Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes.
Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes.
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DOI：
10.1371/journal.pone.0138446
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Biondo C
中科院分区：
文献类型：
--
作者：
Raposo do Amaral F;Neves LG;Resende MF Jr;Mobili F;Miyaki CY;Pellegrino KC;Biondo C
与大规模并行测序相关的超冷冻元件序列捕获(UCES)已成为动物系统学和系统地理学研究中常见的核数据来源。然而，线粒体和微卫星变异仍然普遍用于各种分子研究，并可能在未来几年补充基因组数据。在这里，我们表明，除了提供丰富的基因组数据，UCE测序是微卫星座位设计和高测序深度的完整线粒体基因组的极好来源。这里以来自巴西南部和东南部的三种斑翅雀为例，鉴定了数十个微卫星基因座并组装了完整的有丝基因组。这一战略带来了令人兴奋的机会，可以同时分析全基因组核数据集以及传统上在非模式羊水中使用的mtDNA和微卫星标记，而不需要额外的成本。
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.