The complete mitochondrial genome of Oncorhynchus masou formosanus (Salmoniformes: Salmonidae) and phylogenetic studies of Salmoninae

Masu salmon species complex relationships and sex chromosomes revealed from analyses of the masu salmon (Oncorhynchus masou masou) genome assembly

Masu salmon (Oncorhynchus masou) are the only Pacific salmon endemic to Asia. Some researchers prefer to categorize these salmon into 4 subspecies (masu-Oncorhynchus masou masou, amago-Oncorhynchus masou ishikawae, Biwa-Oncorhynchus masou subsp., and Formosan-Oncorhynchus masou formosanus), while others prefer individual species designations. Even though the masu salmon fishery is thousands of years old, classification of the diversity within the masu salmon species complex remains elusive. In this study, a genetic map and reference genome assembly were generated for 1 species/subspecies (masu) to provide resources for understanding the species complex. In O. m. masou, the sex chromosome was determined to be chromosome 7. Resequenced genomes from 2 other putative subspecies (amago and Biwa) provided evidence that they do not share the same sex chromosome. Principal component and admixture analyses clustered the amago and Biwa salmon close together. This supported previous findings of a close relationship between amago and Biwa salmon and a more distant relationship to masu salmon for both. Additional analyses of the masu salmon species complex will benefit from using the new reference genome assembly.

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.

The complete mitochondrial genome of Sardinella lemuru (Clupeinae, Clupeidae, Clupeoidei) and phylogenetic studies of Clupeoidei

The complete mitochondrial genome of Sardinella lemuru was sequenced using PCR amplification and primer walking sequence method. The complete mitochondrial genome of S. lemuru was 16,616 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). The overall base composition was A 25.04%, C 29.36%, G 20.40%, T 25.20%. In this study, the gene arrangement was consistent with other Sardinella mitochondrial genomes. Additionally, the phylogenetic relationships of 23 Clupeoidei species based on the complete genome was analyzed, and the result showed that S. lemuru firstly clustered with other two Sardinella species, S. albella and S. maderensis. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Clupeoidei.

The complete mitochondrial genome of Gymnogobius Petschiliensis (Gobiiformes; Gobiidae; Gobionellinae) and its phylogenetic implications

Of the goby fishes, many Gymnogobius species have been poor recognized mainly because of the absence of enough molecular information and clear phylogenetic framework. In this study, the complete mitochondrial genome of Gymnogobius petschiliensis was determined and described. The mitogenome is 16,422 bp in length and consists of 22 tRNAs, 13 protein-coding genes, two rRNAs, one control region and a light strand replication origin (O_L). The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 27.5%, 29.5%, 26.1%, and 16.9%, for A, T, C, and G, respectively, with a slight bias on A + T content (57.0%). The 13 protein-coding genes use the initiation codon ATG except COI, which uses GTG. Most of them use TAA or TAG as the stop codon, while COII, COIII, and Cyt b use an incomplete T or TA and ND4 uses an unusual AGA. The maximum-likelihood phylogeny tree of 19 Gobionellinae species demonstrated that G. petschiliensis had a very closely relationship with the same genus G. urotaenia. This study is expected to contributing to the phylogenetic evolution of G. petschiliensis and further phylogenetic relationship of Gobionellinae and Gobiiformes.

The complete mitochondrial genome characterization of Tridentiger obscurus (Gobiiformes: Gobiidae) and phylogenetic analyses of Gobionellinae

The dusky tripletooth goby, Tridentiger obscurus, is a good model organism for the small in size and reaching maturity within a single year. Previous studies mainly focused on the annual reproductive cycle, social behavior and life history, but little information is available of the mitochondrial genome and phylogenetic evolution of this gobioid fish. In this article, we described the complete mitogenome of T. obscurus and reconstructed the phylogenetic relationship of the relative species of Gobionellinae. The genome is 16,501 bp in length including 13 protein-coding, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region and an L-strand replication origin. The overall base composition is 28.1%, 27.0%, 28.0% and 16.9% for A, T, C and G, respectively. This result is expected for better understanding the systematic evolution of the genus Tridentiger and further phylogenetic study of Gobiiformes.