Data from: Ultraconserved elements sequencing as a low-cost source of complete mitochondrial genomes and microsatellite markers in non-model amniotes

Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.

结合大规模并行测序（massively parallel sequencing）的超保守元件（ultraconserved elements, UCEs）序列捕获技术，现已成为动物系统学与系统地理学研究中核基因组数据的常规获取来源。然而，线粒体与微卫星变异仍广泛应用于各类分子生物学研究，且在未来数年仍可能作为基因组数据的重要补充。本研究证实，超保守元件测序不仅可获取丰富的基因组数据，同时也是开发微卫星位点所需序列以及获得高测序深度完整线粒体基因组的优质来源。本文以巴西南部及东南部的3种歌鹀属（Poospiza）鸣禽为例，成功鉴定出数十个微卫星位点并组装得到完整线粒体基因组。该策略为无需额外成本即可同时分析全基因组核数据集以及传统常用的线粒体DNA（mtDNA）与微卫星标记提供了极具前景的研究路径，尤其适用于非模式羊膜动物类群。