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Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group

Author:
Parhi, Janmejay, Tripathy, Partha Sarathi, Priyadarshi, Himanshu, Mandal, Sagar Chandra, Pandey, Pramod Kumar
Source:
Gene 2019 v.713 pp. 143967
ISSN:
0378-1119
Subject:
Cyprinidae, adenosinetriphosphatase, circular DNA, fish, high-throughput nucleotide sequencing, mitochondria, mitochondrial genes, mitochondrial genome, monophyly, paraphyly, polyphyly, ribosomal RNA, taxonomy, transfer RNA, trees
Abstract:
Phylogenetic tree using mitochondrial genes and nuclear genes have long been used for augmenting biological classification and understanding evolutionary processes in different lineage of life. But a basic question still exists for finding the most suitable gene for constructing robust phylogenetic tree. Much of the controversy appears due to monophyletic, paraphyletic and polyphyletic clade making deviations from original taxonomy. In the present study we report the first complete mitochondrial genome (mitogenome) of queen loach, generated through next-generation sequencing methods. The assembled mitogenome is a 16,492 bp circular DNA, comprising of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. Further in this study we also investigated the suitability of different mitochondrial region for phylogenetic analysis in Cyprinidae and loach group. For this genetic tree were constructed on COI, COII, COIII, 16S rRNA, 12S rRNA, Cyt b, ATPase 6, D-loop, ND1, ND2, ND3, ND4, ND5, and ND6 along with complete mitogenome. The complete mitogenome based phylogenetic tree got inclusive support from available classical taxonomy for these groups. On individual gene basis Cyt b, 12S rRNA, ND2 and ND3 also produced perfect clade at family and subfamily level. For rest of the genes polyphyly were observed for the fishes belonging to same family or subfamily which makes their use questionable for phylogenetic tree construction.
Agid:
6510276