Abstract
BackgroundLoaches 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.ResultsIn 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.ConclusionsThe 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.
Highlights
Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value
General features of C. macrostigma mitogenome The mitogenome of C. macrostigma was sequenced, annotated and compared with 57 Cobitinae mitogenomes (Table 1)
Protein coding gene (PCG) range from 168 bp to 1551 bp in size, with a total length of 11,427 bp. Transfer RNA (tRNA) vary from 66 bp (tRNACys(C)) to 76 bp (tRNALys(K)) in size, with a total length of 1557 bp
Summary
Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. Vertebrate mitogenome is a small (16–17 kb) and circular double-stranded molecule [1]. It contains 37 genes including 22 tRNA genes, 13 PCGs and two rRNA genes [1]. Due to its unique features, such as high copy numbers in tissues, simple genomic organization, maternal inheritance, almost unambiguous orthology, haploid inheritance and high nucleotide substitution rate [4,5,6], mitogenome has been widely applied in species identification, i.e., DNA barcoding, as well as population genetics, conservation biology, molecular phylogenetics and evolutionary processes [7,8,9,10,11,12,13]. The genome sequence length, the bias of base composition and start/stop codon, the overlap and IGSs are diverse among different species [14]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
