Complete mitochondrial genome of the natural triploid loach, Misgurnus anguillicaudatus (Teleostei: Cypriniformes: Cobitididae)

Comparative analysis of mitochondrial genomes in genetically distinct groups of the dojo loach Misgurnus anguillicaudatus

Dojo loach (Misgurnus anguillicaudatus) that inhabit Japan are composed of two genetically divergent groups (A and B). Although most individual loach reproduce bisexually, clone lineages exist in certain populations that reproduce gynogenetically. To investigate the molecular phylogenetic relationships among the M. anguillicaudatus groups and clone lineages, complete mitogenomes of members from groups A and B and a clone lineage were sequenced using long range PCR and primer walking methods. The three groups of mitogenomes shared the same gene order and had similar base compositions and codon usage patterns. Phylogenetic analysis indicated group A and the clone lineage were genetically close with group B being genetically divergent.

Complete mitochondrial genomes of five subspecies of the Eurasian magpie Pica pica, obtained with Oxford Nanopore MinION, and their interpretation regarding intraspecific taxonomy

The complete mitochondrial (mt) genomes of five subspecies of the Eurasian (Common) magpie Pica pica were determined for the first time. Lengths of the circular genomes comprise 13 protein-coding genes, two rRNA genes (for 12S rRNA and 16S rRNA), 22 tRNA genes, and the non-coding control region (CR). Gene content and lengths of the genomes (16,936-16,945 bp) are similar to typical vertebrate mt genomes. The subspecies studied differs by several single substitutions and indels, especially in the CR. The phylogenetic tree based on complete mt genomes shows a deep divergence of the two groups of subspecies which supports the proposed division into two distinct species: P. pica and P. serica.

The complete mitochondrial genome sequence of Kichulchoia multifasciata (Teleostei, Cypriniformes, Cobitidae)

The Kichulchoia multifasciata (Teleostei, Cypriniformes, Cobitidae) is one of the loaches and is endemic to Korea. The complete mitochondrial genome sequence consisted of 16 569 base pairs (bp) encoding 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding region. The overall base composition of K. multifasciata was G + C: 42.5% and A + T: 57.5%, apparently with a slight AT bias. Phylogenetic analysis showed that K. multifasciata was closely related to Koreocobitis rotundicaudata.

Sequencing and analysis of the complete mitochondrial genome of Amur minnow from China

The complete mitogenome sequence of Amur minnow (Rhynchocypris lagowskii) was determined using long PCR. The genome was 16,594 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The overall base composition of the heavy strand is A (28.60%), C (26.32%), T (27.40%), and G (17.68%). The control region was 927 bp in length and the A + T content of the region was 63.32%. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur minnow. Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.

The complete mitochondrial genome of Amur bitterling (Rhodeus sericeus) from China

The complete mitogenome sequence of Amur bitterling (Rhodeus sericeus) was determined using long PCR. The genome was 16,581 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand was A (28.9%), C (27.2%), T (26.6%), and G (17.3%). The control region was 925 bp in length and the A + T content of the region was 63.5%. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur bitterling. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity to the 13 Cyprinidae species. It appeared that no less than three major phyletic lineages were present in Cyprinidae. A clade (Rhodeus and Tanakia) with the R. lighti and R. Sinensis as the sister taxon to Acheilognathus was supported by bootstrap values of 100%. The close relationship of Amur bitterling to other Rhodeus species, especially R. pseudosericeus, is consistent with the results confirmed using morphology analysis.