The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems—the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.
more »
« less
Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
more » « less- Award ID(s):
- 2021207
- PAR ID:
- 10540447
- Publisher / Repository:
- Springer Nature
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 14
- Issue:
- 1
- ISSN:
- 2041-1723
- Page Range / eLocation ID:
- 10.1038/s41467-023-41137-5
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
more » « less
Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome of
Pyramimonas parkeae NIES 254 and compared it with that ofP. parkeae CCMP 726, the only other fully sequencedP. parkeae chloroplast genome. The results revealed thatP. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome ofNIES 254 was larger than that ofCCMP 726 by 3,204 bp, theNIES 254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and theIR was 1,086 bp shorter than that ofCCMP 726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein‐coding genes:ycf20 ,psaC , andndhE . Phylogenetic analyses using 16S and 18SrDNA andrbcL sequences resolved a clade consisting of these twoP. parkeae strains and a clade consisting of these plus otherPyramimonas isolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification. -
The infraorder Astacidea, comprising marine clawed lobsters and freshwater crayfish, include some of the most recognizable decapod crustaceans, many being harvested commercially for human consumption and aquaculture. While molecular analyses have elucidated relationships among extant lineages, the composition and placement of several fossil groups within Astacidea remain poorly resolved, with several conflicting phylogenetic hypotheses and taxonomic classifications being proposed in previous works. Among these controversial groups, Erymoidea have variably been placed in Astacidea or Glypheidea, a largely extinct infraorder of predominantly pseudochelate marine lobsters. Cladistic relationships of Stenochiroidea have also been problematic, having been regarded as ancestral to freshwater crayfish (Astacida) or extant marine lobsters (Nephropidae). Failure to reach a consensus regarding these groups can be at least partially attributed to the prevalence of morphological convergence and limited taxon sampling. To clarify evolutionary relationships among fossil and extant taxa, a Bayesian phylogenetic analysis of morphological and molecular data (mitochondrial genes: 12S, 16S and COI; nuclear genes: 18S, 28S and H3) was performed that included extensive taxon sampling of all currently recognized families of Astacidea as well as representatives of several potential sister groups. To overcome error introduced by homoplasy, relationships among extant taxa, as revealed by previous molecular analyses, were used to identify morphological characters with potentially robust phylogenetic signal. The resulting phylogeny places erymids within Glypheidea and supports a sister relationship between Astacidea and Glaessnericarididae. Stenochiroidea was found to be polyphyletic, with most genera forming a clade sister to Nephropidae; Pseudastacus is moved to Protastacidae, which resolves as the sister taxon to freshwater crayfish. The relationships among living and fossil taxa presented here provide new insight into the origins and evolutionary histories of the major lineages of marine clawed lobsters and freshwater crayfish.more » « less
-
Green plants (Viridiplantae) include around 450,000–500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.more » « less
-
Charophytic Green Algae Encode Ancestral Polymerase IV/Polymerase V Subunits and a CLSY/DRD1 Homologmore » « less
Abstract In flowering plants, euchromatic transposons are transcriptionally silenced by RNA-directed DNA Methylation, a small RNA-guided de novo methylation pathway. RNA-directed DNA Methylation requires the activity of the RNA Polymerases IV and V, which produce small RNA precursors and noncoding targets of small RNAs, respectively. These polymerases are distinguished from Polymerase II by multiple plant-specific paralogous subunits. Most RNA-directed DNA Methylation components are present in all land plants, and some have been found in the charophytic green algae, a paraphyletic group that is sister to land plants. However, the evolutionary origin of key RNA-directed DNA Methylation components, including the two largest subunits of Polymerase IV and Polymerase V, remains unclear. Here, we show that multiple lineages of charophytic green algae encode a single-copy precursor of the largest subunits of Polymerase IV and Polymerase V, resolving the two presumed duplications in this gene family. We further demonstrate the presence of a Polymerase V-like C-terminal domain, suggesting that the earliest form of RNA-directed DNA Methylation utilized a single Polymerase V-like polymerase. Finally, we reveal that charophytic green algae encode a single CLSY/DRD1-type chromatin remodeling protein, further supporting the presence of a single specialized polymerase in charophytic green algae.
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1038/s41467-023-41137-5
