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Tuta absoluta is one of the largest threats to tomato agriculture worldwide. Native to South America, it has rapidly spread throughout Europe, Africa, and Asia over the past two decades. To understand how T. absoluta has been so successful and to improve containment strategies, high-quality genomic resources and an understanding of population history are critical. Here, we describe a highly contiguous annotated genome assembly, as well as a genome-wide population analysis of samples collected across Latin America. The new genome assembly has an L50 of 17 with only 132 contigs. Based on hundreds of thousands of single nucleotide polymorphisms, we detect three major population clusters in Latin America with some evidence of admixture along the Andes Mountain range. Based on coalescent simulations, we find these clusters diverged from each other tens of thousands of generations ago prior to domestication of tomatoes. We further identify several genomic loci with patterns consistent with positive selection and that are related to insecticide resistance, immunity, and metabolism. This data will further future research toward genetic control strategies and inform future containment policies., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Chrysodeixis includens (Walker, [1858]) is one of the most important defoliator of soybean in Brazil because of its extensive geographical distribution and high tolerance to insecticides compared with other species of caterpillars. Because of this, we conducted bioassays to evaluate the efficacy of pyrethroid λ-cyhalothrin on a C. includens resistant strain (MS) and a susceptible (LAB) laboratory strain. High throughput RNA sequencing (RNA-seq) of larval head and body tissues were performed to identify potential molecular mechanisms underlying pyrethroid resistance. Insecticide bioassays showed that MS larvae exhibit 28.9-fold resistance to pyrethroid λ-cyhalothrin relative to LAB larvae. RNA-seq identified evidence of metabolic resistance in the head and body tissues: 15 cytochrome P450 transcripts of Cyp6, Cyp9, Cyp4, Cyp304, Cyp307, Cyp337, Cyp321 families, 7 glutathione-S-transferase (Gst) genes, 7 α-esterase genes from intracellular and secreted catalytic classes, and 8 UDP-glucuronosyltransferase (Ugt) were overexpressed in MS as compared with LAB larvae. We also identified overexpression of GPCR genes (CiGPCR64-like and CiGPCRMth2) in the head tissue. To validate RNA-seq results, we performed RT-qPCR to assay selected metabolic genes and confirmed their expression profiles. Specifically, CiCYP9a101v1, CiCYP6ae149, CiCYP6ae106v2, CiGSTe13, CiCOE47, and CiUGT33F21 exhibited significant overexpression in resistant MS larvae. In summary, our findings detailed potential mechanisms of metabolic detoxification underlying pyrethroid resistance in C. includens., (© The Author(s) 2020. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)