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Fungicide use has become a fundamental part of many crop protection systems around the world, including to control blackleg disease on canola (Brassica napus L.). In Australia, most canola growers routinely apply at least one fungicide, and potentially multiple fungicides with different modes of action, in a single growing season. There is evidence for the emergence of fungicide resistance in Leptosphaeria maculans, the causal agent of blackleg disease, to the demethylation inhibitor (DMI) class of fungicides in Australia. However, it is not known whether resistance exists towards other chemical classes such as the succinate dehydrogenase inhibitors (SDHI). In this work, 397 samples were screened for resistance towards seven fungicide treatments in stubble-borne L. maculans populations collected from eight canola-growing agro-ecological regions of Australia from 2018 to 2020, a time frame that bridges the introduction of new chemicals for blackleg control. We confirmed that DMI resistance in L. maculans is pervasive across all of the sampled canola-growing regions, with 15% of fungal populations displaying high levels (resistance scores >0.5) of resistance towards the DMI fungicides. Although resistance to newly introduced SDHI fungicides was low, we found evidence of positive cross-resistance between established DMIonly fungicides and a newly introduced combined DMI and quinone outside inhibitor fungicide, suggesting that the efficacy of the latter may be limited by widespread DMI resistance. Proactive surveillance, as performed here, may provide a means to avoid the rapid loss of fungicide efficacy in the field.

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The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid moulting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown and there is little information on their evolution across all insects. Here, we perform comprehensive phylogenetic analyses on a manually annotated set of EcKL genes from 140 insect genomes, revealing the gene family is comprised of at least 13 subfamilies that differ in retention and stability. Our results show the only two genes known to encode ecdysteroid kinases belong to different subfamilies and therefore ecdysteroid metabolism functions must be spread throughout the EcKL family. We also provide comparative phylogenomic evidence that EcKLs are involved in detoxification across insects, with positive associations between family size and dietary chemical complexity, and also find similar evidence for the cytochrome P450 and glutathione S-transferase gene families. Unexpectedly, we find that the size of the clade containing a known ecdysteroid kinase is positively associated with host plant taxonomic diversity in Lepidoptera, possibly suggesting multiple functional shifts between hormone and xenobiotic metabolism. This work provides a robust framework for future functional studies into the EcKL gene family and opens promising new avenues for exploring the genomic basis of dietary adaptation in insects, including the classically studied co-evolution of butterflies with their host plants.

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1 and cytochrome P450 gene families in Drosophila melanogaster by integrating 2 evolutionary and transcriptomic data 3 4Abstract: The capacity to detoxify toxic compounds is essential for adaptation to the 22 ecological niches of many organisms, especially insects. However, detoxification in 23 insects is often viewed through the lens of mammalian detoxification research, even 24 though the organ and enzyme systems involved have diverged for over half a billion 25 years. Phosphorylation is a non-canonical phase II detoxification reaction that, 26 among animals, occurs near exclusively in insects, but the enzymes responsible 27 have never been cloned or otherwise identified. We propose the hypothesis that 28 members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family 29 encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene 30 family in 12 species of Drosophila and explored their evolution within the genus. 31 Many ancestral EcKL clades are evolutionarily unstable and have experienced 32 repeated gene gain and loss events, while others are conserved as single copy 33 orthologs. Leveraging multiple published gene expression datasets from D. 34 melanogaster, and using the cytochrome P450s-a canonical detoxification family-35 as a test case, we demonstrate relationships between xenobiotic induction, 36 detoxification tissue-enriched expression and evolutionary instability in the EcKLs 37 and the P450s. We also found previously unreported genomic and transcriptomic 38 variation in a number of EcKLs and P450s associated with toxic stress phenotypes 39 using a targeted phenome-wide association study (PheWAS) approach. Lastly, we 40 devised a systematic method for identifying candidate detoxification genes in large 41 gene families that is concordant with experimentally determined functions of P450 42 genes in D. melanogaster. Applying this method to the EcKLs suggested a 43 significant proportion of these genes play roles in detoxification, and that the EcKLs 44 may constitute a detoxification gene family in insects. Additionally, we estimate that 45 between 11-16 uncharacterised D. melanogaster P450s are strong detoxification 46 candidates. 47 48 Highlights 49 50• The poorly characterised ecdysteroid kinase-like (EcKL) gene family is 51 hypothesised to encode enzymes responsible for detoxification by 52 phosphorylation in insects. 53• An integrative 'detoxification score' method accurately categorises the known 54 functions of a canonical detoxification family, the cytochrome P450s, and 55 suggests many EcKLs are also involved in detoxification. 56• A targeted phenome-wide association study finds novel associations between 57 EcKL/P450 variation and a number of toxic stress phenotypes, such as two 58 unlinked EcKL paralogs that are both associated with developmental 59 methylmercury resistance. 60 61 1983 131 132The identification of detoxification genes and enzymes is an important part of 133 bridging the gap between toxicology, chemical ecology and functional genomics in ...