{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T12:12:55Z","timestamp":1789992775781,"version":"4.0.1"},"reference-count":98,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2023,2,10]],"date-time":"2023-02-10T00:00:00Z","timestamp":1675987200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010666","name":"H2020 Research Infrastructures","doi-asserted-by":"publisher","award":["731060"],"award-info":[{"award-number":["731060"]}],"id":[{"id":"10.13039\/100010666","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/P02520X\/1"],"award-info":[{"award-number":["MR\/P02520X\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/R015678\/1"],"award-info":[{"award-number":["MR\/R015678\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01\u2010AI116811"],"award-info":[{"award-number":["R01\u2010AI116811"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","award":["RSWF\\FT\\180003"],"award-info":[{"award-number":["RSWF\\FT\\180003"]}],"id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["203511\/Z\/16\/Z"],"award-info":[{"award-number":["203511\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2023,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    We provide a reproducible and scalable Snakemake workflow, called\n                    <jats:italic>RNA\u2010Seq\u2010Pop<\/jats:italic>\n                    , which provides end\u2010to\u2010end 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\u2010wide selection scans, together with clear visualizations.\n                    <jats:italic>RNA\u2010Seq\u2010Pop<\/jats:italic>\n                    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,\n                    <jats:italic>Anopheles gambiae<\/jats:italic>\n                    . The workflow provides additional modules specifically for\n                    <jats:italic>An.\u00a0gambiae<\/jats:italic>\n                    , 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\u2010selected 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\u2010995S target\u2010site 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.\n                    <jats:italic>RNA\u2010Seq\u2010Pop<\/jats:italic>\n                    is hosted at:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/sanjaynagi\/rna-seq-pop\">github.com\/sanjaynagi\/rna\u2010seq\u2010pop<\/jats:ext-link>\n                    . We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in\n                    <jats:italic>An.\u00a0gambiae<\/jats:italic>\n                    and other taxa.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13759","type":"journal-article","created":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T05:44:16Z","timestamp":1674625456000},"page":"946-961","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["<i>RNA\u2010Seq\u2010Pop<\/i>\n                    : Exploiting the sequence in\n                    <scp>RNA<\/scp>\n                    sequencing\u2014A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector\n                    <i>Anopheles gambiae<\/i>"],"prefix":"10.1111","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1214-8523","authenticated-orcid":false,"given":"Sanjay C.","family":"Nagi","sequence":"first","affiliation":[{"name":"Department of Vector Biology Liverpool School of Tropical Medicine  Liverpool UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ambrose","family":"Oruni","sequence":"additional","affiliation":[{"name":"Uganda Virus Research Institute  Entebbe Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Weetman","sequence":"additional","affiliation":[{"name":"Department of Vector Biology Liverpool School of Tropical Medicine  Liverpool UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5218-1497","authenticated-orcid":false,"given":"Martin J.","family":"Donnelly","sequence":"additional","affiliation":[{"name":"Department of Vector Biology Liverpool School of Tropical Medicine  Liverpool UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,2,10]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.113.006742"},{"key":"e_1_2_9_3_1","unstructured":"Andrews S.(2010).FastQC: A quality control tool for high throughput sequence data.http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.154831.113"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0044607"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u201012\u201082"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071\u2010015\u20101083\u2010z"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.actatropica.2020.105502"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3519"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u20100716\u20102293\u20103_13"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13359"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.117.040089"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0215669"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1186\/1756\u20103305\u20107\u2010314"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0002905"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0910672106"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15845"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms5248"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1590\/0074\u201002760200547"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1077769"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/0035\u20109203(79)90036\u20101"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u201015\u2010174"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep41312"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw354"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0005526"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu314"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1258522"},{"key":"e_1_2_9_30_1","first-page":"1","article-title":"Vcflib and tools for processing the VCF variant call format","author":"Garrison E.","year":"2021","journal-title":"BioRxiv"},{"key":"e_1_2_9_31_1","first-page":"1","article-title":"Haplotype\u2010based variant detection from short\u2010read sequencing","author":"Garrison E.","year":"2012","journal-title":"ArXiv"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005004"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1009253"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa128"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2018.03.014"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/132.2.583"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010018\u201007615\u2010x"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010019\u20101864\u20101"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1009970"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.655707"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1111\/imb.12294"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1093\/jme\/tjaa167"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010019\u20100201\u20104"},{"key":"e_1_2_9_44_1","unstructured":"K\u00f6ster J.(2022).Snakemake: Best practices.https:\/\/snakemake.readthedocs.io\/en\/stable\/snakefiles\/best_practices.html"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes11121487"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2017.00283"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.18\u20100607"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw655"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010014\u20100550\u20108"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.120.401418"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.119.400445"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005457"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00438\u2010015\u20101109\u20104"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071\u2010019\u20103353\u20107"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq002"},{"key":"e_1_2_9_56_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0210586"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.1111\/imb.12735"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ibmb.2021.103655"},{"key":"e_1_2_9_60_1","unstructured":"Miles A. &Harding N. J.(2017).Scikit\u2010Allel.https:\/\/doi.org\/10.5281\/zenodo.3935797"},{"key":"e_1_2_9_61_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature24995"},{"key":"e_1_2_9_62_1","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.29032.2"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.1111\/mve.12310"},{"key":"e_1_2_9_64_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000286"},{"key":"e_1_2_9_65_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010021\u201007551\u2010z"},{"key":"e_1_2_9_66_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1258522"},{"key":"e_1_2_9_67_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576\u2010021\u201000349\u20105"},{"key":"e_1_2_9_68_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365\u20102583.2010.01053.x"},{"key":"e_1_2_9_69_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.16591"},{"key":"e_1_2_9_70_1","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.10501.2"},{"key":"e_1_2_9_71_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4324"},{"key":"e_1_2_9_72_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2013.08.008"},{"key":"e_1_2_9_73_1","doi-asserted-by":"publisher","DOI":"10.1242\/jeb.089508"},{"key":"e_1_2_9_74_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0058815"},{"key":"e_1_2_9_75_1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a026823"},{"key":"e_1_2_9_76_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.25813"},{"key":"e_1_2_9_77_1","doi-asserted-by":"publisher","DOI":"10.1186\/1475\u20102875\u20107\u2010163"},{"key":"e_1_2_9_78_1","doi-asserted-by":"publisher","DOI":"10.1002\/ps.5374"},{"key":"e_1_2_9_79_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576\u2010019\u20100150\u20102"},{"key":"e_1_2_9_80_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0009871"},{"key":"e_1_2_9_81_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010019\u201051181\u20101"},{"key":"e_1_2_9_82_1","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10040415"},{"key":"e_1_2_9_83_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.262790.120.Freely"},{"key":"e_1_2_9_84_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.6418"},{"key":"e_1_2_9_85_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev\u2010biodatasci\u2010072018\u2010021255"},{"key":"e_1_2_9_86_1","doi-asserted-by":"publisher","DOI":"10.3390\/v11060513"},{"key":"e_1_2_9_87_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep46451"},{"key":"e_1_2_9_88_1","doi-asserted-by":"publisher","DOI":"10.1261\/rna.876308"},{"key":"e_1_2_9_89_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2484.RNA\u2010Seq"},{"key":"e_1_2_9_90_1","doi-asserted-by":"publisher","DOI":"10.1016\/0040-5809(75)90020-9"},{"key":"e_1_2_9_91_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010018\u201021265\u20105"},{"key":"e_1_2_9_92_1","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.2007.76.334"},{"key":"e_1_2_9_93_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071\u2010019\u20103774\u20103"},{"key":"e_1_2_9_94_1","doi-asserted-by":"publisher","DOI":"10.3390\/insects13030247"},{"key":"e_1_2_9_95_1","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkab352"},{"key":"e_1_2_9_96_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1190371"},{"key":"e_1_2_9_97_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010020\u20103433\u2010x"},{"key":"e_1_2_9_98_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0078644"},{"key":"e_1_2_9_99_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12936\u2010019\u20102705\u20102"}],"container-title":["Molecular Ecology Resources"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.13759","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/1755-0998.13759","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.13759","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,22]],"date-time":"2023-08-22T16:07:56Z","timestamp":1692720476000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1755-0998.13759"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,10]]},"references-count":98,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,5]]}},"alternative-id":["10.1111\/1755-0998.13759"],"URL":"https:\/\/doi.org\/10.1111\/1755-0998.13759","archive":["Portico"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.06.17.493894","asserted-by":"object"}]},"ISSN":["1755-098X","1755-0998"],"issn-type":[{"value":"1755-098X","type":"print"},{"value":"1755-0998","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,10]]},"assertion":[{"value":"2022-08-03","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-01-06","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-02-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}