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The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.

ABSTRACT: Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3?Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C₄ photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B₁, B₇ and B₁₂ auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.

SUBMITTER: Li L

PROVIDER: S-EPMC7455551 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.

Li Linzhou L Wang Sibo S Wang Hongli H Sahu Sunil Kumar SK Marin Birger B Li Haoyuan H Xu Yan Y Liang Hongping H Li Zhen Z Cheng Shifeng S Reder Tanja T Çebi Zehra Z Wittek Sebastian S Petersen Morten M Melkonian Barbara B Du Hongli H Yang Huanming H Wang Jian J Wong Gane Ka-Shu GK Xu Xun X Liu Xin X Van de Peer Yves Y Melkonian Michael M Liu Huan H

Nature ecology & evolution 20200622 9

Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, mor ...[more]

PMID: 32572216

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Project description:BackgroundMitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups.ResultsThe complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias.ConclusionThe mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the mitochondrial sequences support a basal deuterostome placement, support for this decreases with the use of more sophisticated models of sequence evolution.

Dataset Information

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.

Publications

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.

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