Fuentes-Pardo Angela P, Ruzzante Daniel E
Department of Biology, Dalhousie University, Halifax, NS, Canada.
Mol Ecol. 2017 Oct;26(20):5369-5406. doi: 10.1111/mec.14264. Epub 2017 Sep 5.
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
全基因组重测序（WGR）是一种强大的方法，可用于解决一些尚未通过传统方法完全解决的基础进化生物学问题。WGR包括四种方法：对具有未解析或已解析单倍型的个体进行高深度测序、通过混合等摩尔量的未标记个体DNA对等位基因进行高深度测序（Pool-seq）以及对群体中的多个个体进行低深度测序（lcWGR）。这些技术需要有参考基因组。这一点，再加上鸟枪法测序成本仍然很高以及对计算资源和存储的大量需求，限制了它们在基因组资源稀缺的非模式物种以及保护生物学等领域中的应用。我们在此的目标是描述各种WGR方法、它们的优缺点以及在保护生物学中的潜在应用。WGR提供了前所未有的标记密度，并能检测广泛多样的遗传变异，不限于单核苷酸多态性（例如，结构变异和调控元件中的突变），从而增强了其检测选择特征和局部适应性以及识别表型性状和疾病遗传基础的能力。然而，目前没有一种WGR方法能满足保护遗传学的所有要求，且每种方法都有其自身的局限性和潜在偏差来源。我们讨论了减少此类偏差的建议方法。我们设想在不久的将来，对全基因组的分析将成为许多非模式物种和领域（包括保护生物学）中的常规任务。
