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Abstract The assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study, we show that high‐quality genome assemblies can be produced from samples of multiple wild‐caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae:Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30–100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short‐read assembly standards (N50 = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome‐guided differential expression study of host plant‐specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding onDatura wrightii(Solanaceae) and existing RNA‐seq data fromNicotiana attenuata(Solanaceae)‐fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione‐S‐transferases, cytochrome P450s, and UDP‐glucosyltransferases. Together our results show that long‐read sequencing of pooled samples can provide a cost‐effective genome assembly option for small insects and can provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests.
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A de novo long-read genome assembly of the sacred datura plant (Datura wrightii) reveals a role of tandem gene duplications in the evolution of herbivore-defense response
Abstract The sacred datura plant (Solanales: Solanaceae:Datura wrightii) has been used to study plant–herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novoDatura wrightiigenome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae:Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution ofDatura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes.
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- Award ID(s):
- 2010772
- PAR ID:
- 10483835
- Publisher / Repository:
- Springer Science + Business Media
- Date Published:
- Journal Name:
- BMC Genomics
- Volume:
- 25
- Issue:
- 1
- ISSN:
- 1471-2164
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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