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Urine as a high-quality source of host genomic DNA from wild populations.

尿液作为野生群体宿主基因组DNA的高质量来源。

  • 影响因子:7.01
  • DOI:10.1111/1755-0998.13260
  • 作者列表:"Ozga AT","Webster TH","Gilby IC","Wilson MA","Nockerts RS","Wilson ML","Pusey AE","Li Y","Hahn BH","Stone AC
  • 发表时间:2021-01-01
Abstract

:The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.

摘要

: 从野生动物种群中生成基因组数据的能力有可能对其自然栖息地中的物种的种群历史和动态提供前所未有的见解。然而,对于许多物种,从法律、伦理或逻辑上不可能获得足以用于基因组分析的质量的组织样品。在这项研究中,我们评估了坦桑尼亚贡贝国家公园野生东方黑猩猩 (Pan troglodytes schweinfurthii) 的多种遗传物质来源 (粪便,尿液,牙本质和牙结石) 和几种捕获方法 (鸟枪法,全基因组,外显子组) 在生成基因组规模数据方面的成功。我们发现尿液携带的宿主DNA明显多于其他来源,从而导致整个基因组的覆盖范围越来越广。尿液也表现出较低的等位基因脱落率。我们发现,在从粪便和牙结石等低质量样本中生成可用数据方面,外显子组测序远比鸟枪法测序和全基因组捕获成功。这些结果强调尿液是一种有希望的和尚未开发的DNA来源,可以从许多物种的野生种群中无创地收集。

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