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Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes' sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.

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Abramites hypselonotus, commonly known as marbled headstander, is an important freshwater aquarium fish from Brazil, found in the Orinoco, Amazon, Paraguay and lower Parana River basins. This genus has only two species and only this species occurs in Brazil. The complete mitochondrial genome of Abramites hypselonotus is 16,685 bp in length and it includes 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs genes and a control region with 1,028 bp. It has two PCGs with GTG start codon and the others with ATG start codon. Four of the 13 PCGs appear TAA stop codon, three incomplete TA_ stop codon, four incomplete T_ _ stop codon, one contain AGG stop codon and one TAG stop codon. Phylogenetic analysis showed that Abramites hypselonotus formed a sister group of Leporinus affinis (AP011994.1), thus maintaining the Family Anostomidae as a clade.

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Perciformes is the largest order of fishes and vertebrates. Sooty grunter (Hephaestus fuliginosus) is an economic fish species in the Terapontidae family of Percoidei, a suborder within Perciformes. To conduct molecular-level analysis of the phylogenetic relationships between sooty grunter and major freshwater fishes in Percoidei, we analysed the entire sooty grunter mitochondrial genome sequence and obtained the mitochondrial genome information of 19 fishes from Terapontidae, Serranidae, and Centrarchidae families in Percoidei from GenBank. The complete length of the sooty grunter mitochondrial genome was 16,770 bp; it encoded 13 proteins, 2 rRNAs, 22 tRNAs, and a displacement loop (D-loop). Other than ND6 and eight tRNA genes that are encoded by the light strand, the majority of genes are encoded by the heavy strand. The sequence and distribution of sooty grunter mitochondrial-encoded genes and non-coding segment were similar to those of most vertebrates. The results of neighbour joining, maximum parsimony, and Bayesian inference analyses of the complete mitochondrial genome and six genes, including cytochrome oxidase I, cytochrome B, 12S rRNA, ND2, ND4, and ND5, were consistent. In the phylogenetic trees, fishes in Terapontidae and Centrarchidae formed monophyletic clades, whereas those in Serranidae were divided into two clades, each containing Lateolabrax and Siniperca species. Among the three freshwater fish species in Terapontidae, the freshwater Terapontidae were more closely related to jade perch than with silver perch, suggesting that freshwater Terapontidae fishes originate from marine fishes. In addition, the phylogenetic results indicated that Micropterus salmoides salmoides and Micropterus salmoides floridanus in Centrarchidae should be designated as two independent species, and Siniperca in Serranidae should be considered an independent family. The sooty grunter mitochondrial genome sequence obtained in this study could be used to conduct population genetic diversity and germplasm resource studies. Furthermore, the phylogenetic analysis results of freshwater fishes in Percoidei could provide a molecular basis for cross-breeding.

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Myrmecophaga tridactyla, popularly known as giant anteater, is a member of Xenarthra magnorder which is under the threat of extinction. Herein, we describe the complete mitochondrial genome of M. tridactyla. The circular DNA molecule is 16,546 bp long, contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a non-coding Control Region of 1110 bp. All protein-coding genes are on the heavy strand, except for Nd6. Ten of the 13 PCGs contained an ATG start codon.

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Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European part of Russia and 100 Polish individuals from northern Poland. Nearly complete resolution of mtDNA haplotypes was achieved - about 97% of haplotypes were unique both in Russians and Poles, and no haplotypes overlapped between them when indels were considered. While European populations showed a low, but statistically significant level of between-population differentiation (Fst=0.66%, p=0), Russians demonstrate lack of between-population differences (Fst=0.22%, p=0.15). Results of the Bayesian skyline analysis of Russian mitogenomes demonstrate not only post-Last Glacial Maximum expansion, but also rapid population growth starting from about 4.3kya (95% CI: 2.9-5.8kya), i.e. in the Bronze Age. This expansion strongly correlates with the Kurgan model established by archaeologists and confirmed by paleogeneticists.

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Pimelodus maculatus is an important commercial fish found in the São Francisco and Paraná river basins. NGS was used to sequence the mtDNA of P. maculatus. The mtDNA was annotated and aligned with that of 25 other fish species to enable phylogenetic analysis. The complete mtDNA molecule had 16,561 bp and its GC content was 43.7%; the structure was similar to that of other vertebrates: 2 rRNA, 22 tRNA, 13 protein-coding genes, and a D-loop region containing 914 bp. Phylogenetic analysis yielded a tree with a high bootstrap coefficient that was coherent with the actual phylogeny of the species.

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Prochilodus spp. are important Brazilian freshwater migratory fishes with substantial economic and ecological importance. Prochilodus argenteus and Prochilodus costatus are morphologically similar and a molecular species delimitation is impaired due to high degree of sequence identity among the available genetic markers. Here, the complete mitochondrial genome of P. argenteus and P. costatus and their comparison to the mitogenome of P. lineatus are described. The three species displayed a similar mtDNA annotation. A phylogenetic analysis was performed with other Characiformes species. The genus Prochilodus was recovered as a monophyletic group, as well as the family Prochilodontidae, both with high bootstrap probability.

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Prochilodus lineatus (curimba) is an important Brazilian freshwater migratory fish with substantial economic importance in fishing. The complete mitochondrial genome of P. lineatus is 16,699 bp and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and one control region (D-loop). The mtDNA of P. lineatus is the first mitogenome of the Prochilodontidae family to be fully characterized. All of the PCGs in the mtDNA use the standard ATG start codon, with the exception of Cox1 that utilizes the GTG start codon. Six of the 13 PCGs contain TAA stop codons, two contain the incomplete stop codon TA- (Atp6 and Nd6), and five contain the incomplete stop codon T- - (Nd2, Cox2, Nd3, Nd4 and Cytb).

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