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• W4283076145 abstract "Abstract Background 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 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, Watterson’s θ, and PCA), and genome wide selection scans ( F st , 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 1.04·10 -3 , followed by the selected Busia offspring (7.1·10 -4 ), and finally, Kisumu (6.2·10 -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." @default.
• W4283076145 created "2022-06-19" @default.
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• W4283076145 date "2022-06-17" @default.
• W4283076145 modified "2023-09-26" @default.
• W4283076145 title "<i>RNA-Seq-Pop:</i> Exploiting the sequence in RNA-Seq - a Snakemake workflow reveals patterns of insecticide resistance in the malaria vector <i>Anopheles gambiae</i>" @default.
• W4283076145 cites W1804243006 @default.
• W4283076145 cites W1897349928 @default.
• W4283076145 cites W1907865764 @default.
• W4283076145 cites W1967448179 @default.
• W4283076145 cites W1970707135 @default.
• W4283076145 cites W2005122171 @default.
• W4283076145 cites W2033177710 @default.
• W4283076145 cites W2036272952 @default.
• W4283076145 cites W2036897871 @default.
• W4283076145 cites W2045760616 @default.
• W4283076145 cites W2046310373 @default.
• W4283076145 cites W2064641822 @default.
• W4283076145 cites W2095998476 @default.
• W4283076145 cites W2101317185 @default.
• W4283076145 cites W2106578986 @default.
• W4283076145 cites W2110161291 @default.
• W4283076145 cites W2116548284 @default.
• W4283076145 cites W2123735157 @default.
• W4283076145 cites W2128287083 @default.
• W4283076145 cites W2132378736 @default.
• W4283076145 cites W2136104403 @default.
• W4283076145 cites W2147575903 @default.
• W4283076145 cites W2154883726 @default.
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• W4283076145 cites W2160934269 @default.
• W4283076145 cites W2230709708 @default.
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• W4283076145 cites W2582586511 @default.
• W4283076145 cites W2583577665 @default.
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• W4283076145 cites W2607416563 @default.
• W4283076145 cites W2613745025 @default.
• W4283076145 cites W2620721366 @default.
• W4283076145 cites W2770432019 @default.
• W4283076145 cites W2787596662 @default.
• W4283076145 cites W2805851949 @default.
• W4283076145 cites W2898389114 @default.
• W4283076145 cites W2903531437 @default.
• W4283076145 cites W2912652602 @default.
• W4283076145 cites W2920384872 @default.
• W4283076145 cites W2926046099 @default.
• W4283076145 cites W2933063382 @default.
• W4283076145 cites W2948383743 @default.
• W4283076145 cites W2952768760 @default.
• W4283076145 cites W2963367647 @default.
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• W4283076145 doi "https://doi.org/10.1101/2022.06.17.493894" @default.
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