Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels

Recent studies have demonstrated that deviations from the typical vertebrate mitochondrial gene order are more frequent than initially thought. Such deviations, however, are minor, with inversions and/or translocations of a few genes being involved and tandem duplication of the gene regions followed by deletions of genes having been invoked as mechanisms originating in such novel gene order. During the course of molecular phylogenetic studies on the Elopomorpha (eels and their allies), we found that mitochondrial genomes (mitogenomes) from the two deep-sea gulper eels, Eurypharynx pelecanoides (Eurypharyngidae) and Saccopharynx lavenbergi (Saccopharyngidae), exhibit an identical gene order which greatly differs from that of any other vertebrates. Phylogenetic analysis using the mitogenomic data from 59 species of fish not only confirmed a single origin of such a gene order with confidence but also indicated that it had been derived from the typical vertebrate gene order. Detailed comparisons of the gulper eel gene order with that of typical vertebrates suggested that occurrence of a single step, large-scale duplication of gene region extending >12 kb, followed by deletions of genes in a common ancestor of the two species, most parsimoniously accounts for this unusual gene arrangement.     

Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii"

Higher-level relationships of the basal Euteleostei (=Protacanthopterygii) are so complex and controversial that at least nine different morphology-based phylogenetic hypotheses have been proposed during the last 30 years. Relationships of the Protacanthopterygii were investigated using mitochondrial genomic (mitogenomic) data from 34 purposefully chosen species (data for 12 species being newly determined during the study) that fully represented major basal euteleostean lineages and some basal teleosts plus neoteleosts as outgroups. Unweighted and weighted maximum parsimony (MP) and maximum likelihood (ML) analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and 3rd codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) from the 34 species. The resultant trees were well resolved and largely congruent, with most internal branches being supported by high statistical values. Monophyly of the protacanthopterygians was confidently rejected by the mitogenomic data. Of the five major monophyletic groups that received high statistical support within the protacanthopterygians, a clade comprising members of the alepocephaloids was unexpectedly nested within the Otocephala, sister-group of the euteleosts. The remaining four major monophyletic groups, on the other hand, occupied phylogenetic positions intermediate between the otocephalans and neoteleosts, with a clade comprising esociforms + salmoniforms being more basal to the argentinoids and osmeroids. Although interrelationships of the latter two clades (argentinoids and osmeroids) with the neoteleosts remained ambiguous, the present results indicated explicitly that the protacanthopterygians as currently defined merely represent a collective, polyphyletic group of the basal euteleosts, located between the basal teleosts (elopomorphs and below) and neoteleosts (stomiiforms and above).     

The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S), 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny.