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.

The complete chloroplast and mitochondrial genomes of the diatomNitzschia palea(Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotomDurinskia baltica

“…,b, Pogoda et al. ). As more Nitzschia palea chondriomes are sequenced, the conformation of the chondriome is likely to be resolved.…”

“…It contains all the conserved diatom chondriome genes defined by Pogoda et al. () and all but one, tatA , of the variable genes. Compared to all other publicly available chondriomes, it has very similar features, including GC content, suggesting they have similar nucleotide composition (Table ).…”

“…, Pogoda et al. ). They have a conserved set of 33 genes and so far all but one is described as circular (Kamikawa et al.…”

“…Mitochondrial genomes (chondriomes) are relatively small and useful for phylogenetic comparisons because of their relatively low rate of polymorphisms (Pogoda et al. ). Nearly 20 diatom chondriomes have been sequenced (Armbrust et al.…”

“…Mitochondrial genomes (chondriomes) are relatively small and useful for phylogenetic comparisons because of their relatively low rate of polymorphisms (Pogoda et al 2018). Nearly 20 diatom chondriomes have been sequenced (Armbrust et al 2004, Bowler et al 2008, Ravin et al 2010, Imanian et al 2012, An et al 2016a,b, 2017, Tang and Bi 2016, Villain et al 2017, Pogoda et al 2018. They have a conserved set of 33 genes and so far all but one is described as circular (Kamikawa et al 2018).…”