Genomic Underground: Unraveling NUMTs in Mole Voles

Abstract

Nuclear mitochondrial DNA segments (NUMTs) are pervasive elements of eukaryotic genomes. This study focuses on Ellobius talpinus and Ellobius lutescens, for which we assembled full mitochondrial DNA sequences. Our study identified NUMTs encompassing approximately 0.0052% and 0.0086% of genome assembly length in E. talpinus and E. lutescens, respectively. These NUMTs collectively spanned a total length of 122,294 bp in E. talpinus and 194,875 bp in E. lutescens. Notably, the majority of NUMTs in both species were short, with lengths of less than 500 bp. In E. talpinus, the data indicated the presence of comparatively recent NUMT insertions. More than half of the NUMTs in each species are organized into clusters, primarily situated in intergenic regions or within introns. RNA genes are the most frequently occurring fragments within these NUMTs. Furthermore, our analysis identified LINE, SINE, and LTR retrotransposons within and flanking NUMT clusters. Our results demonstrate the intricate dynamics of NUMT integration and distribution in Ellobius species and provide insights into their genomic architecture and evolutionary history. This study contributes to the broader understanding of mitochondrial DNA contributions to nuclear genomes and underscores the complexity of distinguishing between mtDNA and nuclear DNA in genomic studies.