Divergent NUMT mimicking functional coding region of the mitochondrial genome

Using long read sequencing, we report here a NUMT (nuclear fragment of mitochondrial origin) in a sawfly species Euura vittata (Hymenoptera, Tenthredinidae) that contains the entire coding region with all the genes in the same order as in the mitochondrion. The NUMT is 3.2% different from the mitochondrial sequence (4.1% divergence for COI barcode region), yet appears entirely functional when assuming mitochondrial genetic code. The NUMT is unlikely to be functional because of the usage of standard genetic code in the nuclear genome. Examination of the NUMT containing contig of the whole genome assembly revealed no assembly issues and showed depth of coverage as expected for single copy nuclear genes, strongly suggesting nuclear integration rather than heteroplasmy. Based on mitochondrial COI data, the NUMT is most similar to a cluster of sequences containing mostly Euura tillbergi and related species (but also a few E. vittata specimens). The NUMT, therefore, may result from recent mitochondrial introgression explaining its divergence and misleading functional appearance. The implications are that reports of divergent heteroplasmy need to be validated with long read or RNA sequencing, or by other appropriate experiments.