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Background  Babesiosis, a tick-borne disease caused by protozoans of the genus  Babesia , is widespread in subtropical and tropical countries. Mitochondria are essential organelles that are responsible for energy transduction and metabolism, calcium homeostasis and cell signaling. Mitochondrial genomes could provide new insights to help elucidate and investigate the biological features, genetic evolution and classification of the protozoans. Nevertheless, there are limited data on the mitochondrial genomes of ovine  Babesia  spp. in China.    Methods  Herein, we sequenced, assembled and annotated the mitochondrial genomes of six ovine  Babesia  isolates; analyzed the genome size, gene content, genome structure and cytochrome  b  ( cytb ) amino acid sequences and performed comparative mitochondrial genomics and phylogenomic analyses among apicomplexan parasites.    Results  The mitochondrial genomes range from 5767 to 5946 bp in length with a linear form and contain three protein-encoding genes, cytochrome  c  oxidase subunit 1 ( cox 1), cytochrome  c  oxidase subunit 3 ( cox 3) and  cytb , six large subunit rRNA genes ( LSU ) and two terminal inverted repeats (TIR) on both ends. The  cytb  gene sequence analysis indicated the binding site of anti- Babesia  drugs that targeted the cytochrome  bc 1 complex.  Babesia microti  and  Babesia rodhaini  have a dual flip-flop inversion of 184–1082 bp, whereas other  Babesia  spp. and  Theileria  spp. have one pair of TIRs, 25–1563 bp. Phylogenetic analysis indicated that the six ovine  Babesia  isolates were divided into two clades,  Babesia  sp. and  Babesia motasi .  Babesia motasi  isolates were further separated into two small clades ( B. motasi  Hebei/Ningxian and  B. motasi  Tianzhu/Lintan).    Conclusions  The data provided new insights into the taxonomic relationships and drug targets of apicomplexan parasites.

Insights into the phylogenetic relationships and drug targets of Babesia isolates infective to small ruminants from the mitochondrial genomes