A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect

Abstract

Background Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown. Results A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts. Conclusions Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.

A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

“…2021 ), Diabrotica balteata 47% and 1.61 Gb ( King et al . 2023 ), Diabrotica virgifera 53% and 1.85 Gb ( Coates et al . 2023 ), and Altica viridicyanea 63% and 865 Mb ( Xue et al .…”

The detoxification role of P450 genes implicated in adaptation of Helicoverpa armigera to walnut phytochemistry

“…For example, transcriptomic analysis was used to determine the mechanism of adaptation for the maize pest Diabrotica virgifera to different host plants. The study found that the larvae of this rootworm underwent fewer transcriptional changes when feeding on an alternate host plant than when feeding on a marginal or poor host (Coates et al 2023). Transcriptome pro ling of larvae of the weevil Pagiophloeus tsushimanus exposed to the plant-derived volatile compound linalool showed that linalool exposure induced the expression of genes encoding for P450s, cuticular proteins, antioxidases, heat shock proteins, and digestive enzymes ).…”

A near-complete genome assembly of Monochamus alternatus a major vector beetle of pinewood nematode

“…To perform phylogenomic analysis, the genome assemblies and gene annotations of thirteen Coleoptera insects and an outgroup D. melanogaster were retrieved from several public database, such as A. glabripennis (EnsemblMetazoa: Agla_1.0.48) 37 , Aethina tumida (NCBI RefSeq: GCF_024364675.1) 38 , Altica viridicyanea (NGDC GWH: GWHAMMQ00000000) 39 , Callosobruchus maculatus (NCBI GenBank: GCA_900659725.1) 40 , Dendroctonus ponderosae (NCBI GenBank: GCA_020466635.2) 41 , Dendroctonus valens 42 , Diabrotica virgifera (NCBI RefSeq: GCF_003013835.1) 43 , Gonioctena quinquepunctata (NCBI GenBank: GCA_018342105.1) 44 , Leptinotarsa decemlineata (i5k: OGSv1.2_GCF_000500325) 45 , Nebria riversi 46 , Photinus pyralis (NCBI RefSeq: GCF_008802855.1) 47 , Sitophilus oryzae (NCBI RefSeq: GCF_002938485.1) 48 , and Tribolium castaneum (EnsemblMetazoa: Tcas5.2.48) 49 . For each gene, only the longest transcript was kept for downstream analysis.…”