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Inheritance and phylogenetic analysis of Tylosurus acus melanotus based on the complete mitochondrial genomes.

ABSTRACT: In our research, 17 sets of primers were used to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) of the Tylosurus acus melanotus in order to analyse the inheritance and evolutionary relationship of this species. The total length of the mitochondrial genome is 16,723?bp and deposited in the GenBank with accession numbers KU605633. The gene arrangement was similar to other bony fishes which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region. Most genes were encoded on the H-strand, except for the ND6 and 8 tRNA genes, encoding on the L-strand. The mtDNA may provide some important genetic background information for this valuable fish. The nucleotide skewness for the coding strands of T. acus melanotus (GC-skew?=?-0.21) is biased towards G and the negative GC-skew ranges from -0.53(ATP8) to -0.12(CO2) and the AT-Skew showed more positive varying from?-0.17(ND3) to 0.26(ATP6). The phylogenetic analysis demonstrated that T. acus melanotus was clustered together with Ablennes hians, but far away from Cololabis saira which belongs to Beloniformes, Belonidae.

SUBMITTER: Zhang H

PROVIDER: S-EPMC7799640 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Inheritance and phylogenetic analysis of <i>Tylosurus acus melanotus</i> based on the complete mitochondrial genomes.

Zhang Hong H Zeng Da D Xu Youhou Y Zhang Yanqiu Y Fang Huaiyi H Xu Lili L Gong Bin B

Mitochondrial DNA. Part B, Resources 20160710 1

In our research, 17 sets of primers were used to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) of the <i>Tylosurus acus melanotus</i> in order to analyse the inheritance and evolutionary relationship of this species. The total length of the mitochondrial genome is 16,723 bp and deposited in the GenBank with accession numbers KU605633. The gene arrangement was similar to other bony fishes which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 2 ...[more]

PMID: 33473526

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Project description:The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments.In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths.Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial genomes becomes commonplace in evolutionary studies. "The human factor in classification is nowhere more evident than in dealing with this superfamily (Rhinocerotoidea)." G. G. Simpson (1945).

Project description:BackgroundThe Neogastropoda is a highly diversified group of predatory marine snails (Gastropoda: Caenogastropoda). Traditionally, its monophyly has been widely accepted based on several morphological synapomorphies mostly related with the digestive system. However, recent molecular phylogenetic studies challenged the monophyly of Neogastropoda due to the inclusion of representatives of other caenogastropod lineages (e.g. Littorinimorpha) within the group. Neogastropoda has been classified into up to six superfamilies including Buccinoidea, Muricoidea, Olivoidea, Pseudolivoidea, Conoidea, and Cancellarioidea. Phylogenetic relationships among neogastropod superfamilies remain unresolved.ResultsThe complete mitochondrial (mt) genomes of seven Neogastropoda (Bolinus brandaris, Cancellaria cancellata, Conus borgesi, Cymbium olla, Fusiturris similis, Nassarius reticulatus, and Terebra dimidiata) and of the tonnoidean Cymatium parthenopeum (Littorinimorpha), a putative sister group to Neogastropoda, were sequenced. In addition, the partial sequence of the mitochondrial genome of the calyptraeoidean Calyptraea chinensis (Littorinimorpha) was also determined. All sequenced neogastropod mt genomes shared a highly conserved gene order with only two instances of tRNA gene translocation. Phylogenetic relationships of Neogastropoda were inferred based on the 13 mt protein coding genes (both at the amino acid and nucleotide level) of all available caenogastropod mitochondrial genomes. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses failed to recover the monophyly of Neogastropoda due to the inclusion of the tonnoidean Cymatium parthenopeum within the group. At the superfamily level, all phylogenetic analyses questioned the taxonomic validity of Muricoidea, whereas the monophyly of Conoidea was supported by most phylogenetic analyses, albeit weakly. All analyzed families were recovered as monophyletic except Turridae due to the inclusion of Terebridae. Further phylogenetic analyses based on either a four mt gene data set including two additional Littorinimorpha or combining mt and nuclear sequence data also rejected the monophyly of Neogastropoda but rendered rather unresolved topologies. The phylogenetic performance of each mt gene was evaluated under ML. The total number of resolved internal branches of the reference (whole-mt genome) topology was not recovered in any of the individual gene phylogenetic analysis. The cox2 gene recovered the highest number of congruent internal branches with the reference topology, whereas the combined tRNA genes, cox1, and atp8 showed the lowest phylogenetic performance.ConclusionPhylogenetic analyses based on complete mt genome data resolved a higher number of internal branches of the caenogastropod tree than individual mt genes. All performed phylogenetic analyses agreed in rejecting the monophyly of the Neogastropoda due to the inclusion of Littorinimorpha lineages within the group. This result challenges morphological evidence, and prompts for further re-evaluation of neogastropod morphological synapomorphies. The important increase in number of analyzed positions with respect to previous studies was not enough to achieve conclusive results regarding phylogenetic relationships within Neogastropoda. In this regard, sequencing of complete mtDNAs from all closely related caenogastropod lineages is needed. Nevertheless, the rapid radiation at the origin of Neogastropoda may not allow full resolution of this phylogeny based only on mt data, and in parallel more nuclear sequence data will also need to be incorporated into the phylogenetic analyses.

Dataset Information

Inheritance and phylogenetic analysis of Tylosurus acus melanotus based on the complete mitochondrial genomes.

Publications

Inheritance and phylogenetic analysis of <i>Tylosurus acus melanotus</i> based on the complete mitochondrial genomes.

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