Corn Insects & Crop Genetics Research Unit, USDA-ARS, 2310 Pammel Dr, 532 Science II, Iowa State University, Ames, IA, 50011, USA.
Roy J. Carver Biotechnology Center, University of Illinois at Champaign-Urbana, Urbana, IL, USA.
BMC Genomics. 2023 Jan 13;24(1):19. doi: 10.1186/s12864-022-08990-y.
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.
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.
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.
节肢动物害虫对作物的防御措施的适应能力决定了它们对农业生产的影响。西部玉米根虫（Diabrotica virgifera virgifera）（鞘翅目：金龟子科）的幼虫寄主范围仅限于玉米和少数几种草。D. v. virgifera 对轮作和多种杀虫剂的抗性是其成为北美和欧洲玉米栽培中最具破坏性害虫的原因之一。这种害虫的适应能力在多大程度上导致了对寄主植物的专门化仍然未知。
从短 shotgun 读数组装了一个 2.42 Gb 的西部玉米根虫 D. v. virgifera 基因组草案 Dvir_v2.0，并使用长插入物配对、转录组和连锁读取数据进行了支架构建。K-mer 分析预测重复含量≥61.5%。Dvir_2.0 RefSeq 模型的同源物分配预测了更多的种特异性基因重复，包括 ATP 结合盒转运蛋白和化感基因家族的扩张，而不是其他鞘翅目动物。D. v. virgifera 细胞色素 P450s 的大部分属于 CYP4、6 和 9 族。与替代寄主（芒草）、边缘寄主（潘帕斯草）、不良寄主（高粱）和饥饿处理相比，在以玉米根为食的 D. v. virgifera 幼虫之间有 5404 个转录本差异表达；在差异表达的转录本中，1908 个在所有处理中都有表达，而在芒草与玉米之间表达最少。差异表达的转录本富集了假定的剪接体、蛋白酶体和细胞内运输功能。与主要（玉米）和替代寄主相比，边缘寄主、不良寄主和饥饿反应中的上调转录本中独特且富集了一般应激途径功能。
手动注释 D. v. virgifera Dvir_2.0 RefSeq 模型预测了假定参与杀虫剂抗性和化感感知的基因家族的平行基因扩张。我们的研究还表明，D. v. virgifera 幼虫对替代寄主植物的适应能力导致的转录变化比边缘或不良寄主植物要少。边缘寄主和不良寄主以及饥饿处理之间应激反应途径的上调共享可能反映了营养缺乏。这项研究提供了对幼虫在不同寄主植物和资源上取食的转录组反应的深入了解，为这种对玉米具有重要经济意义的害虫的基因组研究提供了信息。
