Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae

Background: Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and
scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and
controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated
characteristics were not elaborated.
Results: In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma.
Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of
58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA
secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were
observed among different genus and significantly negative linear correlation between AT% and AT-skew were
found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the
atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally,
all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the
paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split
into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur
(14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus.
Conclusions: The current study represents the first comparative mitogenomic and phylogenetic analyses within
Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the
cobitinae family.