Detection and characterization of nuclear mitochondrial DNA (NUMTs) in the alpaca genome

NUMTs are mitochondrial DNA sequences that are inserted into the nuclear genome of almost all eukaryotic organisms, although high interspecific variability regarding abundance, size, and location is observed. In particular, the NUMT amount is highly dependent on the detection method utilized. The aim of this study was to provide the first comprehensive description and annotated collection of NUMTs for the alpaca. We have examined different detection strategies and obtained 267 hits, representing 0.011% of the genome (233,411 bp aligned). By merging these hits, we have identified and characterized 158 NUMTs across the alpaca genome. We found copies from all the mtDNA with variable identity values and two particularly large NUMTs that covered 72-83% of the mitogenome with a mean identity of 80%. Results showed that NUMTs were preferentially inserted in the non-coding region of the nuclear genome and were flanked by repetitive elements. Besides, the main mechanism for NUMT generation in this species seems to be independent insertion events, rather than duplication. Furthermore, we have selected and validated by PCR the presence of four NUMTs in the alpaca genome and proved their presence in the other three South American Camelid species. The results generated by this work represent a useful resource for curating databases and can be used to avoid co-amplification of NUMTs in studies involving mtDNA, like phylogenetics, populations or evolution studies.

Automated summary

This study aimed to provide a comprehensive description and annotation of NUMTs in alpacas. By utilizing different detection strategies, 267 NUMTs were identified, with 158 of them being characterized across the alpaca genome. Results showed that NUMTs preferentially insert in the non-coding region of the nuclear genome and are flanked by repetitive elements. The main mechanism for NUMT generation in this species seems to be independent insertion events rather than duplication. Furthermore, the presence of four NUMTs in the alpaca genome was validated and confirmed in three other South American Camelid species.