A Genome-Wide Analysis of Nuclear Mitochondrial DNA Sequences (NUMTs) in Chrysomelidae Species (Coleoptera)

Nuclear mitochondrial DNA sequences (NUMTs) are mitochondrial DNA fragments in the nuclear genome, and their unclear distribution in Chrysomelidae species hinders the selection of accurate molecular markers for species identification and phylogenetic analysis. Our study presents a genome-wide survey of NUMTs in 32 Chrysomelidae species. Filtering strategies based on sequence length and open reading frame (ORF) features were employed to identify mitochondrial protein-coding genes (PCGs) minimally affected by NUMTs. Phylogenetic relationships were inferred from both mitochondrial PCG datasets and a COX1 dataset containing NUMTs. Our results show that NUMTs are chromosomally specific, species-specific, and widely distributed. ATP8, COX1, ND1, and ND4 are identified as relatively reliable molecular markers. Phylogenetic analysis is influenced by NUMTs and other factors such as sequence type and saturation. A total of 66 independent COX1 gene nuclear integration events were estimated across 32 species, mostly from distinct mitochondrial lineages. These findings suggest that NUMTs reflect key evolutionary processes such as gene flow and mitochondrial lineage diversification. Their prevalence emphasizes the need for refined molecular markers in species identification and phylogenetic analysis, while also highlighting the importance of NUMTs in understanding mitochondrial DNA integration and their contribution to species' evolutionary history.