the selected Busia offspring, and finally, Kisumu. Differential expression and variant analyses reveal that the selected Busia colony exhibits a number of distinct mechanisms of pyrethroid resistance, including the Vgsc-995S target-site mutation, upregulation of SAP genes, P450s and a cluster of carboxylesterases. During deltamethrin selections, the 2La chromosomal inversion rose in frequency (from 33% to 86%), supporting a previous link with pyrethroid resistance. RNA-Seq-Pop is hosted at: github.com/sanja ynagi/ rna-seq-pop. We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in An. gambiae and other taxa.

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Transcriptome profiling reveals sex‐specific gene expressions in pupal and adult stages of the mosquito Culex pipiens

Cited by 3 publications

References 33 publications

Intrinsic factors driving mosquito vector competence and viral evolution: a review

Intrinsic factors driving mosquito vector competence and viral evolution: a review

RNA-Seq-Pop: Exploiting the sequence in RNA-Seq - a Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae

RNA‐Seq‐Pop: Exploiting the sequence in RNA sequencing—A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae

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