An RNA-based approach to sequence the mitogenome of Hypoptopoma incognitum (Siluriformes: Loricariidae)

Abstract

Hypoptopoma incognitum is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.

• Fish
• heteroplasmy
• mtRNA
• RNA-Seq
• transcriptome

Acknowledgements

The authors are thankful to Dr Jansen Zuanon from INPA for fish identification and to Dr Paulo A. Buckup from the Museu Nacional (MN UFRJ) for fish deposit. Authors acknowledge the use of the computer cluster Titan from the Woods Hole Oceanographic Institution (WHOI), where T. P. holds a guest investigator position.

Declaration of interest

The authors report no conflict of interest. This work was supported by Partnerships for Enhanced Engagement in Research (PEER) grant from USAID (PGA-2000003446) to TP.

Supplementary material available online

Supplementary Table 1