The mitochondrial genomes are very diverse, but their evolutionary history is unclear due to the lack of efforts to sequence that of protists (unicellular eukaryotes), which cover a major part of the eukaryotic tree. Cryptista comprises cryptophytes, goniomonads, kathablepharids, and Palpitomonas bilix, and their mitochondrial genomes (mt-genomes) are characterized by various gene contents, particularly the presence/absence of an ancestral (bacterial) system for the cytochrome c maturation system. To shed light on mt-genome evolution in Cryptista, we report the complete mt-genome of Microheliella maris, which was recently revealed to branch at the root of Cryptista. The M. maris mt-genome was reconstructed as a circular mapping chromosome of 61.2 kbp with a pair of inverted repeats (12.9 kbp) and appeared to be the most gene-rich among the mt-genomes of the members of Diaphoretickes (a mega-scale eukaryotic assembly including Archaeplastida, Cryptista, Haptista, and SAR) studied so far, carrying 53 protein-coding genes. With this newly sequenced mt-genome, we inferred and discussed the evolution of the mtgenome in Cryptista and Diaphoretickes.

We prepared cox11 and tufA alignments, of which taxon samplings refer to the cox15 alignments analyzed in He et al. (2016). The cox11 and tufA sequences of M. maris, Marophrys sp. SRT127, several eukaryotes, and several Alphaproteobacteria were also added. The phylogenetic alignment of ccmA, ccmC, and ccmF analyzed by Nishimura et al. (2020) was updated by adding the M. maris sequences retrieved from the genome data. The sequences were aligned using MAFFT with the L-INS-i option. Ambiguously aligned positions were manually removed from each alignment.