# Insights into Nuclear Mitochondrial Sequence Distribution in the Pig Genome Based on the Latest Reference Assembly

## TL;DR

This study identifies and analyzes nuclear mitochondrial sequences in pigs using the latest genome assembly, revealing their non-random distribution and evolutionary patterns.

## Contribution

A comprehensive map of NUMTs in pigs using an improved genome assembly, revealing new insights into their genomic distribution and evolutionary constraints.

## Key findings

- 513 high-confidence NUMTs were identified, with 460 mapped to chromosomes.
- NUMTs preferentially originate from specific mitochondrial regions and integrate into genomic areas with weak selective constraints.
- Improved genome quality significantly enhances NUMT detection, especially in repetitive and GC-rich regions.

## Abstract

During evolution, fragments of mitochondrial DNA occasionally integrate into the nuclear genome, forming nuclear mitochondrial sequences (NUMTs). Pigs are among the earliest domesticated livestock species and display extensive breed diversity. This study used the latest pig genome assembly to systematically find and analyze the distribution and characteristics of the NUMTs in the pig genome. We identified a total of 513 high-quality NUMTs distributed across the chromosomes. Our analyses revealed that these NUMTs were not generated randomly; instead, they preferentially originated from specific regions of the mitochondrial genome, and their nuclear insertion sites were associated with particular repetitive sequences. By leveraging a more accurate genome assembly, this study detected substantially more NUMTs than earlier versions of the pig genome, providing a more comprehensive landscape of NUMT integration. These findings enhance our understanding of pig evolutionary history and offer a valuable foundation for the conservation and utilization of pig genetic resources.

Horizontal transfer of mitochondrial DNA into the nuclear genome generates nuclear mitochondrial sequences (NUMTs), which serve as molecular fossils reflecting long-term mitochondrial–nuclear interactions and genome evolution. However, the biological mechanisms governing NUMT integration, retention, and evolutionary fate remain incompletely understood in domesticated animals. Here, using the latest pig reference genome assembly (Sscrofa11.1), we present a comprehensive genome-wide characterization of NUMTs in pigs and provide new insights into their genomic distribution and evolutionary constraints. We identified 513 high-confidence NUMTs, of which 460 were chromosomally mapped, accounting for 0.0106% of the nuclear genome. Beyond increased detection, our analyses reveal that pig NUMTs exhibit non-random origins, preferentially integrate into genomic regions under weak selective constraint, and are frequently associated with repetitive elements, consistent with a DNA repair-mediated insertion mechanism. NUMTs predominantly occur as short, fragmented sequences and show signatures of long-term neutral evolution, while insertions disrupting coding sequences are strongly selected against. Synteny-based analyses further identified clustered NUMT regions and duplicated NUMTs, suggesting secondary genomic duplication events following initial integration. Comparative analysis with the earlier Sscrofa10.2 assembly demonstrates that improved genome quality substantially enhances NUMT detection, particularly in repetitive and GC-rich regions, clarifying previously ambiguous sequence-context associations. Together, this high-quality pig NUMT map provides a robust foundation for future functional, evolutionary, and population-level investigations and contributes to the conservation and utilization of pig genetic resources.