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The complete mitochondrial genome of an endemic cichlid Etroplus canarensis from Western Ghats, India (Perciformes: Cichlidae) and molecular phylogenetic analysis

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Abstract

Background

The Indian endemic cichlid Etroplus canarensis (Canara pearl spot) is an endangered fish and is one among the three Indian cichlids (Etroplinae) that had a restricted distribution in the South Canara region of Karnataka, India. Despite considerable investigations, the phylogeny of Indian Cichlids and its biogeographical origin is still ambiguous and remains a question under discussion which is scrutinized based on whole mitogenomes in the present study.

Methods and results

We report the 16,339 bp complete mitochondrial genome of E. canarensis for the first time using the next-generation sequencing methods. Comparison of gene arrangement and genome characterization was found to commensurate with the previous reports on two Indian cichlid fishes, E. suratensis and E. maculatus. ND6 has been identified as a gene with the highest evolutionary rate and COI and COII is the most conserved gene based on p-genetic distance calculation. Substitution rate (ka/ks) was found to be very low indicating a reduced rate of evolution among subfamily Etroplinae accounting for its subsided species divergence of Indian cichlids. Phylogenetic analysis of Indian cichlids based on a combined dataset of 12 protein-coding genes representing cichlids generated high posterior probability values pillaring paraphyletic nature of Indian Malagasy lineage and monophyletic Indian genus Etroplus.

Conclusion

The mitogenome sequence of E. canarensis may provide fundamental molecular data useful for further researches on genetic diversity, endemicity and the conservation of this endangered freshwater fish.

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Data availability

The raw sequence data is submitted as SRA (sequence read archives) submission in NCBI (Genbank Accession number SRR10297504) registered under bio project PRJNA575350. Fasta files and annotated sequences submitted through BankIt (Accession number MZ646791). The data information on species selected for phylogenetic analysis is provided in supplementary information.

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Acknowledgements

The authors thank Dr. Beena P.S., OmicsGen Life Sciences Pvt Ltd. and Director, Rajiv Gandhi Centre for Biotechnology for providing the facilities for this work. JJ is also thankful to Director, Trivandrum Natural History Museum for providing facility for depositing specimen.

Funding

JJ thanks Council of Scientific and Industrial research, Govt. of India for a research fellowship (Grant No. 08/450(0008)/2017-EMR-I).

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Authors and Affiliations

  1. Department of Zoology, Research centre, University of Kerala, University College, Thiruvananthapuram, Kerala, India

    Joelin Joseph, Sandeep Sreeedharan & Mano Mohan Antony

  2. Transdisciplinary Biology Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India

    Sanil George

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Contributions

JJ developed the theory conducted experiments, computation analysis and wrote the manuscript. SS helped in performing experiments, bioinformatics analysis and sample collection. SG supervised findings of the work, provided technical support and helped in the manuscript design. MM conceived the present idea, designed manuscript, provided critical feedback and assisted in data interpretation. All the authors read and approved the final manuscript.

Corresponding author

Correspondence to Mano Mohan Antony.

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Conflict of interest

The Authors declare that there is no conflict of interest with any person or institution on subject matter or materials discussed in this manuscript.

Research involving human and animal participants

All applicable institutional and university guidelines for the care and use of animals were followed. This article does not contain any studies with human participants performed by any of the authors. The Departmental Doctoral Committee, Dept. of Zoology, University of Kerala, reviewed, discussed, and granted permission for the present study as part of the Ph.D. program of the principal author, Joelin Joseph under the guidance of Dr. Mano Mohan Antony, Assistant professor, University College, recognized research Centre, University of Kerala, under the Ph.D. dissertation entitled “Karyotyping and chromosomal banding pattern of Etroplus species of South India with special reference to its phylogenetic interrelationships’’ as per UGC (University Grants Commission) and Govt. of India guidelines on 29.03.2017 (Order: No. AcE VI/3/117/ZOO/15146/2017) at Dept. of Zoology, University of Kerala, Kariavattom Campus. The consent for the conduct of research was further approved based on the committee’s report by the Registrar and Vice-chancellor, the University of Kerala on 27/07/2017.

Statement regarding fish collection

The protocol mentioned in the study does not involve any slaughtering of fish and the fish was not collected from any protected area. A portion of the tail fin from a single individual was sufficient to carry out all the experiments and fish was released back to the wild. E. canarensis, though endangered, is an edible fish not protected by any law. Hence no permission was required from the state of Karnataka and Gov. of India for collection. The fish was collected from an open fishing area with the help of local fishermen.

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Joseph, J., Sreeedharan, S., George, S. et al. The complete mitochondrial genome of an endemic cichlid Etroplus canarensis from Western Ghats, India (Perciformes: Cichlidae) and molecular phylogenetic analysis. Mol Biol Rep 49, 3033–3044 (2022). https://doi.org/10.1007/s11033-022-07130-9

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