The integration of nuclear mitochondrial DNA (mtDNA) into the mammalian genomes is an ongoing, yet rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMT). In this study, we identified and analysed NUMT inserted into the pig (Sus scrofa) genome and in the genomes of a few other Suinae species. First, we constructed a comparative distribution map of NUMT in the Sscrofa11.1 reference genome and in 22 other assembled S. scrofa genomes (from Asian and European pig breeds and populations), as well as the assembled genomes of the Visayan warty pig (Sus cebifrons) and warthog (Phacochoerus africanus). We then analysed a total of 485 whole genome sequencing datasets, from different breeds, populations, or Sus species, to discover polymorphic NUMT (inserted/deleted in the pig genome). The insertion age was inferred based on the presence or absence of orthologous NUMT in the genomes of different species, taking into account their evolutionary divergence. Additionally, the age of the NUMT was calculated based on sequence degradation compared to the authentic mtDNA sequence. We also validated a selected set of representative NUMT via PCR amplification. We have constructed an atlas of 418 NUMT regions, 70 of which were not present in any assembled genomes. We identified ancient NUMT regions (older than 55 million years ago, Mya) and NUMT that appeared at different time points along the Suinae evolutionary lineage. We identified very recent polymorphic NUMT (private to S. scrofa, with < 1 Mya), and more ancient polymorphic NUMT (3.5–10 Mya) present in various Sus species. These latest polymorphic NUMT regions, which segregate in European and Asian pig breeds and populations, are likely the results of interspecies admixture within the Sus genus. This study provided a first comprehensive analysis of NUMT present in the Sus scrofa genome, comparing them to NUMT found in other species within the order Cetartiodactyla. The NUMT-based evolutionary window that we reconstructed from NUMT integration ages could be useful to better understand the micro-evolutionary events that shaped the modern pig genome and enriched the genetic diversity of this species.

中文翻译：

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插入猪基因组的线粒体起源核序列 (NUMT) 综合图谱


核线粒体 DNA (mtDNA) 整合到哺乳动物基因组中是一个持续但罕见的进化过程，可产生线粒体起源的核序列 (NUMT)。在这项研究中，我们鉴定并分析了插入猪（Sus scrofa）基因组和其他一些猪亚科物种基因组中的 NUMT。首先，我们构建了 Sscrofa11.1 参考基因组和其他 22 个组装的 Scrofa 基因组（来自亚洲和欧洲猪品种和种群）以及 Visayan 疣猪（Sus）的组装基因组中 NUMT 的比较分布图。 cebifrons）和疣猪（Phacochoerus africanus）。然后，我们分析了来自不同品种、种群或猪种的总共 485 个全基因组测序数据集，以发现多态性 NUMT（在猪基因组中插入/删除）。插入年龄是根据不同物种基因组中是否存在直系同源 NUMT 推断的，同时考虑到它们的进化差异。此外，NUMT 的年龄是根据与真实 mtDNA 序列相比的序列降解来计算的。我们还通过 PCR 扩增验证了一组选定的代表性 NUMT。我们构建了 418 个 NUMT 区域的图谱，其中 70 个区域不存在于任何组装的基因组中。我们确定了古代 NUMT 区域（早于 5500 万年前，Mya）和在 Suinae 进化谱系的不同时间点出现的 NUMT。我们鉴定了最近的多态性 NUMT（S. scrofa 特有的，具有 < 1 Mya），以及存在于各种 Sus 物种中的更古老的多态性 NUMT（3.5-10 Mya）。这些最新的多态性 NUMT 区域在欧洲和亚洲猪品种和种群中分离，很可能是猪属内种间混合的结果。 这项研究首次对野猪基因组中存在的 NUMT 进行了全面分析，并将其与鲸齿目其他物种中发现的 NUMT 进行了比较。我们从 NUMT 整合年龄重建的基于 NUMT 的进化窗口可能有助于更好地理解塑造现代猪基因组并丰富该物种遗传多样性的微进化事件。