Targeted capture in evolutionary and ecological genomics

Abstract

The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole genome sequencing in ecological and evolutionary genomic studies. High throughput targeted capture is one such strategy that involves the parallel enrichment of pre-selected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across labs focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to 1) increase the accessibility of targeted capture to researchers working in non-model taxa by discussing capture methods that circumvent the need of a reference genome, 2) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy, and 3) discuss the future of targeted capture and other genome partitioning approaches in light of the increasing accessibility of whole genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole genome sequencing.

Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution

“…Finally, depending on the level of sample multiplexing, targeted sequencing approaches can be more expensive than using RNAseq for venom discovery ($230.65 per RNAseq sample vs. $285.62 per targeted sequencing sample, supplementary table S7, Supplementary Material online). Therefore, the choice between two sequencing strategies will depend on the overall goal of the research project, as no one next-generation sequencing method is suited for all research applications (Jones and Good 2016).…”

Reticulation, divergence, and the phylogeography–phylogenetics continuum

“…Another comparison (102) found similar phylogeographic resolution between exons (drawn randomly from transcriptomes) vs. anchored hybrid enrichment (AHE) loci, which mostly target conserved exons (96,97). Exon capture has been effectively used to study diverging lineages of both vertebrates and invertebrates (e.g., 12, 98, 103) and is particularly appropriate for retrieving genomic data from museum specimens (80,104,105). Arguably, most UCE, AHE, or exon capture loci that have been used thus far for next-generation phylogeography are under mild or even strong purifying selection.…”

Population Genomics of Marine Zooplankton

“…Nielsen et al (2009) concluded that few published studies have convincingly documented that non-neutral traits reflect local adaptation, citing reviews by Hedrick (2006) and Levasseur et al (2007). Recent advances in statistical analysis of genomic markers are enabling more sensitive and accurate detection of local adaptations (Gayral et al 2013;Savolainen et al 2013;De Wit et al 2015), although these are much more powerful for species with well-characterized genomes, which allows exome capture and sequencing (Jones and Good 2016).…”

“…Although the statistical significance of these findings has been questioned (see Bortolotto et al 2011), small-scale patchiness -or genetic "noise" -may be a consequence of the life history of this unique species and/or evidence of local adaptation. Evidence of micro-evolution and local adaptation by Antarctic krill has been shown in genetic and functional analysis of target genes, including thioredoxin (Li et al 2017), clock genes (Jones and Good 2016), heat shock proteins (Papot et al 2016), and opsins (Biscontin et al 2016), among others. Population genomic analysis of Antarctic krill was introduced by Deagle et al (2015), who examined circum-Antarctic genetic diversity and structure using both RADseq and mitochondrial (ND1 and COI) markers.…”

“…However, significant challenges remain for whole-genome analysis of non-model organisms, thus necessitating and encouraging broad use of approaches that require little or no prior genomic data. These include reduced-representation genomic DNA libraries (Reitzel et al 2013), genotyping-by-sequencing (Elshire et al 2011), and exon-capture (Hodges et al 2007;De Wit et al 2015;Jones and Good 2016), although the latter requires prior knowledge of gene architecture. In broad view, population genomic approaches have enormous potential to yield significant new understanding of the ecological and evolutionary dynamics of zooplankton and other marine organisms.…”