远古人类线粒体DNA的死后分子损伤图谱。

IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Daniel R Cuesta-Aguirre, Cristina Amor-Jimenez, Assumpció Malgosa, Cristina Santos
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引用次数: 0

摘要

线粒体DNA (mtDNA)分析对于了解人类群体结构和遗传多样性至关重要。然而,死后DNA损伤带来了挑战,这使得分析变得困难。DNA保存受到环境条件的影响,环境条件以及其他因素使古代mtDNA混合谱中内源性变异与人工制品的区分复杂化。本研究旨在建立古代mtDNA的分子损伤图谱,为分析古代遗骸mtDNA提供一个有用的工具。从ENA数据库中编译了代表不同历史时期和气候区域的个体的427个全基因组或捕获的mtDNA序列数据集。现在的和udg处理的古代样本也包括在内,并用于确定受损读数的水平。结果表明,来自寒冷地区的样本中,reads的受损比例最低,其次是干旱、寒冷、热带和温带地区,且在寒冷和温带地区之间存在显著差异。生成了一个全球损伤概况,确定了2933个位置(占考虑位置的25%),超过23.8%的分析样本中存在损伤,被视为损伤热点。值得注意的是,这些热点中有2856个从未被报道为损伤或突变热点或异质位点。按位置划分,非编码区损伤热点频率略高于编码区。总之,本研究为古代mtDNA分析提供了分子损伤图谱,有望成为解释古代样品mtDNA变异的有价值的工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.

Mitochondrial DNA (mtDNA) analysis is crucial for understanding human population structure and genetic diversity. However, post-mortem DNA damage poses challenges, that make analysis difficult. DNA preservation is affected by environmental conditions which, among other factors, complicates the differentiation of endogenous variants from artefacts in ancient mtDNA mix profiles. This study aims to develop a molecular damage profile for ancient mtDNA that can become a useful tool in analysing mtDNA from ancient remains. A dataset of 427 whole genomes or capture of mtDNA sequences from individuals representing different historical periods and climatic regions was compiled from the ENA database. Present-day and UDG-treated ancient samples were also included and used to establish levels of damaged reads. Results indicated that samples from cold regions exhibited the lowest percentage of damaged reads, followed by arid, cold, tropical and temperate regions, with significant differences observed between cold and temperate regions. A global damage profile was generated, identifying 2933 positions (25% of the positions considered) with damage in more than 23.8% of the samples analysed, deemed as damage hotspots. Notably, 2856 of these hotspots had never been reported as damage or mutational hotspots, or heteroplasmic positions. Damage hotspot frequency by position was slightly higher in the non-coding region compared with the coding region. In conclusion, this study provides a molecular damage profile for ancient mtDNA analysis that is expected to be a valuable tool in the interpretation of mtDNA variation in ancient samples.

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来源期刊
Molecular Ecology Resources
Molecular Ecology Resources 生物-进化生物学
CiteScore
15.60
自引率
5.20%
发文量
170
审稿时长
3 months
期刊介绍: Molecular Ecology Resources promotes the creation of comprehensive resources for the scientific community, encompassing computer programs, statistical and molecular advancements, and a diverse array of molecular tools. Serving as a conduit for disseminating these resources, the journal targets a broad audience of researchers in the fields of evolution, ecology, and conservation. Articles in Molecular Ecology Resources are crafted to support investigations tackling significant questions within these disciplines. In addition to original resource articles, Molecular Ecology Resources features Reviews, Opinions, and Comments relevant to the field. The journal also periodically releases Special Issues focusing on resource development within specific areas.
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