Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs

Abstract

Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100‐year‐old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by‐product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.

Cost‐saving population genomic investigation of Daphnia longispina complex resting eggs using whole‐genome amplification and pre‐sequencing screening

“…When using WGA strategies, it is also important to consider the impact of the quantity of input DNA that can lead to downwardly biased estimates of heterozygosity and therefore genotyping bias (Medeiros & de Medeiros & Farrell, 2018). This study and others that use very small amounts of input DNA (Campbell et al, 2020;Cruaud et al, 2018;O'Grady et al, 2021) indicate that MDA-WGA does not introduce amplification bias that affects SNP genotyping.…”

“…In addition, Lack et al ( 2018 ) did not use any qualitative diagnostic to assess the amplified Daphnia DNA from a resting egg before performing costly library preparation and sequencing steps. The success rate achieved by O'Grady et al ( 2021 ) was much higher for eggs of Daphnia magna and Daphnia pulicaria (86% and 78%, respectively). Their study also did not include any screening step and so far, no species of the species predominant in European lakes were tested.…”

“…MDA‐WGA uses phi29 DNA polymerase and annealing of random hexamers which does not require species‐specific primers and yields an average DNA product length of >10 kb (Dean et al, 2002 ; Spits et al, 2006 ). It is the preferred method for SNP detection (de Bourcy et al, 2014 ) and has been used in other studies where extremely small specimens hinder genomic investigation to successfully perform RADSeq (Cruaud et al, 2018 ) and whole‐genome sequencing (O'Grady et al, 2021 ). These new methods enabled researchers to study introgression in Schistosome parasites (Platt II et al, 2019 ) and population genomic structure in water mites (Blattner et al, 2022 ) and ghost‐worms (Cerca et al, 2021 ).…”

Tracking aquatic animals with sediment DNA records

“…Nonetheless, comparisons of classical zooplankton taxonomy analyses with metagenomic data based on eDNA extracted from water samples at the same sites, yielded results that were moderately congruent (Monchamp et al 2022). Furthermore, shotgun sequencing can be applied to study Daphnia resting eggs where this analytical platform can provide insight into the differentiation of populations among time points, and identify presence of functional genes and viral pathogens (Hewson et al 2013;Cordellier et al 2021;O'Grady et al 2022). For example, Hewson et al (2013) used a shotgun metagenomic approach on resting eggs and bulk sedDNA from two temperate lakes in the USA to identify viruses suspected to be involved in the ecology of Daphnia spp.…”

A tale of two lakes: divergent evolutionary trajectories of twoDaphniapopulations experiencing distinct environments

“…Specifically, comparing one population experiencing significant ecological disruption to one experiencing relatively stable conditions may provide the ability to specifically account for patterns of local versus global adaptive variation. Such data can be collected for Daphnia , a keystone microcrustacean grazer in freshwater environments, either by direct sequencing of dormant eggs deposited in the layered sediment of lakes (Lack et al, 2018; O’Grady et al, 2022) or by sequencing the extracted DNA of ‘resurrected’ Daphnia isolates (Kerfoot et al, 1999; Kerfoot and Weider, 2004). Here we use the second approach to obtain genomic information on historic and extant populations of Daphnia pulicaria in two lakes located in Minnesota, USA.…”