Comparative analysis of the mitochondrial genomes of six newly sequenced diatoms reveals group II introns in the barcoding region of cox1

Abstract

Diatoms are the most diverse lineage of algae and at the base of most aquatic food webs, but only 11 of their mitochondrial genomes have been described. Herein, we present the mitochondrial genomes of six diatom species, including: Melosira undulata, Nitzschia alba, Surirella sp., Entomoneis sp., Halamphora coffeaeformis, and Halamphora calidilacuna. Comparison of these six genomes to the 11 currently published diatom mitochondrial genomes revealed a novel ubiquitous feature block consisting of tatC-orf157-rps11. The presence of intronic retrotransposable elements in the barcoding region of cox1 in the Halamphora genomes may explain historic difficulty (especially PCR) with cox1 as a universal barcode for diatoms. Our analysis suggests that high rates of variability in number and position of introns, in many commonly used coding sequences, prevent these from being universally viable as barcodes for diatoms. Therefore, we suggest researchers examine the chloroplast and/or nuclear genomes for universal barcoding markers.

Keywords:

• Diatom
• mitochondrial evolution
• genome comparison
• taxonomic barcoding
• group II introns

Acknowledgements

The authors acknowledge the field work facilitated by E. Kociolek and D. Uehling, Vancouver, Washington.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this manuscript.

Additional information

Funding

This work was funded in part by a grant from the University of Colorado Boulder.