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Do all mushrooms have the same multicellular ancestor?

Do all mushrooms have the same multicellular ancestor?


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Do all mushrooms have the same multicellular ancestor? Did that ancestor feature common mushroom elements such as cap, stem, sporofore, vulva, bulb, etc.


All fungal species within the kingdom have the same common ancestor, which is unicellular (thought to be protistan). This common ancestor is the point at which it is thought that animals diverged, as suggested by this article. In their words:

It is now well established that animals share a common single-celled ancestor with fungi, and that in the two sister lineages multicellularity arose independently

A fungal phylogenetic tree is shown below, which originated from this paper.

Note: all colored areas represent different phyla of fungi.

EDIT:

I will respond to a few questions addressed in the comments.

Is there a unique multicellular ancestor to all mushrooms?

I am rather sure (but can't explicitly confirm with a reference) that multicellularity in fungi only evolved once. If this were true, I would also hypothesize that mushroom-like characteristics also evolved only once, thus indicating that there is a multicellular ancestor to all mushrooms.

Are there multicellular fungi outside dikarya?

No. One branch of dikarya seems to consist of only unicellular organisms, suggesting that multicellularity evolved at some point within organism under only one dikaryan branch.

Was the common ancestor of Dykarya multicellular?

No. See previous answer.

Are those unicellular dykaria secondary unicellular or not? Given that the both branches of dykaria show similarities in fruiting bodies, it seems to be plausible that the common ancestors of dykaria had a similar structure.

I am not exactly aware of the similarities in fruiting bodies in both branches, but if the physiology behind fruiting bodies are similar, it is very likely because the dikaryan common ancestor had a similar mechanism.


24.2: Classifications of Fungi

  • Contributed by OpenStax
  • General Biology at OpenStax CNX
  • Classify fungi into the five major phyla
  • Describe each phylum in terms of major representative species and patterns of reproduction

The kingdom Fungi contains five major phyla that were established according to their mode of sexual reproduction or using molecular data. Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are placed for convenience in a sixth group called a &ldquoform phylum&rdquo. Not all mycologists agree with this scheme. Rapid advances in molecular biology and the sequencing of 18S rRNA (a part of RNA) continue to show new and different relationships between the various categories of fungi.

The five true phyla of fungi are the Chytridiomycota (Chytrids), the Zygomycota (conjugated fungi), the Ascomycota (sac fungi), the Basidiomycota (club fungi) and the recently described Phylum Glomeromycota. An older classification scheme grouped fungi that strictly use asexual reproduction into Deuteromycota, a group that is no longer in use.

Note: &ldquo-mycota&rdquo is used to designate a phylum while &ldquo-mycetes&rdquo formally denotes a class or is used informally to refer to all members of the phylum.


What were the first multicellular organisms?

The beginnings of multicellularity have been traced back to a very remote past, more than 1 billion years ago, according to some authors (eg, Selden & Nudds, 2012).

Because transitional forms have been poorly conserved in the fossil record, little is known about them and about their physiology, ecology, and evolution, making the process of constructing a reconstruction of incipient multicellularity difficult.

In fact, it is not known if these first fossils were animals, plants, fungi, or any of these lineages. Fossils are characterized by being flat organisms, with a high surface area / volume.


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When immature and white, this mushroom may be known as common mushroom, white mushroom, [3] button mushroom, [3] cultivated mushroom, table mushroom, and champignon mushroom (or simply champignon). When immature and brown, it may be known variously as Swiss brown mushroom, Roman brown mushroom, Italian brown mushroom, cremini/crimini mushroom, [4] [5] chestnut mushroom (not to be confused with Pholiota adiposa), and baby bella. [4]

When marketed in its mature state, the mushroom is brown with a cap measuring 10–15 centimetres (4–6 inches). [5] This form is commonly sold under the names portobello mushroom, [5] [6] portabella mushroom, [7] and portobella mushroom, but the etymology is disputed. [5] [6]

The common mushroom has a complicated taxonomic history. It was first described by English botanist Mordecai Cubitt Cooke in his 1871 Handbook of British Fungi, as a variety (var. hortensis) of Agaricus campestris. [8] [9] Danish mycologist Jakob Emanuel Lange later reviewed a cultivar specimen, and dubbed it Psalliota hortensis var. bispora in 1926. [10] In 1938, it was promoted to species status and renamed Psalliota bispora. [11] Emil Imbach (1897–1970) imparted the current scientific name of the species, Agaricus bisporus, after the genus Psalliota was renamed to Agaricus in 1946. [2] The specific epithet bispora distinguishes the two-spored basidia from four-spored varieties.

This mushroom is commonly found worldwide in fields and grassy areas following rain, from late spring through to autumn, especially in association with manure. In many parts of the world it is widely collected and eaten however, resemblance to deadly or poisonous lookalikes (see below) should be noted.

Lookalike species Edit

The common mushroom could be confused with young specimens of the deadly poisonous destroying angel (Amanita sp.), but the latter may be distinguished by their volva or cup at the base of the mushroom and pure white gills (as opposed to pinkish or brown of A. bisporus). Thus it is always important to clear away debris and examine the base of such similar mushrooms, as well as cutting open young specimens to check the gills. Furthermore, the destroying angel grows in mossy woods and lives symbiotically with spruce.

A more common and less dangerous mistake is to confuse A. bisporus with Agaricus xanthodermus, an inedible mushroom found worldwide in grassy areas. A. xanthodermus has an odor reminiscent of phenol its flesh turns yellow when bruised. This fungus causes nausea and vomiting in some people.

The poisonous European species Entoloma sinuatum has a passing resemblance as well, but has yellowish gills, turning pink, and it lacks a ring.

Mushroom and truffle
production – 2019
Country Millions of
tonnes
China 8.94
Japan 0.47
United States 0.38
Poland 0.36
Netherlands 0.30
World 11.90
Source: FAOSTAT of the United Nations [16]

The earliest scientific description of the commercial cultivation of A. bisporus was made by French botanist Joseph Pitton de Tournefort in 1707. [17] French agriculturist Olivier de Serres noted that transplanting mushroom mycelia would lead to the propagation of more mushrooms.

Originally, cultivation was unreliable as mushroom growers would watch for good flushes of mushrooms in fields before digging up the mycelium and replanting them in beds of composted manure or inoculating 'bricks' of compressed litter, loam, and manure. Spawn collected this way contained pathogens and crops commonly would be infected or not grow at all. [18] In 1893, sterilized, or pure culture, spawn was discovered and produced by the Pasteur Institute in Paris, for cultivation on composted horse manure. [19]

Modern commercial varieties of the common agaricus mushroom originally were light brown in color. The white mushroom was discovered in 1925 growing among a bed of brown mushrooms at the Keystone Mushroom Farm in Coatesville, Pennsylvania. Louis Ferdinand Lambert, the farm's owner and a mycologist by training, brought the white mushroom back to his laboratory. As with the reception of white bread, it was seen as a more attractive food item and became grown and distributed. [20] Similar to the commercial development history of the navel orange and Red Delicious apple, cultures were grown from the mutant individuals, and most of the cream-colored store mushrooms marketed today are products of this 1925 chance natural mutation.

A. bisporus is now cultivated in at least seventy countries throughout the world. [2]


Mushrooms are macroscopic fruiting bodies of certain fungi. On the other hand, the fungus is any member of the kingdom fungi that mainly includes yeasts, moulds, and mushrooms. Therefore, this is the key difference between mushrooms and fungus. Furthermore, another difference between mushrooms and fungus is that the mushrooms belong to the phylum Basidiomycota while the fungus belongs to the phyla Chytridiomycota, Zygomycota, Ascomycota and Basidiomycota. Also, mushrooms develop above ground while fungus can grow below ground.

Moreover, a further difference between mushrooms and fungus is that the mushroom fungi are filamentous while fungi can be either unicellular or filamentous. Besides, all mushrooms are fungi but, not all fungus produce mushrooms.


Results

High-Resolution Genetic Map.

Cytological evidence has indicated that meiotic exchanges are highly enriched in subtelomeric regions of the 13 chromosomes in C. cinerea (12), suggesting that recombination rates might be non-uniform across the genome. To examine crossover distribution, we used 133 simple sequence repeat (SSR) markers evenly distributed across the genome and four additional markers to construct a genetic map (Fig. 1, SI Text, Fig. S1, and Dataset S1, Table S3). Examination of the marker genotypes of the progeny revealed regions of average, high, and low recombination. The total genetic map length of the 31-Mb physical genome that could be mapped is 948 centimorgans (cM), indicating an average frequency of exchange of 33 kb/cM. However, the “hot” regions (8% of the genome) exhibit an elevated rate of recombination (6 kb/cM on average), whereas the “cold” regions (44% of the genome) exhibit very little recombination (198 kb/cM).

Summary plots of chromosome II of C. cinerea. The plot shows the location of (Top panel) telomeres in red and centromere as black oval (Second panel) the density of transposable elements (brown) (Third panel) tRNA genes (light green) (Fourth panel) recombination rates (the position of the SSR markers is indicated by vertical black bars, white is unmapped, red is high recombination, gray is average recombination, blue is low recombination) (Fifth panel) the density of all genes (orange) (Sixth panel), the density of orphan genes (light orange) (Seventh panel), the density of orthologous genes (blue) (Eighth panel) the density of paralogous genes (red) (Ninth panel) similarity of paralog families represented as 1/dS (10th panel) syntenic regions (all regions of synteny between C. cinerea and L. bicolor are indicated in green, and blocks with >15 anchors are indicated in dark green). Vertical scales are defined for each bar in the bar title. Horizontal scale is Mb.

The hot regions are located predominantly in subtelomeric regions (16/18 are within the 15% of the nearest telomere Fisher's exact test, P = 0.0002) (Fig. S1). Although the frequency of chiasmata (cross-overs) per bivalent ranges from 1 to 12 in both fungi and other organisms (reviewed in ref. 15), species with both low and high levels of exchange exhibit an elevated rate of recombination in subtelomeric regions (16–18). This elevation may reflect associations between the initiation of chromosome synapsis at subterminal regions and chiasma formation in these species (15, 19).

Retrotransposon Distribution.

Transposon sequences (2.5% of genomic sequence) are not distributed uniformly across the genome (Fig. 1, Fig. S1, and Dataset S1, Tables S4a and S4b). Each chromosome contains a distinctive internal transposon cluster whose position is highly correlated (R 2 = 0.89) with the cytological centromere (12) on the nine chromosomes that extend telomere to telomere (Fig. S1). These transposon clusters (20% of all transposon-related sequences) could represent sequence-independent centromeres that are common in other fungi such as Neurospora crassa and Cryptococcus neoformans (20, 21). Many of these transposon clusters lie within regions that are cold for meiotic recombination. With the exception of the transposon clusters, the cold regions lack retrotransposon-related sequences. They contain only 3 of the 44 full-length retrotransposons (χ 2 = 23.7, P < 0.001), and all of the cold regions contain extensive stretches (over 1 Mb on the larger chromosomes) that lack any retrotransposon-related sequences (Fig. S1). The complexity of factors influencing the genome-wide distribution of transposons has been noted (22, 23), but the pattern we see in C. cinerea with an exclusion of retrotransposons from most but not all regions of low recombination has not been reported previously. Retrotransposons outnumber DNA transposons by a factor of 10 in C. cinerea (SI Text). Retrotransposon-related sequences are found either in the presumed centromere clusters or in regions of average or high recombination, whereas the distribution of DNA transposons is more uniform.

Ortholog and Paralog Distribution.

To predict 13,342 protein-coding genes, 267 tRNA genes, and 10 snRNA genes (Dataset S1, Table S5), we used computational tools in combination with evidence that included proteins from related species and 5,612 ESTs (SI Text). Gene calls were confirmed further by 5′ serial analysis of gene expression (SAGE) from two tissue types (5,130 gene models Dataset S1, Table S6). Comparative analyses of the available basidiomycete genomes reveals a dramatic increase in gene number from less than 7,000 genes in C. neoformans and Ustilago maydis to more than 13,000 in the sequenced Agaricomycete fungi including C. cinerea (Dataset S1, Table S7). To understand better the mechanism of the observed gene increase and to ask if expansions of gene families are equally likely at different chromosomal locations, we constructed gene families based on sequence similarity using TribeMCL (24) (SI Text and Dataset S1, Table S8). We determined which C. cinerea genes are orphan (no homologs), orthologous (single-copy in C. cinerea and at least one Laccaria bicolor ortholog), or paralogous (multicopy in C. cinerea). We plotted the distribution of these three categories along the chromosomes (Fig. 1 and Fig. S1). It is striking that, whereas the distribution of orphan genes is relatively uniform, orthologous single-copy genes are overrepresented in regions with low rates of meiotic recombination, and paralogous multicopy genes are found primarily in regions with average or high rates of meiotic recombination (Table 1). We conclude that several factors, including high recombination rates, tolerance of transposable elements, telomere proximity, and chromatin structure, potentially could contribute positively to the creation and maintenance of duplicated paralogous genes in the discrete regions that we observe in C. cinerea.

Non-uniform gene distribution in chromosome regions with different rates of meiotic recombination

Paralogous Gene Families.

Inspection of Dataset S1, Table S8 reveals that the largest paralogous expansion involves genes encoding proteins with protein kinase domains. Because kinases in many organisms mediate sophisticated control mechanisms essential for complex structure and developmental patterns, we focused on this family in more detail. BLAST and hidden Markov model (HMM) screening of the C. cinerea transcriptome indicates the presence of 380 kinases (SI Text and Dataset S1, Tables S9a and S9b), including 12 classes not present in Saccharomyces cerevisiae, three of which have not been previously observed outside the Metazoa (Dataset S1, Table S9c). The largest family, with 133 members, FunK1, has unusual modifications in conserved kinase motifs, expanding the documented diversity of this important catalytic domain (Fig. 2). Catalytic residues D166, N171, and D184 are conserved [1ATP.pdb numbering (25)], suggesting that FunK1 family members use a catalytic mechanism similar to that of conventional protein kinases and are enzymatically active. There are some notable changes in the FunK1 motifs. A highly conserved lysine corresponding to K168 is replaced by an invariant serine in FunK1. This lysine, which donates a hydrogen bond to the transferred gamma phosphate group, presumably is replaced by a basic residue from elsewhere in the FunK1 sequence if efficient catalysis is to be retained. Several very highly conserved residues without direct catalytic roles also are missing from FunK1, including H158, F185, and G186. However, conservation of R165 and K189, which form intramolecular interactions with phosphorylated amino acids in some protein kinases, suggests that members of the FunK1 family are regulated by phosphorylation (25). The FunK1 family has homologs in the Agaricomycotina and Pezizomycotina, but not in other fungi, suggesting a potential link between this kinase family and the multicellularity of these fungi. We observed that the left subterminal region of chromosome IX contains 59 FunK1 kinases in all orientations (head to head, head to tail, and tail to tail) with only two transposon clusters and very few interspersed nonkinase genes. In contrast, the distribution of protein kinases from families with widely distributed orthologs is more scattered, with the vast majority occurring in regions with low rates of meiotic recombination (Fig. S2).

HMM logos of protein kinase active site regions. (A) Conventional protein kinases. (B) FunK1 protein kinases. Conserved residues positions in both conventional and FunK1 kinases are indicated with blue circles. Residue positions that are nearly universally conserved in conventional ePK domains but are altered in FunK1 kinases are indicated with red circles.

There also are copy-number changes within conserved fungal kinase families. Phylogenetic analysis of the MAPK cascade revealed Basidiomycota-specific duplications in the MAPK genes (S. cerevisiae FUS3/KSS1) which are involved in the pheromone response, whereas HOG1 a p38 kinase, is single copy throughout the sampled fungi (Fig. S3).

We examined two additional gene families of significant size (cytochrome P450 and hydrophobins) to ask if duplicated paralogs from these families also are found in restricted chromosome regions. The P450 gene family (125 genes contain the Pfam domain) includes genes with metabolic roles in monooxygenase metabolism, and the family is implicated in the degradation capabilities of Phanerochaete chrysosporium on substrates ranging from lignin to diesel fuel (26, 27). Phylogenetic analysis shows that the expansion of the family was independent in P. chrysosporium and C. cinerea (SI Text and Fig. S4). Although scattered members of the P450 and other expanded families are found within cold regions, tandem repeats of these genes are found exclusively in genomic regions with higher recombination rates. In contrast to the FunK1 family, many P450 gene paralogs are found in head-to-tail orientation with a maximum of four copies in any one chromosomal location. A similar pattern is observed for the hydrophobin gene family (34 genes). Hydrophobins are small, secreted proteins that self-assemble at hydrophilic–hydrophobic interfaces to form amphipathic films (28, 29). These films help hyphae emerge from moist substrates to form aerial structures and also line internal cavities in the fruiting body (28). We have found that C. cinerea has the largest described hydrophobin gene family for any fungus. Phylogenetic analysis (Fig. S5) shows independent expansions of the gene family in P. chrysosporium, L. bicolor, and C. cinerea. The hydrophobin paralogs often are found in head-to-tail orientation with a maximum of seven genes in one cluster. These clusters are found in regions with high rates of recombination, whereas hydrophobins that are unique within their contigs occur in regions with low rates of recombination.

The patterns of gene duplication have important implications for adaptation and evolution in some species where pathogenic factors like adhesins and cell-surface variation genes tend to be found in the highly recombining regions near chromosome ends (4, 30). In C. cinerea, gene ontology (GO) terms are correlated with local recombination rates along the chromosomes (SI Text and Dataset S1, Table S10). In addition, we have found that the age of gene duplicates, as measured by calculating synonymous substitution rates (dS), correlates well with the recombination rate classes. We identified 3,796 duplicated gene pairs and found that pairs residing in cold regions are significantly older (P < 1E -16 , Kolmogorov-Smirnov test median dS 2.2) than the pairs that reside in regions of average or elevated recombination (median dS 1.95), as illustrated in Fig. 1 and Fig. S1. The genomic orientation of paralogous gene pairs also is highly nonrandom. Overall, 49% of all adjacent genes are in tandem orientation, as expected from a random distribution, whereas 88% of adjacent paralogous genes are in tandem orientation (P < 1E -16 Fisher's exact test). The increased age in the cold regions of the genome indicates a lower generation rate of gene duplicates and confirms that an unequal rate of sequence evolution is a general property of all gene families in C. cinerea.

Transcriptional Program Associated with Mating Behavior.

Coordinated gene expression of adjacent FunK1 kinases, P450 genes, and hydrophobins might provide a selective advantage that contributes to the maintenance of the clusters. Alternatively, individual members of these paralogous gene families may play important roles at discrete stages in C. cinerea development. The ease of culture and synchronous development (under the control of light and nutritional cues) of C. cinerea greatly facilitates studies of transcriptional regulation. Accordingly, we designed a 13,230-feature microarray that includes at least one 70-mer oligonucleotide for each known and predicted gene, EST, and repeated element. We used the validated arrays to investigate the transcriptional program that occurs during mating (SI Text). In the typical basidiomycete life cycle, nuclear fusion does not occur immediately after mating cell fusion. Instead, a nucleus from each mating partner is maintained in a common cytoplasm (the “dikaryotic cell”), and all tissues (except for the multinucleate stipe cells) of the highly differentiated mushroom fruiting bodies of C. cinerea (Fig. 3A) are composed of dikaryotic cells. The formation of the dikaryotic mycelium in mushrooms is initiated by fusion of undifferentiated hyphal cells and is maintained by a complex cell division in which both nuclei divide in synchrony in the tip cell, and daughter nuclei then are partitioned equally into the new tip and subterminal cells. Partitioning involves the formation of a structure known as the “clamp connection” (Fig. 3D) through which one of the daughter nuclei must pass. The steps of dikaryon formation are controlled by two sets of unlinked, multiallelic mating-type genes called “A” and “B” (Fig. S6). Many details of the process, including the different steps that are under the control of the A genes (which encode homeodomain proteins that heterodimerize in a compatible mating) and the B genes (which encode pheromones and receptors that activate each other in a compatible mating) are understood from classical genetics and more recent molecular studies (10).

Photograph and micrographs of C. cinerea. (A) Mature C. cinerea fruiting body that is shedding spores. The upper surface of the cap has loosely adhering “veil cells.” The lower surface of the cap is composed of “gills” which support the basidia (meiotic cells). The cap is elevated several centimeters above the Petri dish by the “stipe” (stalk). (B) Simple septum between two cells in a monokaryotic hypha. (C) “False clamp” between two cells in an “A-on” hypha. (D) True clamp connection between two cells in a dikaryotic hypha (“A-on B-on”). Magnification in BD is the same.

We examined mycelia in which targets of the A locus (the “A-on” strain Fig. 3C) and the B locus (the “B-on” strain, which has a morphology similar to the strain shown in Fig. 3B) were expressed separately and compared these with transcripts expressed in the dikaryon (Fig. 3D) and in the unmated monokaryotic strain (Fig. 3B). We observed 877 transcripts with significant differences in expression levels in one or more of these conditions (SI Text and Dataset S1, Table S11). Of particular interest was a FunK1 kinase (CC1G_04033) with an ortholog in L. bicolor, which was significantly up-regulated in the A-on mycelium, along with a FunK1 paralog (CC1G_13267), suggesting that these may have a unique role in cell signaling in the A-regulated part of the pathway that requires synchronization of nuclear division. Other differentially regulated genes of interest include the previously characterized genes clp1 and pcc1, 12 transcription factors, five additional kinases including S. cerevisiae HOG1 and RCK2 orthologs, STE3 receptors, major facilitator superfamily transporters, and many genes involved in cell-cycle regulation, the cytoskeleton, and cell wall biogenesis (SI Text and Dataset S1, Table S11). A MAPK signaling complex, which includes the HOG1 homolog Fus3, plays a central role in the yeast pheromone response (31). However, the Fus3 MAPK cascade does not occur outside of the Saccharomycetales (32). We did observe that HOG1 a p38 MAPK, and RCK2 a calcium/calmodulin-dependent protein kinase, are both strongly down-regulated in A-on and B-on cells. Orthologs of these protein kinases are involved in the hyperosmotic response of yeast (33, 34). HOG1 is down-regulated in S. cerevisiae a1/α2 cells (35), but in contrast to what we observe in C. cinerea, its target, RCK2 (34), is not (35). It has been suggested that when FUS3 transcription is shut down in a1/α2 cells, HOG1 is down-regulated so it is not spuriously activated in the site vacated by its homolog (35). In C. cinerea, down-regulation of HOG1 and its target RCK2 must serve a different purpose, because the Fus3 is absent (32). We conclude that our high-throughput approach to identifying potential regulators and targets in the A-on and B-on pathways is essential for understanding this complex morphogenetic process, especially because very few of the downstream targets of the mating factors have been identified in any basidiomycete (36).

Overall, we found very few examples of coordinated regulation of adjacent paralogous gene duplicates in these experiments. Despite the presence of 59 adjacent FunK1 family members in the genome, scattered members of this cluster were coordinately regulated during dikaryon formation. We did observe significantly coordinated expression of a single paralogous tandem array of hydrophobins and of a paralogous tandem array of P450 genes during dikaryon formation. However, examination of expression patterns of all paralogous pairs indicated that adjacent pairs were no more likely to be coordinately regulated than nonadjacent pairs. We conclude that adjacent gene duplicates have diverged in expression timing and perhaps function.

Synteny.

Although there is larger number of genes in the currently sampled Agaricomycotina genomes (

10,000–15,000) than in Cryptococcus or Ustilaginomycotina (

6,000), there is no evidence for a whole-genome duplication, because no substantial region of duplication was identified through dot-plot or gene-based comparisons of self-vs.-self of the C. cinerea genome. A comparative approach also was used to ask if the key genomic features present in C. cinerea, particularly the potential for similar large genomic clusters with limited meiotic recombination, are represented in other Agaricomycetes. The genome of L. bicolor (37) provides an appropriate test case, because these Agaricomycetes last shared a common ancestor 200 Mya (SI Text). L. bicolor is an important ectomycorrhizal symbiont of hardwood and conifer species, although it also can adopt a transient saprotrophic lifestyle similar to that of C. cinerea. The genome of L. bicolor is 1.8 times larger than the C. cinerea genome, contains 1.6 times the number of predicted gene models, and is estimated to contain 13.65 Mb of transposons and transposon relics (in contrast to the 0.86 Mb in the assembled C. cinerea genome).

To identify blocks of synteny between these species, we employed the program (for “Fast Identification of Segmental Homology”), because the Manhattan distance metric it employs allows very asymmetric intervals between the syntenic “anchors” (38) (SI Text). We found that 39% of the assembled C. cinerea genome is syntenic with L. bicolor (Fig. S1 and Dataset S1, Table S12a). To estimate the total number of chromosomal rearrangement events that have occurred since their split from a common ancestor, we fit our data to the Nadeau-Taylor model (39, 40), which assumes that genes and chromosomal rearrangement breakpoints are uniformly distributed at random along the chromosomes. We calculate a rate of 3.5–4.5 chromosomal rearrangements per million years have accumulated along each lineage since separation. This rate is at the high end of the range described previously for eukaryotes (41) and is approximately 3-fold higher than in S. cerevisiae (42).

Despite the prevalence of rearrangements in these lineages, we observed 10 blocks with more than 15 anchors (SI Text and Dataset S1, Table S12b). Because these are highly unlikely (P < 0.0016) if rearrangements are tolerated equally, it was of interest to determine the nature of these chromosomal regions that are unusually refractory to rearrangement in mushrooms. These regions (3.4 Mb) are found primarily in genomic regions with low meiotic recombination rates on the five largest chromosomes (Fig. 1 and Fig. S1). GO analysis of these regions revealed that they are enriched (P < 0.0005 to P < 0.01) in genes annotated to basic structures and processes such as nitrogen metabolism, the cytoskeleton, and metabolic regulation, as well as in particular G protein-coupled receptors (Dataset S1, Table S13). These regions contain 2.4 times the number of expected transcription factors (χ 2 = 67.7, P < 0.001) and lack transposable elements. Interestingly, the 1,378 genes in these blocks are spaced on average only 872 bp apart, in contrast to the average gene spacing in the genome (1,261 bp) and in sharp contrast to the average gene spacing in regions that display elevated rates of recombination (1,655 bp).


Some mushrooms glow, and here's why

Did you know that there are mushrooms that actually glow? Aristotle was aware of this intriguing fact more than 2,000 years ago. He also was the first person to ask a simple question in print: Why? Now, researchers reporting in the Cell Press journal Current Biology on March 19 finally have a good answer. The light emitted from those fungi attracts the attention of insects, including beetles, flies, wasps, and ants. Those insect visitors are apparently good for the fungi because they spread the fungal spores around.

The new study also shows that the mushrooms' bioluminescence is under the control of the circadian clock. In fact, it was that discovery that led the researchers to suspect that the mushrooms' light must serve some useful purpose.

"Regulation implies an adaptive function for bioluminescence," explains Jay Dunlap of Dartmouth's Geisel School of Medicine.

"It appears that fungi make light so they are noticed by insects who can help the fungus colonize new habitats," says Cassius Stevani of Brazil's Instituto de Química-Universidade de São Paulo. The circadian control of bioluminescence makes the process more efficient.

There are many examples of living things that generate light in various ways. Among bioluminescent organisms, fungi are the most rare and least well understood. Only 71 of more than 100,000 described fungal species produce green light in a biochemical process that requires oxygen and energy. Researchers had believed in most cases that fungi produce light around the clock, suggesting that perhaps it was a simple, if expensive, metabolic byproduct.

The new work led by Dunlap and Stevani suggests that just isn't so, at least not in the case of Neonothopanus gardneri, one of the biggest and brightest of bioluminescent mushrooms. N. gardneri is also called "flor de coco," meaning coconut flower, by locals in Brazil, where the mushroom can be found attached to leaves at the base of young palm trees in coconut forests.

The researchers found that the mushrooms' glow is under the control of a temperature-compensated circadian clock. They suggest that this level of control probably helps the mushrooms save energy by turning on the light only when it's easy to see.

To find out what that green glow might do for the mushrooms, the researchers made sticky, fake mushrooms out of acrylic resin and lit some from the inside with green LED lights. When those pretend fungi were placed in the forest where the real bioluminescent mushrooms are found, the ones that were lit led many more staphilinid rove beetles, as well as flies, wasps, ants, and "true bugs," to get stuck than did sticky dark mushrooms.

Dunlap says they are interested in identifying the genes responsible for the mushrooms' bioluminescence and exploring their interaction with the circadian clock that controls them. They are also using infrared cameras to watch the interaction between N. gardneri mushrooms and arthropods, especially larger ones, more closely.

The findings are not only cool, they are also important in understanding how mushrooms are dispersed in the environment, the researchers say. That's key because mushrooms such as N. gardneri play an important role in the forest ecosystem.

"Without them, cellulose would be stuck in its form, which would impact the whole carbon cycle on Earth," Stevani says. "I dare to say that life on Earth depends on organisms like these."

Some fungi in the group known as basidiomycetes, including two bioluminescent mushrooms, are also parasites of coffee and pine trees. As a result, Stevani says, "it is very important to know how basidiomycetes grow and consequently how they spread their spores."


Five Kingdom Classification of Organisms

In this article we will discuss about the Five Kingdom Classification of Organisms (From 1969 to 1990):- 1. Criteria for Delimiting Kingdoms 2. Monera— Kingdom of Prokaryotes 3. Protista— Kingdom of Unicellular Eukaryotes 4. Fungi— Kingdom of Multicellular Decomposers 5. Plantae — Kingdom of Multicellular Producers or Metaphyta 6. Animalia — Kingdom of Multicellular Consumers or Metazoa 7. Advantages of Five Kingdom Classification 8. Drawbacks of Five Kingdom Classification.

Criteria for Delimiting Kingdoms:

Whittaker has used five criteria for delimiting the different kingdoms:

(i) Complexity of cell structure, prokaryotic and eukaryotic

(ii) Complexity of body structure or structural organisation, unicellular and multicellular.

(iii) Mode of nutrition which is divergent in multicellular kingdoms— photo-autotrophy in plantae, absorptive heterotrophy in fungi and ingestive heterotrophyin animalia. Photoautotrophic nutrition is also called holophytic nutrition while absorptive heterotrophy is known as holozoic nutrition. Absorptive heterotrophy is saprobiotic (= saprophytic) nu­trition.

(iv) Ecological life style like producers (plantae), decomposers (fungi) and consum­ers (animalia).

(v) Phylogenetic relationships.

Whittaker’s five kingdoms are Monera, Protista, Plantae, Fungi and Animalia.

Monera— Kingdom of Prokaryotes:

The kingdom includes all prokaryotes— mycoplasma, bacteria, actinomycetes and cyanobacteria or blue green alge. Along with fungi, they are decomposers and mineralizers of the biosphere.

(i) Monerans are basically unicellular (monos-single) prokaryotes and contain the most primitive of living forms,

(ii) They are varied in their nutrition— saprobic, parasitic, chemoautotrophic, photoautotrophic and symbiotic. The photoautotrophs include both aerobes and anaerobes,

(iii) The cells are microscopic (0.1 to a few microns in length),

(iv) Cell wall is generally present. It contains peptidoglycan and polysaccharides Other than Cellulose,

(v) Cells have one envelope type of organisation, i.e., the whole protoplast is covered by plasma membrane but internal compartmentalization is absent,

(vi) Genetic material is not organised into a nucleus,

(vii) DNA is naked, i.e., it is not associated with histone proteins. DNA lies coiled inside the cytoplasm. The coiled mass is known as nucleoid. It is equivalent to a single chromosome,

(viii) All membrane bound cell organelles are absent, e.g., mitochondria, lysosomes, spherosomes, Golgi bodies, plastids, etc.

(ix) The flagella, if present, are single stranded instead of being 11 stranded in eukaryotes. They are formed of protein called flagellin.

(x) Mitotic spindle is absent,

(xi) Gametes are absent. Gene recombination has been discovered in certain cases. Otherwise reproduction is by asexual methods,

(xii) Some of the monerans have the ability to convert di-nitrogen into ammonia state.

Protista— Kingdom of Unicellular Eukaryotes:

All prokaryotic organisms were grouped together under Kingdom Monera and the uni­cellular eukaryotic organisms were placed in Kingdom Protista.

Kingdom Protista has brought together Chlamydomonas, Chlorella (earlier placed in Algae within Plants and both having cell walls) with Paramecium and Amoeba (which were earlier placed in the animal kingdom which lack cell wall. It has put together organisms which, in earlier clas­sifications, were placed in different kingdoms.

This happened because the criteria for clas­sification changed. This kind of changes will take place in future too depending on the improvement in our understanding of characteristics and evolutionary relationships.

Over time, an attempt has been made to evolve a classification system which reflects not only the morphological physiological and reproductive similarities, but is also phylogenetic, i.e., is based on evolutionary relationships. Kingdom protista includes flagellates (euglenophyceae), diatoms, dinoflagellates, slime moulds, sarcodines, ciliates, sporozoans, etc.

The important characteristics are:

(i) It in­cludes all unicellular and colonial eukaryotes,

(ii) Mostly they are aquatic organisms forming plankton,

(iii) They have diverse modes of nutrition— photosynthetic, saprobic, parasitic, ingestive, or holozoic etc.

(iv) The photosynthetic plankton are called phytoplankton. They usually possess cell wall and constitute an important group of producers. The non-photosyn­thetic, wall-less and holozoic plankton are called zooplankton. Holozoic nutrition involves ingestion of particulate food. The protistans having holozoic nutrition are collectively called protozoa, though they have been excluded from kingdom animalia.

(v) There is a group of Euglena-like organisms which have a dual mode of nutrition, holophytic or photosynthetic in light and holozoic in absence of light or presence of abundant organic matter.

Slime moulds are a group of protista which are intermediate between wall-less and walled organisms. They are devoid of a wall in vegetative phase. In the vegetative phase, the nutrition is of ingestive type. In the repro­ductive phase, the slime moulds come to have cell walls,

(vi) The cellular organisation is of two envelope type, i.e., besides plasma membrane, internal membranes occur around certain organelles,

(vii) Genetic material is organised in the form of nucleus. DNA is associated with histone proteins,

(viii) The aerobic forms possess mitochondria. Endoplasmic reticulum, golgi bodies, lysosomes and centrioles occur,

(ix) Flagella, if present, are 11 stranded with 9 + 2 organisation of microtubules that are composed of a protein named tubulin,

(x) Both sexual and asexual modes of reproduction are present. However, an embryo stage is absent,

(xi) Tissue system is, absent.

Kingdom protista does not seem to be a natural group due to:

(i) Dinoflagellates are mesokaryotic and not eukaryotic.

(ii) A distinction of unicellular protistan algae and green algae included in volvocales is not valid,

(iii) Slime moulds are quite distinct from rest of the protists.

(iv) There are several evolutionary lines in protista,

(v) Protists of this kingdom have diverse modes of form, structure and life.

Fungi— Kingdom of Multicellular Decomposers:

The kingdom includes moulds, mildews, yeasts, rust causing fungi, pencillium, morels, mushrooms, puffballs, bracket fungi, etc., i.e., all the fungi of the two kingdom classification except slime moulds:

(i) It contains achlorophyllous, spore producing, multicellular or multinucleate eukaryotic organisms. Basically unicellular yeasts are also included amongst fungi because their sexual reproduction is similar to that of some fungi,

(ii) The organism: are heterotrophic with absorptive type of nutrition. It is either saprobic or parasitic. Symbiotic association occurs with some algae and higher plants, e.g., lichens, mycorrhiza. The saprobic fungi excrete hydrolytic or digestive enzymes in the external medium for digesting complex organic compounds. The parasitic fungi absorb nourishment directly from another living organism called host,

(iii) The body of fungus is filamentous and is called mycelium. The filaments are known as hyphae.

(iv) Hyphae are either multicellular or multinucleate. Nuclei are very small and show intra-nuclear spindle,

(v) The wall contains chitin and non-cellulosic polysaccharides. Cellulose also occurs in a few cases,

(vi) The cellular organisation is two envelope type,

(vii) In most cases, Golgi bodies are unicistemal.

(viii) Reproduction is both asexual and sexual,

(ix) Vegetative body or mycelium is not clear externally in most of the cases due to its subterranean nature. Reproductive bodies, are, however, apparent as in mushrooms, toadstools, puff balls, bracket fungi,

(x) Tissue differentiation is absent,

(xi) Food reserve is glycogen and fat.

The kingdom is important in nutrient cycling because along with some protistans and monerans, fungi are decomposers and mineralizers of the biosphere.

Plantae — Kingdom of Multicellular Producers or Metaphyta:

The kingdom contains all photosynthetic eukaryotic multicellular plants and their non-photosynthetic relatives. At the lower level it contains multicellular algae— green, brown and red algae. Other groups included in the kingdom plantae are bryophytes, pteridophytes and spermatophytes.

Important characters of this kingdom are as follows:

(i) Organisms are multicellular.

(iii) Body form is less regular,

(iv) Growth is usually indefinite,

(v) Organs are commonly external,

(vii) Mode of nutrition is autotrophic.

(viii) The photosynthetic regions contain plastids in their cells. Due to photo­synthetic activity, plants are called producers,

(ix) Most of the plants are restricted to land, sea-shores and fresh water reservoirs.

(x) The plants are usually fixed or free floating. Active locomotion is generally absent,

(xi) Structural differentiation into tissues is found except for certain algae,

(xii) Food reserve is usually starch and fat.

(xiii) Some of the plants are heterotrophic. They are mostly parasitic. A few are saprobes. A small group of au­totrophic plants catch small animals and insects for obtaining extra nitrogen. They are called carnivorous or insectivorous plants,

(xiv) Reproduction is both asexual and sexual. Acces­sory spores are present in lower plants. An embryo stage is absent in the algal group but is present in others.

Animalia — Kingdom of Multicellular Consumers or Metazoa:

Members of this kingdom are also known as metazoa or multicellular animals. The kingdom has maximum number and most diverse types of organisms. It includes all the animals of the two kingdom classification except Protozoa.

Groups included are sponges, coelenterates, worms, molluscs, arthropods, star fishes and vertebrates like fishes, amphib­ians, reptiles, birds and mammals. Insects, a group of arthropods, outnumber all other organisms in variety and number.

The important characteristics of animalia are:

(i) Organ­isms are multicellular eukaryotes,

(iv) Growth is definite. Well defined growing points are absent,

(v) Cellular, tissue and organ- system levels of organisation occurs in different groups,

(vi) Response to stimuli is quick,

(vii) A cell does not possess central vacuole. Instead small vacuoles may occur,

(viii) Centrioles occur in the ceils,

(x) Plastids and photosynthetic pigments are absent,

(xi) The organisms have holozoic or ingestive type of nutrition. A few animals are, however, parasitic. They live on or inside the bodies of other eukaryotes,

(xii) Animals are motile or mobile as they have to search for their food. Sponges and corals are an exception,

(xiii) The organisms possess muscle cells for their mobility and nerve cells for conduction of impulses. They are, however, absent in sponges,

(xiv) Reproduction is mostly sexual. Regeneration of whole organism and formation of spores are found in lower animals,

(xv) Embryo stage is present,

(xvi) Ecologically animals are consumers. These consumers constitute links in the food chains and food webs.

Advantages of Five Kingdom Classification:

1. Separation of prokaryotes in a separate kingdom of Monera is a wise step because prokaryotes differ from all other organisms in their genetic, cellular, reproductive and physi­ological organisation.

2. Many transitional or intermediate forms are present in the unicellular eukaryotes which had been included both amongst plants and animals. Separation of unicellular eukaryotes into kingdom protista has removed this anomaly.

3. Fungi have never been related to plants. They have their own biochemical, physi­ological and structural organisation. Separation of fungi into a separate kingdom was long overdue.

4. The five kingdom classification is based on levels of organisation and nutrition which evolved very early and became established in later groups that are existing today.

5. In this classification, animal and plant kingdoms are more homogeneous than they are in two-kingdom classification.

6. It has tried to bring out phylogenetic relationships even amongst the primitive forms.

Drawbacks of Five Kingdom Classification:

1. In real terms the phylogenetic system cannot be established till all the distinct evolu­tionary tendencies are separated. This is not possible at the lower level.

For example, certain green algae are known to obtain hydrogen from sources other than water like pho­tosynthetic bacteria, Similarly, Euglena can be photosynthetic as well as saprotrophic. Its relatives can have absorptive as well as ingestive type of heterotrophic nutrition.

2. A distinction between unicellular and multicellular organisms is not possible in case of algae. It is because of this that unicellular green algae have not been included in kingdom Protista by Whittaker.

3. Each group has so many diversities that it is difficult to keep them together. For example, monera and protista contain both walled and wall-less organisms, photosynthetic and non-photosynthetic organisms, unicellular and filamentous or mycelial organisms.

4. Viruses have not been included in this system of classification.

5. Archaebacteria differ from other bacteria in structure, composition and physiology.

6. Mycoplasmas are quite different from bacteria where they have been placed along with prokaryotes.


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