• YUSUKE YAMANOUE

      Articles written in Journal of Genetics

    • Mitogenome analysis of dwarf pufferfish (Carinotetraodon travancoricus) endemic to southwest India and its implications in the phylogeny of Tetraodontidae

      CHANDHINI SATHYAJITH YUSUKE YAMANOUE SHIN-ICHI YOKOBORI SUNESH THAMPY REJISH KUMAR VATTIRINGAL JAYADRADHAN

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      The Tetraodontidae (pufferfishes), is primarily a family of marine and estuarine fishes with a limited number of freshwater species. Freshwater invasions can be observed in South America, Southeast Asia and central Africa. In the present study, we have analysed the complete mitogenome of freshwater pufferfish, Carinotetraodon travancoricus (dwarf pufferfish or Malabar pufferfish) endemic to southwest India. The genome is 16487 bp in length and consist of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region like all the other vertebrate mitogenomes. The protein-coding genes ranged from 165 bp (ATP synthase subunit 8) to 1812 bp (NADH dehydrogenase subunit 5) and comprised of 11310 bp in total, constituting 68.5% of the complete mitogenome. Some overlaps have been observed in protein-coding genes by a total of 7 bp. The AT skew (0.032166) and GC skew (-0.29746) of the mitogenome indicated that heavy strand consists equal amount of A and T, but the overall base composition was mainly C skewed. The noncoding D-loop region comprised 869 bp. The conserved motifs ATGTA and its complement TACAT associated with thermostable hairpin structure formation were identified in the control region. The phylogenetic analysis depicted a sister group relationship of C. travancoricus with euryhaline species Dichotomyctere nigroviridis and D. ocellatus with 100% bootstrap value rather than with the other freshwater members of Carinotetraodon species from Southeast Asia. The data from this study will be useful for proper identification, genetic differentiation, management and conservation of the dwarf Indian pufferfish.

    • Whole mitogenome analysis and phylogeny of freshwater fish red-finned catopra (Pristolepis rubripinnis) endemic to Kerala, India

      S. CHANDHINI YUSUKE YAMANOUE SNEHA VARGHESE P. H. ANVAR ALI V. M. ARJUNAN V. J. REJISH KUMAR

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      The freshwater leaf fish Pristolepis rubripinnis belongs to the family Pristolepididae, restricted to Pamba and Chalakudy rivers of Kerala, India. In the present study, we sequenced the complete mitogenome of P. rubripinnis and analysed its phylogeny in the order Anabantiformes. The 16622-bp long genome comprised of 13 protein-coding genes, two rRNA genes, 22 transfer RNAs (tRNAs) genes and had a noncoding control region. All the protein-coding genes, tRNA and rRNA were located on the heavy strand, except nad6 and eighttRNAs (glutamine, alanine, asparagine, cysteine, tyrosine, serine, glutamic acid and proline) transcribed from L strand. The genome exhibited an overlapping between atp8 and atp6 (2 bp), nad4 and nad4l (2 bp), tRNAIle and tRNAGln (1 bp), tRNAThr and tRNAPro (1 bp).Around 157 bp, an intergenic spacer was identified. The overall GC-skews and AT-skews of the H-strand mitogenome were –0.35 and 0.079, respectively, revealing that the H-strand consisted of equal amounts of A and T and that the overall nucleotide composition was Cskewed. All tRNA genes exhibited cloverleaf secondary structures, while the secondary structure of tRNASer lacked a discernible dihydrouridine stem. The phylogenetic analysis of available mitogenomes of Anabantiformes revealed a sister group relationship between Pristolepididae and Channidae. The whole mitogenome of Pristolepis rubripinnis will form a molecular resource for further taxonomic and conservation studies on this endemic freshwater fish.

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