The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range

Abstract

We present the first draft genome for an invasive mite, the redlegged earth mite, Halotydeus destructor (Tucker, 1925), a major pest of Australian grains and pasture. Our de novo assembly comprised 132 contigs, with a total length of 48.90 Mb, an N50 of 874,492, an L50 of 14, a GC content of 45.3%, 14,583 putative genes, and a high level of completeness as assessed through benchmark single copy orthologs (BUSCO >89%). We use our draft genome to gain insights into the unresolved genetic mechanism of organophosphate resistance and demographic processes in the invasive Australian populations. We found that the acetylcholinesterase gene (ace), the target of organophosphate pesticides, has undergone a large amplification event in H. destructor. Copy number of this gene is considerably larger compared to most other arthropod pests and is likely to contribute to organophosphate resistance in this species. Congruent with a stepping-stone invasion pathway, we found that western populations were more genetically diverse (higher genomic heterozygosity) and had larger population sizes (as inferred from demographic analyses) relative to eastern populations. Our demographic analyses were, however, equivocal on the role of gene flow in shaping these genetic patterns. Due to the short evolutionary timescale since the H. destructor Australian invasion, it is challenging to discern between recent divergence with isolation versus ongoing gene flow. Our draft genome for H. destructor is the first assembled for mites in the family Penthaleidae of the order Trombidiformes, an under-represented group with few available reference genomes.

Aceandace-like genes of invasive redlegged earth mite: Copy number variation, target-site mutations, and their associations with organophosphate insensitivity

“…This ace amplification may be the product of a long history of organophosphate selection. In that prior work, we observed clear presence/absence patterns between organophosphate resistant/susceptible populations for target-site mutations at the ancestral ace HDE_14279 gene: G119S, A201S, and F331Y (Thia et al, 2022). However, the role of different ace genes in organophosphate insensitivity has not been tested.…”

“…Victoria populations included two from Colbinabbin, one with evolved resistance to organophosphates (herein referred to as Colbinabbin Res) and the other susceptible to organophosphates (herein referred to as Colbinabbin Sus). A third Victorian population was collected from Wantirna South and previously used to assemble the reference genome for H. destructor (Thia et al ., 2022). Although not phenotypically screened in this study, mites from Wantirna South are known to be susceptible to organophosphates (Paul Umina, personal communication).…”

“…Mapping was limited to contigs >0.2 Mb in length. We limited mapping to these larger contigs because prior work had identified more variable, unreliable mapping to smaller contigs (Thia et al ., 2022). S am TOOLS (Li et al ., 2009; Danecek et al ., 2021) was used to discard reads with mapping quality <30 and those that were found to be PCR duplicates.…”

“…We used mapped read depth ratios as an estimate of ace copy number. We compiled a single copy gene list containing the 866 reference genes verified as single copies in prior BUSCO analyses of the H. destructor genome (Thia et al ., 2022) that resided on genomic contigs >0.2 Mb in length. We extracted mean read depth information for these single copy genes and 19 ace genes with the SAMTOOLS COVERAGE function.…”

“…Whilst the molecular mechanism of pyrethroid resistance in H. destructor has mostly been linked to target-site mutations (Edwards et al ., 2018; Cheng et al ., 2019; Yang et al ., 2020), the molecular mechanism of organophosphate resistance has been difficult to elucidate. The recently assembled draft genome for H. destructor (Thia et al ., 2022) revealed a large ace gene amplification event, which has led to the formation of an ace gene complex. This ace amplification may be the product of a long history of organophosphate selection.…”