Research paper
Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group
Graphical abstract
Introduction
The phylogeny based on molecular data are being used extensively for understanding and placing more accurately the evolution of gene and genome in conjunction with origin and divergence of species (Brown, 2002). But not limited to this scope, phylogenetics is also being used in the field of understanding molecular mechanism of disease (Harris et al., 2010), development of medicine (Espiritu et al., 2001; Fenical et al., 2009), Bioprospecting (Smith and Wheeler, 2006), organisms' metabolic networks (Forst and Schulten, 2001), etc. However, different genes such as mitochondrial (e.g. COI, Cyt-b, 16S rRNA) and nuclear (e.g.RAG, ATPS-α) are used for studying evolutionary history, produces different kind of topology or clade in phylogenetic tree for different group of life and further inference (Castresana, 2007; Powell et al., 2013; Farias et al., 2001). Since the process or technique of drawing phylogenetic relationship among the species is still establishing, hunt for a better gene continues. However, this is not so straightforward, as we analyses the final established sequence for different regions (genes) which has already gone through some convergent, divergent and independent evolution in different branches of life for better adaptation, selection and speciation (Zuckerkandl and Pauling, 1965; Zakon, 2002; Hasselmann et al., 2008; Castoe et al., 2009; Arbuckle and Speed, 2016) resulting in contrasting phylogenetic tree. Hence, in the present study, we compared and evaluated different mitochondrial regions along with complete mitogenome for making the phylogenetic tree in some selected group of fishes with concurrence note with the classical taxonomic position. For this purpose, we also sequenced complete mitochondrial DNA of the queen loach, Botia dario.
B. dario belongs to the family Botiidae of order Cypriniformes and found in Brahmaputra and Ganges basins of Bangladesh, Bhutan and Northeast India (Talwar and Jhingran, 1991). The species has a great demand for the aquarium trade in many countries due to its unique band pattern and bright color (Froese and Pauly, 2015). This species is considered to be endangered in Bangladesh (IUCN Bangladesh, 2000) and near endangered in lower Brahmaputra basin of Assam, India due to habitat destruction and overexploitation for ornamental trade (CAMP, 1998). So its conservation measures are of a great concern now.
Section snippets
Ethical statement
All the fish specimens of B. dario used in this study were collected from the College of Fisheries, CAU (I) tank. Ethical approval, specimen collection, and maintenance were performed in strict accordance with the recommendations of the ethical standards of the Institute of Animal Ethics Committee, College of Fisheries, Central Agricultural University, Imphal.
Tissue collection and DNA isolation
The mitochondrial DNA, used in this study, was isolated from muscle tissue of B. dario fish species, after following the method of
Characteristics of the B. dario mitogenome
We determined the first complete mitochondrial genome sequence of B. dario by next-generation sequencing method. A uniform coverage of ~1500× was obtained for most of the mitogenome segments, except a few places in the control region where the presence of the repeat sequences resulted in slightly low coverage. A total of 31,52,420 reads were found from the mitochondrial DNA sample, used with a total data size of approximately 939 Mb. Size of the assembled mitogenome, as generated from CLC
Discussion
The fishes of Cobitidae, Nemacheilidae and Balitoridae family clearly formed a separate clade in the phylogenetic tree based on complete mitogenome (Fig. 3). All the three families have very similar morphometric characters and commonly known as loach. The other species of Cyprinidae family formed a paraphyletic clade with loach group which exhibits the evolutionary relatedness and sharing of a common ancestor between Cyprinidae and loach group. This finding is in agreement with a previous
Conclusion
In the present study, the complete mitochondrial DNA sequence of B. dario found will help in studying its biology, molecular studies, evolutionary studies, species confirmation and will be useful in conservation management. The whole mitogenome will also help in population studies of this fish species. The complete mitogenome of B. dario found in this study has been submitted to NCBI GenBank with accession number MG751071.The phylogenetic analysis of individual mitochondrial genes along with
Declaration of Competing Interest
The authors declare no conflict of interest.
Acknowledgments
The authors thank the Centre of Excellence (COE) (Grant number- DBT-NER/LIVE/05/2011) and Department of Biotechnology, Government of India (Grant number- BT/22/NE/2011) for providing instruments for the experiment.
References (67)
- et al.
Genetic cryptic species as biological invaders: the case of a Lessepsian fish migrant, the hardyhead silverside Atherinomorus lacunosus
J. Exp. Mar. Biol. Ecol.
(2002) - et al.
Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny
Mol. Phylogenet. Evol.
(2004) - et al.
Venomous cone snails: molecular phylogeny and the generation of toxin diversity
Toxicon
(2001) - et al.
Discovery and development of the anticancer agent salinosporamide A (NPI-0052)
Bioorg. Med. Chem.
(2009) - et al.
A phylogenetic and biogeographic perspective on the evolution of poeciliid fishes
Mol. Phylogenet. Evol.
(2007) - et al.
Similar morphologies of cichlid fish in Lakes Tanganyika and Malawi are due to convergence
Mol. Phylogenet. Evol.
(1993) - et al.
Phylogenetic signal in the COI, 16S, and 28S genes for inferring relationships among genera of Microgastrinae (Hymenoptera; Braconidae): evidence of a high diversification rate in this group of parasitoids
Mol. Phylogenet. Evol.
(1999) - et al.
Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion
Mol. Phylogenet. Evol.
(2000) - et al.
Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study
Mol. Phylogenet. Evol.
(2013) - et al.
Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes)
Mol. Phylogenet. Evol.
(2006)
Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae)
Mol. Phylogenet. Evol.
Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae
Gene
Evolutionary divergence and convergence in proteins
Genetic structure and history of populations of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence analysis
Mol. Ecol.
Analysing convergent evolution: a practical guide to methods
Trimmomatic: a flexible trimmer for Illumina sequence data
Bioinformatics
The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA
Genome Res.
Genomes
Evidence for an ancient adaptive episode of convergent molecular evolution
Proc. Natl. Acad. Sci.
Topological variation in single-gene phylogenetic trees
Genome Biol.
A method for the rapid isolation of mitochondrial DNA from fishes
Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes
J. Fish Biol.
Standard percent DNA sequence difference for insects does not predict species boundaries
J. Econ. Entomol.
Species identification by means of mitochondrial cytochrome b DNA sequencing in processed anchovy, sardine and tuna products
Food Nutr. Sci.
Evidence for AT-transversion bias in wasp (Hymenoptera: Symphyta) mitochondrial genes and its implications for the origin of parasitism
J. Mol. Evol.
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Nucleic Acids Res.
The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes
J. Mol. Evol.
Evolutionary trees from DNA sequences: a maximum likelihood approach
J. Mol. Evol.
Phylogenetic analysis of metabolic pathways
J. Mol. Evol.
FishBase 2015: World Wide Web electronic publication
The correlation between saprobity and mitochondrial genes of indicator fish species based on molecular phylogeny
Int. J. Green Pharm
Comparing thousands of circular genomes using the CGView Comparison Tool
BMC Genomics
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