Genomic landscape of mitochondrial DNA insertions in 23 bat genomes: characteristics, loci, phylogeny, and polymorphism

The transfer of mitochondrial DNA to the nuclear genome gives rise to the nuclear DNA sequences of mitochondrial origin (NUMTs), considered as a driving force in genome evolution. In this study, NUMTs in 23 bat genomes were investigated and compared systematically. The results showed that NUMTs existed in 22 genomes except for Noctilio leporinus, suggesting that mitochondrial fragment insertion in the nuclear genome was a common event in bat genomes. However, remarkable variations in NUMTs number, cumulative length, and proportion in the nuclear genome were discovered across bat species. Further orthologous NUMT loci analysis of the Phyllostomidae family indicated that the NUMTs insertion events in bat genomes were homoplasy-free. The NUMTs were mainly inserted into the intergenic regions, particularly, co-localized with repetitive sequences (especially transposable elements). However, several NUMTs were inserted into genes, some of which were in the exon region of functional genes. One NUMT in the genome of Pteropus alecto surprisingly matched with cDNA of ATP8B3 that provided evidence of NUMTs with coding function. Phylogenic analysis on NUMTs originating from COXI and COXII loci highlighted 2 clusters of Yinpterochiroptera and Yangochiroptera for Chiroptera. Seven NUMTs from Rhinolophus ferrumequinum were amplified, and the sequencing results confirmed the reliability of the NUMT analysis. One of them was polymorphic for the presence or absence of the NUMT insertion, and each genotype of NUMT loci showed a distinct regional distribution pattern. The information obtained in this study provides novel insights into the NUMT organization and features in bat genomes and establishes a basis for further studying of the evolution of bat species.