Reduced Representation Methods for Subgenomic Enrichment and Next-Generation Sequencing

Good, Jeffrey M.

doi:10.1007/978-1-61779-228-1_5

Cited by 29 publications

(30 citation statements)

References 59 publications

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“…Rather, sequencing strategies should be tailored to specific research aims (Davey et al 2011; Good 2011; Ekblom & Galindo 2011). Thus, the benefits and limits of sequencing approaches are best discussed in the context of a specific research aim.…”

Section: When Should Targeted Capture Be Used?mentioning

confidence: 99%

Targeted capture in evolutionary and ecological genomics

2015

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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.

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Section: When Should Targeted Capture Be Used?mentioning

confidence: 99%

Targeted capture in evolutionary and ecological genomics

2015

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“…Most of these issues will require some form of comparative genomic data to be addressed. Powerful next-generation sequencing techniques now enable the collection of large-scale genomic data in non-model species (Good, 2011), including the recent development of large-scale targeted resequencing tools for chipmunks (Bi et al, 2012(Bi et al, , 2013.…”

Section: Future Directionsmentioning

confidence: 99%

Divergence with gene flow within the recent chipmunk radiation (Tamias)

et al. 2014

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Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para-and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection.

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“…The reduced genome representation can be achieved in several ways: (1) by using various steps for reducing genome complexity such as RAD (restriction-site associated DNA) sequencing and related approaches (Miller et al, 2007;Baird et al, 2008;Peterson et al, 2012;Toonen et al, 2013); (2) by targeting only the expressed parts of the genome (i.e., RNAseq, Wang et al, 2009);or (3) by isolating specific known regions of the genome through hybridization-based sequence capture or targeted amplification (Good, 2011;Grover et al, 2012), although the latter approach requires a pre-existing reference sequence from the target species or a close relative. Alternative approaches combine transcriptome and genome sequence data (e.g., Lamichaney et al,.…”

Section: Next-generation Population Genomicsmentioning

confidence: 99%