One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade

Abstract

Mantamonads were long considered to represent an “orphan” lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the “CRuMs” supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.

A gene-rich mitochondrion with a unique ancestral protein transport system

“…With 49 protein-coding genes, D. rotans also has a gene-rich mitogenome 9 compared to most eukaryotes, but significantly below the 62 protein-coding genes found in Mantamonas . Interestingly, these two species are the most distant representatives of the CRuMs 15,16 . Mantamonas sphyraenae and D. rotans are the only eukaryotes that encode the ribosomal protein rpl23 in their mitogenomes, a shared character that provides additional support for the monophyly of CRuMs (Figure 1C).…”

“…The genome sequence of M. sphyraenae was generated as described in Blaz et al . 16 . Briefly, whole DNA from this protist was sequenced using both long (PacBio) and short (Illumina) read sequencing, with a coverage of 112x for PacBio and 115x for Illumina.…”

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Results and DiscussionMantamonas sphyraenae possesses one of the most gene-rich mitogenomes Mantamonas sphyraenae is a protist species belonging to the CRuMs supergroup 15,16 . Our analysis of its complete mitochondrial genome revealed a 53,051 bp long molecule (Figure 1A) with an A+T content of 73.45%.

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“…At the other end of the spectrum, Jakobids harbor the largest mitogenomes, encoding 60-66 proteins 8 . Here, we introduce the mitogenome of Mantamonas sphyraenae , a protist from the deep-branching CRuMs supergroup 15,16 . Remarkably, it boasts the most gene-rich mitogenome outside of jakobids, by housing 91 genes, including 62 protein-coding ones.…”

Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life

“…M. plastica) do bear pseudopodia 57 and, accordingly, the ancestor of the group. Mantamonadida have a stable phylogenetic position 58 and might have retained some of the ancestral features of CRuMs; indeed, Mantamonas share some similarities with ancyromonads, notably the possession of small flattened cells with a short anterior flagellum and benthic/soil-associated lifestyles. However, the other CRuM linages (Diphyllatea and Hilomonadea) include larger, freshwater planktonic species, also possessing a ventral groove 56,59 .…”