Assessing the utility of whole genome amplified DNA for next-generation molecular ecology

DNA quantity can be a hindrance in ecological and evolutionary research programmes due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential solution to low-quantity DNA lies in whole genome amplification (WGA) techniques that can substantially increase DNA yield. To date, few studies have rigorously examined sequence bias that might result from WGA and next-generation sequencing of nonmodel taxa. To address this knowledge deficit, we use multiple displacement amplification (MDA) and double-digest RAD sequencing on the grey mouse lemur (Microcebus murinus) to quantify bias in genome coverage and SNP calls when compared to raw genomic DNA (gDNA). We focus our efforts in providing baseline estimates of potential bias by following manufacturer's recommendations for starting DNA quantities (>100 ng). Our results are strongly suggestive that MDA enrichment does not introduce sys...DNA 含量不足常成为生态与进化研究的阻碍，其影响因素涵盖目标物种的濒危等级、可获取的组织类型，以及野外条件对样本保存方式的制约。针对低含量DNA的可行解决方案之一是全基因组扩增（whole genome amplification, WGA）技术，该技术可显著提升DNA产出量。截至目前，鲜有研究针对非模式类群，严格评估WGA与下一代测序可能引发的序列偏差。为填补这一研究空白，本研究以灰鼠狐猴（Microcebus murinus）为研究对象，采用多重置换扩增（multiple displacement amplification, MDA）与双酶切RAD测序技术，以原始基因组DNA（raw genomic DNA, gDNA）为对照，量化基因组覆盖度与单核苷酸多态性（SNP）分型过程中的偏差。本研究严格遵循厂商推荐的起始DNA用量（＞100 ng）标准，旨在为潜在偏差提供基准评估数据。本研究结果强烈提示，MDA富集过程不会引入系统性（sys...）