The closest lineage of Archaeplastida is revealed by phylogenomics analyses that include Microheliella maris

Abstract

By clarifying the phylogenetic positions of ‘orphan’ protists (unicellular micro-eukaryotes with no affinity to extant lineages), we may uncover the novel affiliation between two (or more) major lineages in eukaryotes. Microheliella maris was an orphan protist, which failed to be placed within the previously described lineages by pioneering phylogenetic analyses. In this study, we analysed a 319-gene alignment and demonstrated that M. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name ‘Pancryptista’ for Cryptista plus M. maris . The 319-gene analyses also indicated that M. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called ‘CAM clade’ here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia) and the particular phylogenetic ‘signal’ most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies.

Microheliella maris possesses the most gene-rich mitochondrial genome in Diaphoretickes

“…The Mm mt-genome possesses a pair of inverted repeats, 12,850 bp in length, and contains 22 genes (three ribosomal RNAs, seven tRNAs, and 12 protein-coding genes; Figure 1). We could not detect nad10 and ccmB in the Mm mt-genome, which were found in the mitochondrial genome of P. bilix (Pb mt-genome), but detected nad10 transcripts in the RNA-seq data generated by Yazaki et al (2022). The protein sequence of M. maris nad10 showed an extension at the N-terminus compared to that of P. bilix encoded in its mt-genome.…”

“…In the phylogenetic analyses based on alignments comprising 319 genes, M. maris branched at the base of Cryptista, and the clade of M. maris plus Cryptista was further united with Archaeplastida (Yazaki et al, 2022). The clade of M. maris plus Cryptista was proposed to be called Pancryptista, and the union of Pancryptista and Archaeplastida was named the CAM clade (Yazaki et al, 2022). In the present study, we sequenced the mitochondrial genome of M. maris.…”

“…Thus, the shift from System I to System III (or that from System III to System I) needs to be invoked multiple times during Cryptista evolution (Nishimura et al, 2016(Nishimura et al, , 2020. To precisely understand the distribution of System I/III in Cryptista, we need the mitochondrial genomes of more diverse cryptists as well as other eukaryotes, including Microheliella maris, which showed an intimate affinity to Cryptista in a recent phylogenomic study (Yazaki et al, 2022).…”

“…Microheliella maris is a protist that was originally classified into the phylum Heliozoa (centroheliozoans) based on several characteristics, such as the radiating axopodia with tiny granules and the centroplast, which are similar to those of centroheliozoans (Cavalier-Smith and von der Heyden, 2007;Yabuki et al, 2012;Cavalier-Smith et al, 2015). In the phylogenetic analyses based on alignments comprising 319 genes, M. maris branched at the base of Cryptista, and the clade of M. maris plus Cryptista was further united with Archaeplastida (Yazaki et al, 2022). The clade of M. maris plus Cryptista was proposed to be called Pancryptista, and the union of Pancryptista and Archaeplastida was named the CAM clade (Yazaki et al, 2022).…”

The complete mitochondrial genome of Isochrysis galbana harbors a unique repeat structure and a specific trans-spliced cox1 gene

“…These four groups were once collectively known as the chromalveolates or CASH based on a uniting biological feature of plastids, but their evolutionary history had long been a bone of contention ( Cavalier-Smith, 1999 ; Petersen et al, 2014 ; Ponce-Toledo et al, 2019 ). Recently the monophyly of CASH was overturned by addition of other previously unrelated groups: a lveolates and s tramenopiles branches with r hizarians forming SAR supergroup ( Keeling and Burki, 2019 ), even T-SAR clade with the subsequent addition of t elonemids ( Strassert et al, 2019 ); h aptophytes have merged with centrohelids to form Haptista supergroup while c ryptophytes saw a coalescence of a few lineages ( Palplitomonas and katablepharids) around them to form Cryptista ( Keeling and Burki, 2019 ), even the newly proposed clade Pancrytista plus Microheliella maris ( Yazaki et al, 2022 ). With the maturation of genomic methods and uncovering of new species, clarifying and confirming the phylogenetic positions of these major eukaryotic lineages will continue, which will facilitate the better understanding of distant and murky past of early evolution.…”