Which protest was the ancestor to plants

Their sequences form a clade that is sister to fungal phytochromes Fig. Interestingly, the phytochrome from the brown algal virus EsV-1 ref. This relationship was not supported in a bootstrapping analysis Supplementary Fig. Additional phytochrome data from stramenopiles will be necessary to clarify the origin of these viral phytochromes. We also examined haptophytes, a predominantly marine lineage of phytoplankton their relationships with stramenopiles and other protists are unclear 27 , No phytochrome could be found in the haptophyte transcriptomes.

Terminal clades are collapsed into higher taxonomic units usually orders or classes for display purposes. Orange circles indicate inferred gene duplications.

Canonical plant phytochromes originated in an ancestor of streptophytes green star , and some charophyte algae retain non-canonical phytochromes PHYX1 and PHYX2.

Phytochrome domain architectures are shown on the right. Domains that are not always present are indicated by dashed outlines. Red algae are mostly multicellular, marine species that include many coralline reef-building algae. No phytochromes were found in the 28 red algal transcriptomes we examined, nor in the published genomes of Porphyridium purpureum , Chondrus crispus , Cyanidioschyzon merolae , Galdieria sulphuraria and Pyropia yezoensis Supplementary Table 1.

This result, based on data from all Rhodophyta classes 34 , provides compelling evidence for the absence of phytochromes from red algae Supplementary Fig. Glaucophytes are a small clade of freshwater, unicellular algae with unusual plastids referred to as cyanelles, which, unlike plastids in rhodophytes and green plants, retain a peptidoglycan layer GPS, in contrast with canonical plant phytochromes, have a single PAS domain in the C-terminal module, and the conserved histidine residue is present in the kinase domain, suggesting it retains histidine kinase activity The phylogenetic position of cryptophytes remains controversial.

They were once thought to be related to stramenopiles and haptophytes belonging to the kingdom Chromalveolata , but some recent phylogenomic studies place them either as nested within, or sister to, Archaeplastida 26 , 27 , These cryptophyte phytochromes differ from the canonical phytochromes in their retention of the conserved histidine phosphorylation site in the kinase domain Figs 1 and 2.

Despite this variation in the C terminus, the N-terminal photosensory modules of all cryptophyte phytochromes are monophyletic Fig. The tree depicts the organismal phylogeny of all the phytochrome-containing lineages. The domain architecture of the C-terminal regulatory module characteristic of each lineage is indicated on the right connected by dashed lines. The substitution of the histidine phosphorylation site H in the histidine kinase domain KD occurred subsequent to the divergence of prasinophytes.

The canonical plant phytochrome is restricted to streptophytes in grey box ; Zygnematales and Coleochaetales also have non-canonical plant phytochromes. Viridiplantae comprise two lineages, Chlorophyta and Streptophyta. Chlorophytes appear to lack phytochromes entirely; we did not find homologues in any of the chlorophyte transcriptomes examined, including 14 Trebouxiophyceae, 21 Ulvophyceae, 59 Chlorophyceae and 2 Pedinophyceae. This result is consistent with available whole-genome sequence data; the genomes of Chlamydomonas reinhardtii , Volvox carteri and Chlorella variabilis Chlorophyceae lack phytochromes.

Prasinophytes, on the other hand, do have phytochromes. Prasinophyte phytochromes are monophyletic and are the sister group to streptophyte phytochromes Fig. Streptophyta or streptophytes are an assemblage of the charophytes a paraphyletic grade of algae and the land plants 22 Supplementary Fig.

We found phytochrome homologues in all land plant clades, as well as in all charophyte lineages: Mesostigmatales including Chlorokybales , Klebsormidiales, Coleochaetales, Charales, Zygnematales and Desmidiales Fig.

The Charales phytochromes were not included in our final phylogenetic analyses because the transcriptome contigs and also the data currently available on GenBank are too short to be informative about their relationships. All streptophytes have canonical plant phytochromes, including Mesostigmatales, the earliest diverging charophyte lineage Figs 1 and 2 , Supplementary Fig. This result suggests that the origin of the canonical plant phytochrome took place in the ancestor of extant streptophytes.

Within charophyte algae we identified several gene duplication events. Members of the charophyte PHY1 clade are not common in our algal transcriptomes, and were found only in Desmidiales and in Entransia of the early-diverging Klebsormidiales Supplementary Fig. On the other hand, the charophyte PHY2 homologue is found consistently across algal transcriptomes.

Relationships recovered within each of these phytochrome subclades correspond well to species phylogenies for Desmidiales Some PHYX1 have a response regulator domain at the C terminus, similar to prasinophyte, cryptophyte and glaucophyte phytochromes Figs 1 and 2. Our data suggest that the phytochrome module of neochrome had a single origin Fig. Published data indicate that the phototropin module of neochromes, in contrast, had independent origins in algae and hornworts 18 , implying two separate fusion events involving phytochromes that shared a common ancestor.

To further explore this finding, we analysed the neochrome nucleotide data set see above using several nucleotide, codon and amino acid models, and performed a topology test. We consistently recovered the monophyly of the phytochrome module of neochromes, and usually with high support, from analyses using all models Fig. Although Anthoceros a hornwort neochrome was resolved as sister to a Zygnematales algal neochrome, this relationship was not supported except in the MrBayes analysis of the nucleotide data set.

Phytochromes from mosses, liverworts and hornworts each form a monophyletic group Fig. We detected single phytochrome homologues in hornwort and liverwort transcriptomes. The gene phylogenies match the species relationships 30 , 31 , consistent with the presence of single orthologous genes in these taxa.

Indeed, a single phytochrome has been identified via cloning methods in the liverwort, Marchantia paleacea var. We also searched the low-coverage draft genome of the hornwort Anthoceros punctatus 20X; Li et al. To further evaluate gene copy number, we hybridized the A. The same phytochrome contig and only that contig was recovered, suggesting that this hornwort does not harbour additional, divergent phytochrome copies.

Previously identified phytochromes are in bold font. The position of orange circles indicates inferred gene duplications.

In contrast, phytochromes in mosses are diverse, with at least four distinct clades resulting from three gene duplications Fig. The phylogeny reveals those moss phytochromes that are orthologous to the previously named P. Because Takakia Takakiopsida represents the earliest diverging lineage in the moss species phylogeny 36 , the first phytochrome duplication probably predates the origin of all extant mosses.

Previously identified phytochromes are shown in bold. The position of orange circles estimates the origin of inferred gene duplications. Our results show that the phytochrome copies previously cloned from Ceratodon purpureus , which were named CpPHY1—4 ref. These results suggest that the four known C. Lycophyte phytochromes are resolved as monophyletic and are sister to the fern plus seed-plant phytochromes Figs 1 and 5 , Supplementary Fig.

Selaginella and Isoetes Isoetopsida each have a single phytochrome, with the exception of Selaginella mollendorffii , where two nearly identical phytochromes are apparent in the whole-genome sequence data. Their high degree of similarity suggests that they might be products of a species-specific gene duplication. Fern phytochromes form a clade that is sister to the seed plant phytochromes Figs 1 and 5 , Supplementary Fig.

The name PHY3 was used previously to denote the chimeric photoreceptor that is now recognized as neochrome 17 , However, the amino acid data set included fewer sequences from ferns, which could reduce phylogenetic accuracy It is likely that that the phylogeny Fig.

PHY4B is a novel phytochrome clade that has not been documented before; it is not common in the fern transcriptomes we examined. Seed plant phytochromes cluster into three clades Supplementary Fig.

Organismal relationships within the gene subclades largely are consistent with those inferred in phylogenetic studies of angiosperms Notably, however, support for the monophyly of gymnosperms was low. Our phylogenetic results refute previous hypotheses suggesting that plants acquired phytochrome from cyanobacteria via endosymbiotic gene transfer 41 , 42 , because streptophyte and cyanobacterial phytochromes are not closest relatives in our phytochrome trees Fig.

Instead, plant phytochromes evolved from a precursor shared with other Archaeplastida. We clearly placed the origin of canonical plant phytochromes in a common ancestor of extant streptophytes Figs 1 and 2. Our data, moreover, show that the origin of this structure required multiple steps. As noted above, the position of cryptophytes is uncertain, and its inclusion in Archaeplastida is not strongly supported in published studies 26 , 27 , The topology of our phytochrome trees is consistent with a sister-group relationship between Viridiplantae and cryptophytes, but the topology also could result from endosymbiotic or horizontal gene transfer.

The loss of the histidine phosphorylation site in the histidine kinase domain—hence the attainment of the canonical form—occurred later, in the ancestor of streptophytes, and seems to have been accompanied by a permanent dissociation with the response regulator at the C-terminal end Fig.

Some streptophytes have additional, non-canonical phytochromes. Our findings highlight the different evolutionary modes of the phytochrome N- and C-terminal modules. In contrast, the evolution of the C-terminal regulatory module has been much more dynamic Fig. For example, the C-terminal PAS may be absent, may occur singly, or may occur as a tandem repeat Fig. The successful linkage of the phytochrome photosensory module with a variety of C-terminal modules has promoted phytochrome functional diversity.

Certainly the most compelling example is that of the neochromes. Neochrome was first discovered in ferns 16 and postulated to be a driver of the modern fern radiation under low light, angiosperm-dominated forest canopies 45 , 46 , Suetsugu et al. A recent study identified yet another neochrome from hornworts, and demonstrated that ferns acquired their neochromes from hornworts via horizontal gene transfer By placing the phototropin portion of neochrome into a broad phylogeny of phototropins, Li et al.

In contrast, the phytochrome portion of neochrome has had a different evolutionary history, with Zygnematales, hornworts and ferns forming a single monophyletic group Fig. This result is robust, and is supported by most of the analyses and by a topology test.

Our results thus suggest that neochromes originated via two separate fusion events, involving two distinct sources of phototropin but the same phytochrome progenitor. This is a fascinating extension of the capacity and propensity of the phytochrome photosensory module to be linked with functionally distinct downstream domains.

The major clades of land plants differ markedly with respect to phytochrome gene diversity. It appears that phytochromes are single copy in most liverworts, hornworts and Isoetopsida Isoetaceae and Selaginellaceae , whereas they have independently diversified in Lycopodiales, mosses, ferns and seed plants Fig. Interestingly, we observed a relationship between phytochrome copy number and species richness.

It is possible that the evolution of phytochrome structural and functional diversity enhanced the ability of polypod ferns and Bryopsida mosses to adapt to diverse light environments. Indeed, seed plants, ferns and mosses each have at least one phytochrome duplicate that convergently evolved or retained the role of mediating high-irradiance responses 48 , 49 , 50 , 51 , a trait likely to be important for surviving under deep canopy shade 52 see below.

The independent phytochrome diversification events in seed plants, ferns, mosses and Lycopodiales have significant implications for phytochrome functional studies. Moss phytochromes, for example, are more closely related to each other than to any of the seed-plant phytochromes and the same is true, of course, for phytochromes from ferns and those from Lycopodiales.

Seed-plant phytochromes have undergone significant differentiation into two major types. One is represented by phyA of A. It degrades rapidly in light, mediates very-low fluence and high-irradiance responses, and depends on protein partners FHY1 far-red elongated hypocoytl 1 and FHL FHY1 like for nuclear translocation.

The other is represented by phyB-E of A. They have a longer half-life than phyA in light, mediate low-fluence responses, and in the case of phyB, nuclear translocation does not require FHY1 or FHL 4 , 5.

The first instinct of scientists was to relate these organisms to plants and animals by relying on morphological characteristics. The term protozoan plural: protozoa or protozoans , meaning "early animals," was introduced in by naturalist Georg A. Goldfuss, according to a article published in the journal International Microbiology.

This term was used to describe a collection of organisms including ciliates and corals. By , Protozoa was established as a phylum or subset of the animal kingdom by German scientist Carl Theodor von Seibold. This phylum included certain ciliates and amoebas, which were described by von Seibold as single-celled animals.

In , the concept of protozoans was further refined and they were elevated to the level of a taxonomic kingdom by paleontologist Richard Owen. The members of this Kingdom Protozoa, in Owen's view, had characteristics common to both plants and animals. Though the scientific rationale behind each of these classifications implied that protozoans were rudimentary versions of plants and animals, there was no scientific evidence of the evolutionary relationships between these organisms International Microbiology, According to Simpson, nowadays "protozoa" is a term of convenience used in reference to a subset of protists, and is not a taxonomic group.

The term protista, meaning "the first of all or primordial" was introduced in by German scientist Ernst Haeckel. He suggested Protista as a third taxonomic kingdom, in addition to Plantae and Animalia, consisting of all "primitive forms" of organisms, including bacteria International Microbiology, Since then, the kingdom Protista has been refined and redefined many times.

Different organisms moved in and out notably, bacteria moved into a taxonomic kingdom of their own. American scientist John Corliss proposed one of the modern iterations of Protista in the s.

His version included the multicellular red and brown algae, which are considered to be protists even today. Scientists, often concurrently, have debated kingdom names and which organisms were eligible for example, versions of yet another kingdom, Protoctista had been proposed over the years.

However, it is important to note the lack of correlation between taxonomy and evolutionary relationships in these groupings.

According to Simpson, these groupings were not monophyletic, meaning that they did not represent a single, whole branch of the tree of life; that is, an ancestor and all of its descendants.

Today's classification has shifted away from a system built on morphology to one based on genetic similarities and differences. Entrepreneurs from throughout California are working to create the next generation of biofuels from algae. But will you ever be able to run your car off it? Many people, if not most, believe seaweed to be a plant. Is it? Plant-Like Protists: Algae Plant-like protists are called algae singular, alga. Diatoms are single-celled algae.

Other forms of algae are multicellular. Ecology of Algae Algae play significant roles as producers in aquatic ecosystems. Classification of Algae Types of algae include red and green algae, and euglenids , and dinoflagellates see Table below for examples. Type of Algae Origin of Chloroplast Type of Chloroplast Red algae cyanobacteria two membranes, chlorophyll like the majority of cyanobacteria Green algae cyanobacteria two membranes, chlorophyll like a minority of cyanobacteria Euglenids green algae three membranes, chlorophyll like green algae Dinoflagellates red algae three membranes, chlorophyll like red algae.

Reproduction of Algae Algae have varied life cycles. Summary Plant-like protists are called algae. They include single-celled diatoms and multicellular seaweed. Like plants, algae contain chlorophyll and make food by photosynthesis. Types of algae include red and green algae, euglenids, and dinoflagellates. Ciliates also are surrounded by a pellicle, providing protection without compromising agility.

The genus Paramecium includes protists that have organized their cilia into a plate-like primitive mouth, called an oral groove, which is used to capture and digest bacteria Figure 7. Food captured in the oral groove enters a food vacuole, where it combines with digestive enzymes.

Waste particles are expelled by an exocytic vesicle that fuses at a specific region on the cell membrane, called the anal pore.

In addition to a vacuole-based digestive system, Paramecium also uses contractile vacuoles , which are osmoregulatory vesicles that fill with water as it enters the cell by osmosis and then contract to squeeze water from the cell. Figure 7. Paramecium has a primitive mouth called an oral groove to ingest food, and an anal pore to excrete it. Contractile vacuoles allow the organism to excrete excess water. Cilia enable the organism to move. Watch the video of the contractile vacuole of Paramecium expelling water to keep the cell osmotically balanced.

Paramecium has two nuclei, a macronucleus and a micronucleus, in each cell. The micronucleus is essential for sexual reproduction, whereas the macronucleus directs asexual binary fission and all other biological functions.

The process of sexual reproduction in Paramecium underscores the importance of the micronucleus to these protists. Paramecium and most other ciliates reproduce sexually by conjugation. This process begins when two different mating types of Paramecium make physical contact and join with a cytoplasmic bridge Figure 8. The diploid micronucleus in each cell then undergoes meiosis to produce four haploid micronuclei. Three of these degenerate in each cell, leaving one micronucleus that then undergoes mitosis, generating two haploid micronuclei.

The cells each exchange one of these haploid nuclei and move away from each other. A similar process occurs in bacteria that have plasmids. Fusion of the haploid micronuclei generates a completely novel diploid pre-micronucleus in each conjugative cell. This pre-micronucleus undergoes three rounds of mitosis to produce eight copies, and the original macronucleus disintegrates. Four of the eight pre-micronuclei become full-fledged micronuclei, whereas the other four perform multiple rounds of DNA replication and go on to become new macronuclei.

Two cell divisions then yield four new Paramecia from each original conjugative cell. Figure 8. The complex process of sexual reproduction in Paramecium creates eight daughter cells from two original cells. Each cell has a macronucleus and a micronucleus. During sexual reproduction, the macronucleus dissolves and is replaced by a micronucleus.

Figure 9. This stramenopile cell has a single hairy flagellum and a secondary smooth flagellum. The other subgroup of chromalveolates, the stramenopiles, includes photosynthetic marine algae and heterotrophic protists. Many stramenopiles also have an additional flagellum that lacks hair-like projections Figure 9. Members of this subgroup range in size from single-celled diatoms to the massive and multicellular kelp. The diatoms are unicellular photosynthetic protists that encase themselves in intricately patterned, glassy cell walls composed of silicon dioxide in a matrix of organic particles Figure These protists are a component of freshwater and marine plankton.

Most species of diatoms reproduce asexually, although some instances of sexual reproduction and sporulation also exist. Some diatoms exhibit a slit in their silica shell, called a raphe. By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction. Figure Assorted diatoms, visualized here using light microscopy, live among annual sea ice in McMurdo Sound, Antarctica.

Gordon T. During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms. The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms.

As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels. Like diatoms, golden algae are largely unicellular, although some species can form large colonies.

Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community. The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds.

Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis. The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity.

Compare this life cycle to that of humans, for instance. Haploid gametes produced by meiosis sperm and egg combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus. However, the individual sperm and egg themselves never become multicellular beings.

Terrestrial plants also have evolved alternation of generations. In the brown algae genus Laminaria , haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form Figure Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.

Several species of brown algae, such as the Laminaria shown here, have evolved life cycles in which both the haploid gametophyte and diploid sporophyte forms are multicellular.