The enigmatic Betadevario ramachandrani (Teleostei: Cyprinidae: Danioninae): phylogenetic position resolved by mitogenome analysis, with remarks on the prevalence of chimeric mitogenomes in GenBank

Abstract

We present the complete mitochondrial genome and a phylogenetic analysis of the danionine cyprinid Betadevario ramachandrani, endemic to the Western Ghats in India. Bayesian phylogenetic analysis of all available mitochondrial genomes of Danionina show that B. ramachandrani is the most basal member of a clade also containing Devario, Microdevario and Microrasbora, and this clade is the sister group of Danio. Seven of 20 mitochondrial genomes downloaded from GenBank for phylogenetic analysis were found to be chimeric, including five curated reference genomes, and this did affect our phylogenetic analysis. At least three of these erroneous sequences have been used in other studies. There is reason to suspect that there are numerous chimeric mitogenomes in GenBank.

Keywords:

• DNA barcoding
• next generation sequencing
• phylogeny

PUBLIC INTEREST STATEMENT

This study reports on the first sequencing of the whole mitochondrial genome of the rare carpfish Betadevario ramachandrani, and performs an analysis which confirms that it is a primitive relative of the genus Devario. During analysis, it was found that 7 out of 20 mitochondrial genomes downloaded from GenBank for inclusion in this study were amalgams (“chimeras”) from several different species; in one case, the genome is comprised of sequences from three different species from three different subfamilies of Cyprinidae. The erroneous genomes affected the outcome of the analysis, at least three of the erroneous genomes have been used in other studies, and further analysis suggests that the problem of chimeric genomes in GenBank may be widespread.

Competing Interest

The authors report no conflicts of interest.

Acknowledgements

Te Yu Liao (National Sun Yat-sen University, Taiwan) made the extraction used in this study, and Mazen Sarhan (Macrogen Europe, Netherlands) provided help with high-throughput sequencing.

Additional information

Funding

The authors received no direct funding for this research.

Notes on contributors

Michael Norén

Dr. Michael Norén and Professor Sven Kullander are members of the ichthyology team at the Swedish Museum of Natural History (NRM) in Stockholm, Sweden. Professor Kullander (ORCID: 0000-0001-6075-0266) is the Scientific Curator for the ichthyological and herpetological collections of the NRM, team leader for FishBase Sweden, and an expert on fish taxonomy, specializing in Cichlidae and Cyprinidae. Dr. Norén (ORCID: 0000-0003-2561-6760) is Curator of FishBase Sweden, and specializes in molecular systematics.