The Complete Mitochondrial Genome of Eurasian Minnow (Phoxinus cf. Phoxinus) from the Heilongjiang River, and Its Phylogenetic Implications

SIMPLE SUMMARY: Fishes of genus Phoxinus belong to the family Leusciscidae and are widely distributed in Eurasia. Since the early 20th century, it has generally been accepted that the European minnow (P. phoxinus) was the only valid species of Phoxinus in Europe. After the loss of most species from North America and Asia, only those taxa in Euasia originally placed under the name P. phoxinus remain in the genus. In recent years, more than 20 lineages of genus Phoxinus have been identified in Europe, more than 10 of which have been considered as valid species in taxonomy. Existing morphological and genetic cues suggest distinct differences between Asian and European members of Phoxinus. Mitochondrial DNA from European Phoxinus spp. and their Asian relatives provide evidence that Far Eastern phoxinins should be divided into two genera: Phoxinus and Rhynchocypris. The updated phylogeny of Phoxinus indicates five mtDNA lineages in Asia. The validity of some of these lineages have been supported previously by morphological evidence. ABSTRACT: Over the past two decades, the genus Phoxinus has undergone extensive taxonomic revision and many new species or mitochondrial lineages have been found in Europe. However, Asian populations of Phoxinus spp. have received less attention and have rarely been compared with their European relatives. In this study, we deciphered the 16,789-nucleotide mitochondrial genome of Phoxinus cf. phoxinus from the Heilongjiang River (HLJ) and compared it with other known mitogenomes or partial mitochondrial DNA (mtDNA) sequences of Phoxinus spp. We discovered that all known mitochondrial genomes of Phoxinus had a typical mtDNA architecture across vertebrates, but their D-loop regions varied greatly in length. A repetitive motif of ~130 bp was identified in the D-loop regions of Phoxinus spp. The unusual repetitive structure was revealed at the beginning of D-loop regions of all known mitogenomes of Phoxinus spp. The length differences of the D-loop region were attributed mainly to the number of repetitive motifs and the inserted sequences among them. However, this repetitive structure was absent in the other Far East phoxinins. This is further evidence for the notion that Far Eastern phoxinins should be divided into two genera: Phoxinus and Rhynchocypris. All mtDNA sequences (including three mitogenomes) from South Korea represent the same genetic lineage, as there were only slight differences among them. The remaining six mtDNA sequences are highly divergent and represent different lineages of the genus, as supported by partial mtDNA sequences. The updated phylogeny of genus Phoxinus suggests that there are five distinct mtDNA lineages in Asia. The Asian lineages have diverged markedly from their European relatives and should not be included with the European minnow (P. phoxinus).