The complete genome assemblies of 19 insect pests of worldwide importance to agriculture

Amey, 2015, An evolutionarily unique heterodimeric voltage-gated cation channel found in aphids, FEBS Letts., 589, 598, 10.1016/j.febslet.2015.01.020 Cheng, 2021, Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm, Nat. Methods, 18, 170, 10.1038/s41592-020-01056-5 Chin, 2016, Phased diploid genome assembly with single-molecule real-time sequencing, Nat. Methods, 13, 1050, 10.1038/nmeth.4035 Dermauw, 2012, A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae, Proc. Natl. Acad. Sci., 110, E113 Deutsch, 2018, Increase in crop losses to insect pests in a warming climate, Science, 361, 916, 10.1126/science.aat3466 Douris, 2020, Using CRISPR/Cas9 genome modification to understand the genetic basis of insecticide resistance: Drosophila and beyond, Pestic. Biochem. Physiol., 167, 10.1016/j.pestbp.2020.104595 Eddy, 2009, A new generation of homology search tools based on probabilistic inference, Genome Inform., 23, 105 Feron, 2022, Exploring new genomic territories with emerging model insects, Curr. Op. Ins. Sci., 51 Garrison, 2012, Haplotype-based variant detection from short-read sequencing Gilbert, 2012, Perfect arthropod genes constructed with Gigabases of RNA Grabherr, 2011, Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat. Biotechnol., 29, 644, 10.1038/nbt.1883 Haas, 2003, Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucleic Acids Res., 31, 5654, 10.1093/nar/gkg770 Haas, 2022, Phylogenomic and functional characterization of an evolutionary conserved cytochrome P450-based insecticide detoxification mechanism in bees, PNAS U.S.A., 119, 10.1073/pnas.2205850119 Harvey, 2022, Scientists’ warning on climate change and insects Hawkins, 2019, The evolutionary origins of pesticide resistance, Biol. Rev. Camb. Philos. Soc., 94, 135, 10.1111/brv.12440 Holt, 2011, MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects, BMC Bioinformat., 12, 491, 10.1186/1471-2105-12-491 Homem, 2020, Evolutionary trade-offs of insecticide resistance – the fitness costs associated with target-site mutations in the nAChR of Drosophila melanogaster, Mol. Ecol., 29, 2661, 10.1111/mec.15503 Hotaling, 2021, Long reads are revolutionizing 20 years of insect genome sequencing, Genome Biol. Evol, 13 Kurlovs, 2019, Trait mapping in diverse arthropods by bulked segregant analysis, Curr. Opinion Insect Sci., 36, 57, 10.1016/j.cois.2019.08.004 Kurlovs, 2022, Trans- driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae, PLoS Genet., 18, 10.1371/journal.pgen.1010333 Lehmann, 2020, Complex responses of global insect pests to climate warming, Ecol. Environ., 18, 141, 10.1002/fee.2160 Li, 2009, Fast and accurate short read alignment with burrows-wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 Manjon, 2018, Unravelling the molecular determinants of bee sensitivity to neonicotinoid insecticides, Curr. Biol., 28, 114, 10.1016/j.cub.2018.02.045 Nauen, 2022, The role of cytochrome P450s in insect toxicology and resistance, Annu. Rev. Entomol., 67, 105, 10.1146/annurev-ento-070621-061328 Nawrocki, 2013, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, 29, 2933, 10.1093/bioinformatics/btt509 Njiru, 2022, Intradiol ring cleavage dioxygenases from herbivorous spider mites as a new detoxification enzyme family in animals, BMC Biol., 20, 131, 10.1186/s12915-022-01323-1 Northey, 2016, Crystal structures and binding dynamics of odorant-binding protein 3 from two aphid species Megoura viciae and Nasonia ribisnigri, Nat. Sci. Rep., 6, 24739 Pertea, 2020, GFF utilities: GffRead and GffCompare, F1000Research, 10.12688/f1000research.23297.1 Pym, 2019, Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides, BMC Genomics, 20 Richardson, 2021, Chimeric investigations into the diamide binding site on the lepidopteran ryanodine receptor, Int. J. Mol. Sci., 22, 10.3390/ijms222313033 Roach, 2018, Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies, BMC Bioinformat., 19, 460, 10.1186/s12859-018-2485-7 Robinson, 2018, Juicebox.Js provides a cloud-based visualization system for hi-C data, Cell Systems, 6, 256, 10.1016/j.cels.2018.01.001 Samantsidis, 2020, What I cannot create, I do not understand’: functionally validated synergism of metabolic and target site insecticide resistance, B287, 20200838 Savary, 2019, The global burden of pathogens and pests on major food crops, Nat. Ecol. Evol., 3, 430, 10.1038/s41559-018-0793-y Secretariat, 2021, Scientific review of the impact of climate change on plant pests – A global challenge to prevent and mitigate plant pest risks in agriculture, forestry and ecosystems Simão, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthlogs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351 Sims, 2022, Computational investigation of aphid odorant receptor structure and binding function, J. Biomol. Struct. Dyn., 30, 1, 10.1080/07391102.2022.2053743 Sonnhammer, 1997, Pfam: a comprehensive database of protein families based on seed alignments, Proteins, 28, 405, 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L Zimin, 2013, The MaSuRCA genome assembler, Bioinformatics, 29, 2669, 10.1093/bioinformatics/btt476