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131 results for “green algae”
Data from: Turning defence into offence? intrusion of cladoceran brood chambers by a green alga leads to reproductive failure
Microalgae are the foundation of aquatic food webs. Their ability to defend against grazers is paramount to their survival, and modulates their ecological functions. Here we report a novel anti-grazer strategy in the common green alga Chlorella vulgaris against two grazers, Daphnia magna and Simocephalus sp. The algal cells entered the brood chamber of both grazers, presumably using the brood current generated by the grazer's abdominal appendages. Once inside, the alga densely colonised the eggs, significantly reducing reproductive success. The effect was apparent under continuous light or higher light intensity. The algal cells remained viable following removal from the brood chamber, continuing to grow when inoculated in fresh medium. No brood chamber colonisation was found when the grazers were fed the reference diet Raphidocelis subcapitata under the same experimental conditions, despite the fact that both algal species were readily ingested by the grazers and were small enough to enter their brood chambers. These observations suggest that C. vulgaris can directly inflict harm on the grazers' reproductive structure. There is no known prior example of brood chamber colonisation by a microalgal prey; our results point to a new type of grazer-algae interaction in the plankton that fundamentally differs from other antagonistic ecological interactions.
Data from: From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have been useful for reconstructing the phylogeny of numerous clades of photosynthetic organisms (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome data. Results: We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. Conclusions: Analyses of the plastid data recovered a strongly supported framework of relationships for green plants. This includes the placement of Zygnematophyceace as sister to land plants (Embryophyta) and a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining members and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees); within the monilophyte clade (Monilophyta), relationships are strongly supported with Equisetales + Psilotales sister to Marattiales + leptosporangiate ferns. We also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses and provide suggestions for future analyses that will likely incorporate plastid genome data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding protocols for the entire data set as well as subsets of the data.
Data from: The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization
To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed unique protein families involved in osmotic stress tolerance and saccharide metabolism that support phenomic studies. Our results reveal the robust and flexible biology utilized by a green alga to successfully inhabit a desert coastline.
Data from: Static allometry of unicellular green algae: scaling of cellular surface area and volume in the genus Micrasterias (Desmidiales)
The surface area-to-volume ratio of cells is one of the key factors affecting fundamental biological processes and, thus, fitness of unicellular organisms. One of the general models for allometric increase in surface-to-volume scaling involves fractal-like elaboration of cellular surfaces. However, specific data illustrating this pattern in natural populations of the unicellular organisms have not previously been available. This study shows that unicellular green algae of the genus Micrasterias (Desmidiales) have positive allometric surface-to-volume scaling caused by changes in morphology of individual species, especially in the degree of cell lobulation. This allometric pattern was also detected within most of the cultured and natural populations analysed. Values of the allometric S:V scaling within individual populations were closely correlated to the phylogenetic structure of the clade. In addition, they were related to species-specific cellular morphology. Individual populations differed in their allometric patterns, and their position in the allometric space was strongly correlated with the degree of allometric S:V scaling. This result illustrates that allometric shape patterns are an important correlate of the capacity of individual populations to compensate for increases in their cell volumes by increasing the surface area. However, variation in allometric patterns was not associated with phylogenetic structure. This indicates that the position of the populations in the allometric space was not evolutionarily conserved and might be influenced by environmental factors.
Data from: Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae
Phenotypic variation controls the species interactions which determine whether or not species coexist. Long-standing hypotheses in ecology and evolution posit that phenotypic differentiation enables coexistence by increasing the size of niche differentiation. This hypothesis has only been tested using macroscopic traits to date, but niche differentiation, particularly of microscopic organisms, also occurs at the molecular and metabolic level. We examined how phenotypic variation that arises at the level of gene expression over evolutionary time affects phytoplankton species interactions and coexistence. We predicted that similarity in gene expression among species would decline with phylogenetic distance, and that reduced similarity in gene expression would weaken competition, increase facilitation and promote coexistence. To test this, we grew eight species of freshwater green algae in monocultures and bicultures for 46 days in a laboratory microcosm experiment. We quantified the strength of species interactions by: (i) fitting Lotka–Volterra models to time-series densities and estimating interaction coefficients, and (ii) calculating relative densities that compare species' steady-state densities in biculture to those in monoculture. We used Illumina high throughput sequencing to quantify the expression of 1253 families of homologous genes, including a set of 17 candidate genes that we hypothesized a priori to be involved in competition or facilitation. Synthesis. We found that closely related species had greater similarity in gene expression than did distantly related species, but as gene expression became more similar, species experienced weaker competition or greater facilitation, and were more likely to coexist. We identified gene functional categories that were uniquely differentially regulated in association with particular species interaction types. Contrary to common thinking in ecology and evolution, similarity in gene expression, and not differentiation, was associated with weaker competition, facilitation and coexistence.
Data from: Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae
The competition-relatedness hypothesis (CRH) predicts that the strength of competition is the strongest among closely related species and decreases as species become less related. This hypothesis is based on the assumption that common ancestry causes close relatives to share biological traits that lead to greater ecological similarity. Although intuitively appealing, the extent to which phylogeny can predict competition and co-occurrence among species has only recently been rigorously tested, with mixed results. When studies have failed to support the CRH, critics have pointed out at least three limitations: (i) the use of data poor phylogenies that provide inaccurate estimates of species relatedness, (ii) the use of inappropriate statistical models that fail to detect relationships between relatedness and species interactions amidst nonlinearities and heteroskedastic variances, and (iii) overly simplified laboratory conditions that fail to allow eco-evolutionary relationships to emerge. Here, we address these limitations and find they do not explain why evolutionary relatedness fails to predict the strength of species interactions or probabilities of coexistence among freshwater green algae. First, we construct a new data-rich, transcriptome-based phylogeny of common freshwater green algae that are commonly cultured and used for laboratory experiments. Using this new phylogeny, we re-analyse ecological data from three previously published laboratory experiments. After accounting for the possibility of nonlinearities and heterogeneity of variances across levels of relatedness, we find no relationship between phylogenetic distance and ecological traits. In addition, we show that communities of North American green algae are randomly composed with respect to their evolutionary relationships in 99% of 1077 lakes spanning the continental United States. Together, these analyses result in one of the most comprehensive case studies of how evolutionary history influences species interactions and community assembly in both natural and experimental systems. Our results challenge the generality of the CRH and suggest it may be time to re-evaluate the validity and assumptions of this hypothesis.
Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii
We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.
FIGURE. Macro- and microscopic structures of Multiclavula caput-serpentis (KaiR699, holotype). a. Thallus with basidiocarps. b. Basidiospores. c. Hymenium with basidia at different developmental stages and subhymenial hyphae. d. Bulbils of green algae wrapped in hyphae, different developmental stages. Bars a = 2 mm, b, c and d = 10 µm. Drawings by H. Lotz-Winter. in New and interesting species of Agaricomycetes from Panama
FIGURE. Macro- and microscopic structures of Multiclavula caput-serpentis (KaiR699, holotype). a. Thallus with basidiocarps. b. Basidiospores. c. Hymenium with basidia at different developmental stages and subhymenial hyphae. d. Bulbils of green algae wrapped in hyphae, different developmental stages. Bars a = 2 mm, b, c and d = 10 µm. Drawings by H. Lotz-Winter.
Dataset - Selection of cyanobacteria over green algae in a photo-sequencing batch bioreactor fed with wastewater
<p>The data set attached consists of an excel file where the data from the article “<strong>Selection of cyanobacteria over green algae in a photo-sequencing batch bioreactor fed with wastewater”</strong>, published in Science of the Total Environment (vol. 653, 25<sup>th</sup> February 2019, 485-495.) can be found, as well as the different equations and formulae that were used to obtain the published results.</p>
FIGURE 4 in Polulichloris henanensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga
FIGURE 4. Phylogenetic position of Polulichloris henanensis within class Trebouxiophyceae (Chlorophyta), based on 18S rDNA + rbcL sequences. The analysis was based on reduced alignment with an outgroup formed by the chlorophycean Chlamydomonas bilatus. The tree was inferred using PAUP*4.0 with the GTR + I + G evolutionary model. Numbers at branches correspond to MrBayes posterior probabilities (BPP)/maximum likelihood (ML) bootstrap values. Values below 0.95 BPP and 50% ML bootstrap support are not shown. Scale bar shows estimated number of substitutions per site.
FIGURE 1 in Polulichloris henanensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga
FIGURE 1. Morphology of Polulichloris henanensis strain FACHB-1765. A–G: young vegetative cells. H, I: mature vegetative cell. J‒O: autosporangium. P: vegetative cells and liberation of autospores. Scale bars: A‒D = 2 μm, E–P = 5 μm.
FIGURE 2 in Polulichloris henanensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga
FIGURE 2. Ultrastructure of Polulichloris henanensis. C: chloroplast, P: pyrenoid, SE: starch envelope, S: starch grains. Cell of P. henanensis with a parietal and cup-shaped chloroplast, pyrenoid bisected by a few thylakoid bands, and starch envelope composed of 2–4 plates surrounding the pyrenoid. A. Young cell. B–D. Vegetative cell.
FIGURE 3 in Polulichloris henanensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga
FIGURE 3. Phylogenetic position of Polulichloris henanensis within class Trebouxiophyceae (Chlorophyta), based on 18S rDNA sequences. The analysis was based on reduced alignment with an outgroup formed by the chlorophycean species Chlamdomonas rosae. The tree was inferred using PAUP*4.0 with the TrNef + I + G evolutionary model. Numbers at branches correspond to MrBayes posterior probabilities (BPP)/maximum likelihood (ML) bootstrap values. Values below 0.95 BPP and 50% ML bootstrap support are not shown. Scale bar shows estimated number of substitutions per site.
FIGURE 1 in Typification of the marine siphonous green algae Caulerpa prolifera (Bryopsidales, Chlorophyta)
FIGURE 1. Lectotype of Caulerpa prolifera (Forsskål) J.V. Lamouroux [Herbarium Forsskålii nº 878 C (barcode C–A–93369)]. © Herbarium C, reproduced with permission.
FIGURE 2 in Typification of the marine siphonous green algae Caulerpa prolifera (Bryopsidales, Chlorophyta)
FIGURE 2. Lectotype of Caulerpa prolifera f. obovata J. Agardh [Herbarium Agardh at LD (LD-Ag-16391)]. © Herbarium LD, reproduced with permission.
FIGURE 3 in Typification of the marine siphonous green algae Caulerpa prolifera (Bryopsidales, Chlorophyta)
FIGURE 3. Lectotype of Caulerpa prolifera f. zosterifolia Børgesen [St. Croix, I. Havgraesformation vest for Krauses Lagun, F. BØrgesen Nº 1650 iter tertium 1905-06, C (barcode C-A-92172)]. © Herbarium C, reproduced with permission.
FIGURE 8 in Two new green algae, Rhizoclonium fractum sp. nov. and R. umbraticum sp. nov., from tropical and subtropical brackish waters of Japan
FIGURE 8. Cultured material of Cladophoraceae sp. 2 (Rhizoclonium minutissimum). (A, B) Morphology of filamentous thalli. (C) Filamentous thalli with rhizoid-like structure. (D, E) Spindle- and band-shaped chloroplasts with pyrenoids (arrowheads). (F) Autofluorescence of chloroplasts. (G) Cells stained with DAPI, showing nuclei. (H) Cells stained with Lugol's iodine, showing the pyrenoids. (I) Mature sporangia with spores and vegetative cells. Arrowhead points to a mature sporangium. (J) Detail of a hapteroid attachment cell. Scale bar = 20 μm (A–C, G–I); Scale bars = 10 μm (D–F, K).
FIGURE 10 in Two new green algae, Rhizoclonium fractum sp. nov. and R. umbraticum sp. nov., from tropical and subtropical brackish waters of Japan
FIGURE 10. Cultured material of Cladophoraceae sp. 3 (Rhizoclonium umbraticum). (A, B) Morphology of filamentous thalli. (C) Tip of filamentous thalli. (D) Filamentous thalli with rhizoidal structures. (E–G) Spindle- and band-shaped chloroplasts. (H) Autofluorescence of chloroplasts. (I) Cells stained with DAPI, showing nuclei. (J) Cells stained with Lugol's iodine, showing the pyrenoids. (K) Detail of hapteroid attachment cell. Scale bars = 10 μm (A, B, D, F–H, K); Scale bars = 20 μm (C, E, J).
FIGURE 7 in Two new green algae, Rhizoclonium fractum sp. nov. and R. umbraticum sp. nov., from tropical and subtropical brackish waters of Japan
FIGURE 7. Field-collected specimens of Cladophoraceae sp. 2 (Rhizoclonium minutissimum). (A) Field-collected specimens. (B, C) Morphology of field-collected specimens. (D, E) Filamentous thalli with non-septate rhizoids. (F) Tip of filamentous thalli. (G–I) Spindle- and band-shaped chloroplasts. Arrowhead points to a pyrenoid. (J) Autofluorescence of chloroplasts. (K) Cells stained with DAPI, showing nuclei. (L) Cells stained with Lugol's iodine, showing pyrenoids. (M, N) Pyrenoids observed by transmission electron microscopy. Pyrenoids have starch plates. (M) Three or two thylakoid membranes traversing a pyrenoid. (33) One thylakoid membrane. Scale bar = 5 mm (A); Scale bars = 40 μm (B, C); Scale bars = 20 μm (D–G, K, L); Scale bars = 10 μm (H–J); Scale bars = 0.5 μm (M); Scale bars = 1 μm (N).
FIGURE 5 in Two new green algae, Rhizoclonium fractum sp. nov. and R. umbraticum sp. nov., from tropical and subtropical brackish waters of Japan
FIGURE 5. Field-collected specimens of Cladophoraceae sp. 1 (Rhizoclonium fractum). (A, B) Field-collected specimens. (C–E) Range of morphological types in field-collected specimens. (E) Arrowhead pointing to rhizoidal structure. (F, G) Cells of field-collected materials. (H, I) Spindle- or band-shaped chloroplasts. Arrowheads indicate pyrenoids. (J, K) Autofluorescence of chloroplasts. (L) Cells stained with DAPI, showing nuclei. (M) Cells stained with Lugol's iodine, showing the pyrenoids. (N) Polypyramidal pyrenoid observed by transmission electron microscopy. Scale bar = 5 mm (A, B,); Scale bars = 20 μm (C–F, L, M); Scale bar = 10 μm (G–K).; Scale bar = 0.5 μm (N).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.