scholarly journals The Glaucophyta: the blue-green plants in a nutshell

2015 ◽  
Vol 84 (2) ◽  
pp. 149-165 ◽  
Author(s):  
Christopher Jackson ◽  
Susan Clayden ◽  
Adrian Reyes-Prieto
Keyword(s):  
Red Algae ◽  
Functional Data ◽  
Nuclear Genome ◽  
Cyanophora Paradoxa ◽  
Transcriptomic Data ◽  
Ultrastructural Studies ◽  
Photosynthetic Eukaryotes ◽  
Algal Group ◽  
Basic Biology ◽  
The Common

The Glaucophyta is one of the three major lineages of photosynthetic eukaryotes, together with viridiplants and red algae, united in the presumed monophyletic supergroup Archaeplastida. Glaucophytes constitute a key algal lineage to investigate both the origin of primary plastids and the evolution of algae and plants. Glaucophyte plastids possess exceptional characteristics retained from their cyanobacterial ancestor: phycobilisome antennas, a vestigial peptidoglycan wall, and carboxysome-like bodies. These latter two traits are unique among the Archaeplastida and have been suggested as evidence that the glaucophytes diverged earliest during the diversification of this supergroup. Our knowledge of glaucophytes is limited compared to viridiplants and red algae, and this has restricted our capacity to untangle the early evolution of the Archaeplastida. However, in recent years novel genomic and functional data are increasing our understanding of glaucophyte biology. Diverse comparative studies using information from the nuclear genome of <em>Cyanophora paradoxa</em> and recent transcriptomic data from other glaucophyte species provide support for the common origin of Archaeplastida. Molecular and ultrastructural studies have revealed previously unrecognized diversity in the genera <em>Cyanophora</em> and <em>Glaucocystis</em>. Overall, a series of recent findings are modifying our perspective of glaucophyte diversity and providing fresh approaches to investigate the basic biology of this rare algal group in detail.

scholarly journals Analysis of an improved Cyanophora paradoxa genome assembly

DNA Research ◽  
2019 ◽  
Vol 26 (4) ◽  
pp. 287-299 ◽  
Author(s):  
Dana C Price ◽  
Ursula W Goodenough ◽  
Robyn Roth ◽  
Jae-Hyeok Lee ◽  
Thamali Kariyawasam ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Nuclear Genome ◽  
Cleavage Furrow ◽  
Cyanophora Paradoxa ◽  
Model Species ◽  
Night Time ◽  
High Quality ◽  
Genome Data ◽  
Photosynthetic Eukaryotes ◽  
Long Read

Abstract Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organisms. Using the genome data, we generated a resolved 115-taxon eukaryotic tree of life that includes a well-supported, monophyletic Archaeplastida. Analysis of muroplast peptidoglycan (PG) ultrastructure using QFDEEM shows that PG is most dense at the cleavage-furrow. Analysis of the chlamydial contribution to glaucophytes and other Archaeplastida shows that these foreign sequences likely played a key role in anaerobic glycolysis in primordial algae to alleviate ATP starvation under night-time hypoxia. The robust genome assembly of C. paradoxa significantly advances knowledge about this model species and provides a reference for exploring the panoply of traits associated with the anciently diverged glaucophyte lineage.

scholarly journals Cytometric Analysis of Diverse Glaucophyte Species Reveals Distinctive Signals Useful for Fluorescence-Based Detection and Sorting

2021 ◽  
Author(s):  
Rossella Calvaruso ◽  
Janice Lawrence ◽  
Adrian Reyes-Prieto
Keyword(s):  
Red Algae ◽  
Cell Sorting ◽  
Fluorescence Signal ◽  
Algal Group ◽  
Representative Species ◽  
Freshwater Habitats ◽  
The Common ◽  
Competing Hypotheses ◽  
Comprehensive Evaluations ◽  
Photosynthetic Cells

Glaucophytes, red algae and viridiplants (green algae and land plants) are formally united in the supergroup Archaeplastida. Although diverse molecular and genomic evidence suggest the common origin of the three Archaeplastida lineages, the lack of a robust glaucophyte knowledgebase has limited comprehensive evaluations of competing hypotheses. Glaucophytes are rare and apparently confined to freshwater habitats. However, the distribution and diversity of these algae have not been thoroughly explored owing to challenges with detecting and isolating novel specimens. Here we examined the cytometric signatures of representative species of the genera Cyanophora, Cyanoptyche, Glaucocystis and Gloeochaete for a distinctive signal that would aid identification. Most glaucophytes analyzed presented a relatively high red fluorescence signal due to the presence of the blue phycobiliproteins C-phycocyanin and allophycocyanin. Cell-size differences and the concurrent presence of the red phycobiliprotein phycoerythrin in other algal lineages, such as red algae and cryptophytes, allowed us to distinguish glaucophytes from other photosynthetic cells containing blue phycobiliproteins. We used fluorescence-assisted cell sorting (FACS) to isolate viable Cyanophora and Glaucocystis individuals from existing cultures. Our results indicate that the peculiar autofluorescence signal of glaucophytes will facilitate further identification and isolation on novel specimens of this scarce but important algal group.

scholarly journals Loss of plastid developmental genes coincides with a reversion to monoplastidy in hornworts

2022 ◽  
Author(s):  
Alexander Istvan MacLeod ◽  
Parth K Raval ◽  
Simon Stockhorst ◽  
Michael Knopp ◽  
Eftychios Frangedakis ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Nuclear Division ◽  
Developmental Pathways ◽  
Ancestral State ◽  
Plastid Division ◽  
Plastid Development ◽  
State Reconstruction ◽  
Transcriptomic Data ◽  
The Common ◽  
Almost All

The first plastid evolved from an endosymbiotic cyanobacterium in the common ancestor of the Archaeplastida. The transformative steps from cyanobacterium to organelle included the transfer of control over developmental processes; a necessity for the host to orchestrate, for example, the fission of the organelle. The plastids of almost all embryophytes divide independent from nuclear division, leading to cells housing multiple plastids. Hornworts, however, are monoplastidic (or near-monoplastidic) and their photosynthetic organelles are a curious exception among embryophytes for reasons such as the occasional presence of pyrenoids. Here we screened genomic and transcriptomic data of eleven hornworts for components of plastid developmental pathways. We find intriguing differences among hornworts and specifically highlight that pathway components involved in regulating plastid development and biogenesis were differentially lost in this group of bryophytes. In combination with ancestral state reconstruction, our data suggest that hornworts have reverted back to a monoplastidic phenotype due to the combined loss of two plastid division-associated genes: ARC3 and FtsZ2.

scholarly journals Introgression from Gorilla caused the Human-Chimpanzee split

2018 ◽  
Author(s):  
Johan Nygren
Keyword(s):  
Common Ancestor ◽  
Nuclear Genome ◽  
Genome Project ◽  
Lineage Sorting ◽  
Chromosome 5 ◽  
Speciation Model ◽  
Introgression Event ◽  
The Common

ABSTRACT: The Gorilla Genome Project (Scally, 2012) showed that 30% of the gorilla genome introgressed into the ancestor of humans and chimpanzees, and that the two species diverged through lineage sorting with 15% ending up in Pan and another 15% in Homo. That introgression is the Pan-Homo split, hybridization, which led to speciation as the new hybrid lineages became reproductively isolated from one another. The NUMT on chromosome 5 (“ps5”) (Popadin, 2017) fits perfectly with the introgression speciation model, it was formed from mtDNA that had diverged from the common ancestor of Pan-Homo for 1.8 Myr at the time of insertion into the nuclear genome, and originated in the Gorilla lineage. The ps5 pseudogene was transferred to Pan and Homo during the introgression event that led to the Pan-Homo split, 6 million years ago.

scholarly journals Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes

2005 ◽  
Vol 15 (14) ◽  
pp. 1325-1330 ◽  
Author(s):  
Naiara Rodríguez-Ezpeleta ◽  
Henner Brinkmann ◽  
Suzanne C. Burey ◽  
Béatrice Roure ◽  
Gertraud Burger ◽  
...  
Keyword(s):  
Red Algae ◽  
Green Plants ◽  
Photosynthetic Eukaryotes

scholarly journals Protein translocons in photosynthetic organelles of Paulinella chromatophora

2014 ◽  
Vol 83 (4) ◽  
pp. 399-407 ◽  
Author(s):  
Przemysław Gagat ◽  
Paweł Mackiewicz
Keyword(s):  
Protein Import ◽  
Nuclear Genome ◽  
Vesicular Trafficking ◽  
Plastid Gene ◽  
Endosymbiotic Gene Transfer ◽  
Redox Sensor ◽  
Proposed Model ◽  
Number Of Genes ◽  
The Common ◽  
Chromatophore Membrane

The rhizarian amoeba <em>Paulinella chromatophora</em> harbors two photosynthetic cyanobacterial endosymbionts (chromatophores), acquired independently of primary plastids of glaucophytes, red algae and green plants. These endosymbionts have lost many essential genes, and transferred substantial number of genes to the host nuclear genome via endosymbiotic gene transfer (EGT), including those involved in photosynthesis. This indicates that, similar to primary plastids, <em>Paulinella</em> endosymbionts must have evolved a transport system to import their EGT-derived proteins. This system involves vesicular trafficking to the outer chromatophore membrane and presumably a simplified Tic-like complex at the inner chromatophore membrane. Since both sequenced <em>Paulinella</em> strains have been shown to undergo differential plastid gene losses, they do not have to possess the same set of Toc and Tic homologs. We searched the genome of <em>Paulinella</em> FK01 strain for potential Toc and Tic homologs, and compared the results with the data obtained for <em>Paulinella</em> CCAC 0185 strain, and 72 cyanobacteria, eight Archaeplastida as well as some other bacteria. Our studies revealed that chromatophore genomes from both <em>Paulinella</em> strains encode the same set of translocons that could potentially create a simplified but fully-functional Tic-like complex at the inner chromatophore membranes. The common maintenance of the same set of translocon proteins in two <em>Paulinella</em> strains suggests a similar import mechanism and/or supports the proposed model of protein import. Moreover, we have discovered a new putative Tic component, Tic62, a redox sensor protein not identified in previous comparative studies of <em>Paulinella</em> translocons.

scholarly journals Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer

2021 ◽  
Author(s):  
Laszlo Bartha ◽  
Terezie Mandakova ◽  
Ales Kovarik ◽  
Paul Adrian Bulzu ◽  
Nathalie Rodde ◽  
...  
Keyword(s):  
Southern Blotting ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Molecular Cytogenetics ◽  
Nuclear Genome ◽  
Phylogenetic Distance ◽  
Bac Clone ◽  
Intimate Association ◽  
The Common ◽  
Naturally Transgenic Plants

The occurrence of horizontal gene transfer (HGT) in Eukarya is increasingly gaining recognition. Nuclear-to-nuclear jump of DNA between plant species at high phylogenetic distance and devoid of intimate association (e.g., parasitism) is still scarcely reported. Within eukaryotes, components of ribosomal DNA (rDNA) multigene family have been found to be horizontally transferred in protists, fungi and grasses. However, in neither case HGT occurred between phylogenetic families, nor the transferred rDNA remained tandemly arrayed and transcriptionally active in the recipient organism. This study aimed to characterize an alien eudicot-type of 45S nuclear rDNA, assumingly transferred horizontally to the genome of monocot European Erythronium (Liliaceae). Genome skimming coupled by PacBio HiFi sequencing of a BAC clone were applied to determine DNA sequence of the alien rDNA. A clear phylogenetic signal traced the origin of the alien rDNA of Erythronium back to the Argentea clade of Potentilla (Rosaceae) and deemed the transfer to have occurred in the common ancestor of E. dens-canis and E. caucasicum. Though being discontinuous, transferred rDNA preserved its general tandemly arrayed feature in the host organism. Southern blotting, molecular cytogenetics, and sequencing of a BAC clone derived from flow-sorted nuclei indicated integration of the alien rDNA into the recipient's nuclear genome. Unprecedently, dicot-type alien rDNA was found to be transcribed in the monocot Erythronium albeit much less efficiently than the native counterpart. This study adds a new example to the growing list of naturally transgenic plants while holding the scientific community continually in suspense about the mode of DNA transfer.

scholarly journals Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome

2016 ◽  
Vol 113 (52) ◽  
pp. 15036-15041 ◽  
Author(s):  
Sébastien Leclercq ◽  
Julien Thézé ◽  
Mohamed Amine Chebbi ◽  
Isabelle Giraud ◽  
Bouziane Moumen ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Nuclear Genome ◽  
Closely Related Species ◽  
Evolutionary Transitions ◽  
Female Sex ◽  
Bacterial Endosymbionts ◽  
The Common ◽  
And Behavior

Sex determination is a fundamental developmental pathway governing male and female differentiation, with profound implications for morphology, reproductive strategies, and behavior. In animals, sex differences between males and females are generally determined by genetic factors carried by sex chromosomes. Sex chromosomes are remarkably variable in origin and can differ even between closely related species, indicating that transitions occur frequently and independently in different groups of organisms. The evolutionary causes underlying sex chromosome turnover are poorly understood, however. Here we provide evidence indicating that Wolbachia bacterial endosymbionts triggered the evolution of new sex chromosomes in the common pillbug Armadillidium vulgare. We identified a 3-Mb insert of a feminizing Wolbachia genome that was recently transferred into the pillbug nuclear genome. The Wolbachia insert shows perfect linkage to the female sex, occurs in a male genetic background (i.e., lacking the ancestral W female sex chromosome), and is hemizygous. Our results support the conclusion that the Wolbachia insert is now acting as a female sex-determining region in pillbugs, and that the chromosome carrying the insert is a new W sex chromosome. Thus, bacteria-to-animal horizontal genome transfer represents a remarkable mechanism underpinning the birth of sex chromosomes. We conclude that sex ratio distorters, such as Wolbachia endosymbionts, can be powerful agents of evolutionary transitions in sex determination systems in animals.

scholarly journals A single loss of photosynthesis in diatoms

2018 ◽  
Author(s):  
Anastasiia Onyshchenko ◽  
Elizabeth C. Ruck ◽  
Teofil Nakov ◽  
Andrew J. Alverson
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Diversity ◽  
Phylogenetic Analyses ◽  
Rare Event ◽  
Small Subset ◽  
Plastid Genomes ◽  
Photosynthetic Eukaryotes ◽  
Large Numbers ◽  
Group A ◽  
The Common

AbstractLoss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of ‘apochloritic’ diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic diatoms suggests a single loss of photosynthesis in the common ancestor of these species, previous phylogenetic analyses suggested that photosynthesis was lost multiple times. We sequenced additional phylogenetic markers from the nuclear and mitochondrial genomes for a larger set of taxa and found that the best trees for datasets representing all three genetic compartments provided low to moderate support for monophyly of apochloritic Nitzschia, consistent with a single loss of photosynthesis in diatoms. We sequenced the plastid genome of one apochloritic species and found that it was highly similar in all respects to the plastid genome of another apochloritic Nitzschia species, indicating that streamlining of the plastid genome had completed prior to the split of these two species. Finally, it is increasingly clear that some locales host relatively large numbers apochloritic Nitzschia species that span the phylogenetic diversity of the group, indicating that these species co-exist because of resource abundance or resource partitioning in ecologically favorable habitats. A better understanding of the phylogeny and ecology of this group, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group, a rare event in diatoms.

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