Fragmented and on the move - the enigmatic mitochondrial genome sequences of Toxoplasma and Sarcocystis

Recently we have reported on two remarkable aspects of the Toxoplasma gondii mitochondrial genome. First it exists as a redundant and highly fragmented sequence of unknown topology¹. Second, ~10,000 relatively small pieces of the mitochondrial genome (NUMTs) have been transferred to the nuclear genome². These transferred fragments account for an astonishing 1.4% of the nuclear genome sequence and appear to have contributed to evolutionary innovation. We find very similar mtDNA genome sequence novelties in Hammondia and Neospora, including very large numbers of NUMTs¹. Thus, we decided to examine the more distantly related Sarcocystis neurona SN3. We assembled a new S. neurona SN3 genome sequence using ONT, Illumina and Hi-C. It is 127 Mb and we were able to observe at least 10 putative chromosomes, the largest of which is 24 Mb. The assembly has been annotated using orthology, as well as RNA-seq and ISO-seq from different lifecycle stages. We used this new assembly to study the distribution of NUMTs and characterize the mtDNA. We find a markedly reduced number of mtDNA insertions, 1077 or about 0.06% of the nuclear genome content. Interestingly, we find a redundant, fragmented mtDNA that cannot be assembled, as was the case in T. gondii. However, the fragments in S. neurona are quite different from those observed in other related tissue coccidians. This is significant, because as reported by Tetzlaff et al.,³ the T. gondii mtDNA breakpoints are associated with transcription initiation for the generation of small ribosomal RNAs in Toxoplasma.

¹Namasivayam et al., doi: 10.1101/gr.266403.120

²Namasivayam et al., doi: 10.1101/2023.05.22.539837

³Tetzlaff et al., doi: 10.1101/2023.09.02.556019