Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol

Abstract

20Enriching subsets of the genome prior to sequencing allows focusing effort on regions that are 21 relevant to answer specific questions. As experimental design can be adapted to sequence 22 many samples simultaneously, using such approach also contributes to reduce cost. In the 23 field of ecology and evolution, target enrichment is increasingly used for genotyping of plant 24 and animal species or to better understand the evolutionary history of important lineages 25 40 41

Ultra‐Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

“…Besides Hymenoptera, universal probe sets have been designed for Arachnida, Coleoptera, Diptera, Hemiptera and Lepidoptera (Faircloth and Gilbert 2017) that could likely be used to infer relationships within many other poorly known insect groups. Easy to set-up and affordable protocols are freely available (http://ultraconserved.org; Faircloth et al 2015, Cruaud et al 2019, that do not require advanced skills or the use of an expensive robotic molecular biology platform. A software with a detailed tutorial (Faircloth 2016) exists for the easy analysis of raw data.…”

“…We chose to infer the molecular phylogeny of the family using Ultra-Conserved Elements (UCEs) and their flanking regions (Faircloth et al 2012) that are increasingly used to solve ancient and recent divergences in insects (Blaimer et al 2015, Faircloth et al 2015, Blaimer et al 2016a, Bossert et al 2017, Branstetter et al 2017a, Branstetter et al 2017b, Jesovnik et al 2017, Prebus 2017, Van Dam et al 2017, Ward and Branstetter 2017, Bossert et al 2019, Cruaud et al 2019, Kieran et al 2019.…”

Metaphycus macadamiae (Hymenoptera: Encyrtidae) – a biological control agent of macadamia felted coccid Acanthococcus ironsidei (Hemiptera: Eriococcidae) in Hawaii

“…Genomic DNA extraction was undertaken using the protocol in Polaszek et al [10] and Cruaud et al [11], which leaves the sclerotized parts of the specimen intact. Specimens were then critical point dried and card-mounted, with selected individuals then dissected and mounted in Canada balsam on microscope slides.…”

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies

“…In other insect groups that hold sufficient starting material for DNA isolation in particular tissues, such as muscles in the massive legs of Orthoptera (grasshoppers, locusts, crickets) and large beetles, grinding one leg might not be a significant loss to the collection (Tagliavia et al, 2011). Inminute insects such asmicrohymenopterans (tiny wasps in the superfamily Chalcidoidea), the use of non-destructive DNA extraction protocols can be complemented with whole genome amplification prior to library preparation for highthroughput sequencing (Cruaud et al, 2018, 2019).…”

“…Highly-degraded DNA material, such as those coming from museum specimens, might not be suitable for single-molecule DNA sequencing or by certain short-read sequencing protocols such as RADseq (but see protocols that use whole genome amplification prior to reduced-representation sequencing, Cruaud et al, 2018, and targeted sequencing, Cruaud et al, 2019). High molecular weight is only ensured from fresh specimens that have been stored at low temperatures.…”