Fungal genome

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Fungal genomes are among the smallest genomes of eukaryotes. The sizes of fungal genomes range from less than 10 Mbp to hundreds of Mbp. [1] [2] The average genome size is approximately 37 Mbp in Ascomycota, 47 Mbp in Basidiomycota and 75 Mbp in Oomycota. [1] The sizes and gene numbers of the smallest genomes of free-living fungi such as those of Wallemia ichthyophaga , Wallemia mellicola or Malassezia restricta are comparable to bacterial genomes. [3] [4] [5] The genome of the extensively researched yeast Saccharomyces cerevisiae contains approximately 12 Mbp and was the first completely sequenced eukaryotic genome. [6] Due to their compact size fungal genomes can be sequenced with less resources than most other eukaryotic genomes and are thus important models for research. [7] Some fungi exist as stable haploid, diploid, or polyploid cells, others change ploidy in response to environmental conditions and aneuploidy is also observed in novel environments or during periods of stress. [8]

Contents

Genome comparisons

The comparison of fungal genomes has been used to study the evolution of fungi, to improve the resolution of the phylogeny of fungal species, and to determine the time of the emergence and changes in species traits and lifestyles, such as the evolution symbiotic or pathogenic interactions, and the evolution of different morphologies. [2] Major chromosomal rearrangements in fungi were found to be more frequent than in other eukaryotes, thus macrosynteny in fungi is rare. [9] However, in filamentous ascomycetes genes were found to be conserved within homologous chromosomes, but with randomized orders and orientations, a phenomenon named mesosynteny. [9] Mesosynteny was also observed in the basidiomycetous genus Rhodotorula . [10] A comparison of more than 1000 Saccharomyces cerevisiae genomes was used to identify the geographical origin and several domestication events of the species as well as map genomic variants to the species-wide phenotypic landscape of the yeast. [11] Comparisons of several genomes of the same species led to discovery of high levels of recombination in species that were previously considered asexual. [12] [13] [14] In the extremely halotolerant black yeast Hortaea werneckii it was discovered that while the species is clonal, both haploid and diploid strains can be found in nature and the diploid strains are highly heterozygous hybrids, which appear to be stable over large time scales and geographical distances. [15]

Use in taxonomy

While genomic distance measures such as the average nucleotide identity (ANI) are used routinely to distinguish bacterial species, the use of fungal genomes in taxonomy is currently rare. Genome sequences can be used to expand the number of genes used in phylogenetic analyses, but many publicly available genomes lack gene annotations and popular rDNA markers are typically missing from genomic sequences or are incorrectly assembled. [16] Suggested measures of overall genome related indices in yeast include ANI, digital DNA–DNA hybridization (dDDH) and Kr distance. [17] Genomic collinearity was suggested as a possible source of markers to resolve species complexes. [18] Pairwise Kr genomic distances and average nucleotide identity were used in the description of new species within the genera Aureobasidium and Tilletia . [19] [20]

Alternatively, quick and simple to calculate similarity measures based on MinHash also appear to produce usefully accurate estimates of distance between genomes. For example, a fixed threshold genomic distance calculated tools such as Mash and Dashing was able to determine whether two genomes belong to the same or to different species with over 90% accuracy, indicating that simple measures of genomic distance might be useful to delineate fungal species and still largely support the existing fungal taxonomy. [21]

Related Research Articles

Halotolerance is the adaptation of living organisms to conditions of high salinity. Halotolerant species tend to live in areas such as hypersaline lakes, coastal dunes, saline deserts, salt marshes, and inland salt seas and springs. Halophiles are organisms that live in highly saline environments, and require the salinity to survive, while halotolerant organisms can grow under saline conditions, but do not require elevated concentrations of salt for growth. Halophytes are salt-tolerant higher plants. Halotolerant microorganisms are of considerable biotechnological interest.

<span class="mw-page-title-main">Basidiomycota</span> Division of fungi

Basidiomycota is one of two large divisions that, together with the Ascomycota, constitute the subkingdom Dikarya within the kingdom Fungi. Members are known as basidiomycetes. More specifically, Basidiomycota includes these groups: agarics, puffballs, stinkhorns, bracket fungi, other polypores, jelly fungi, boletes, chanterelles, earth stars, smuts, bunts, rusts, mirror yeasts, and Cryptococcus, the human pathogenic yeast.

<span class="mw-page-title-main">GC-content</span> Percentage of guanine and cytosine in DNA or RNA molecules

In molecular biology and genetics, GC-content is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out of an implied four total bases, also including adenine and thymine in DNA and adenine and uracil in RNA.

The Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. Further information is located at the Yeastract curated repository.

<i>Eremothecium gossypii</i> Species of fungus

Eremothecium gossypii (also known as Ashbya gossypii) is a filamentous fungus or mold closely related to yeast, but growing exclusively in a filamentous way. It was originally isolated from cotton as a pathogen causing stigmatomycosis by Ashby and Nowell in 1926. This disease affects the development of hair cells in cotton bolls and can be transmitted to citrus fruits, which thereupon dry out and collapse (dry rot disease). In the first part of the 20th century, E. gossypii and two other fungi causing stigmatomycosis (Eremothecium coryli, Aureobasidium pullulans) made it virtually impossible to grow cotton in certain regions of the subtropics, causing severe economical losses. Control of the spore-transmitting insects - cotton stainer (Dysdercus suturellus) and Antestiopsis (antestia bugs) - permitted full eradication of infections. E. gossypii was recognized as a natural overproducer of riboflavin (vitamin B2), which protects its spores against ultraviolet light. This made it an interesting organism for industries, where genetically modified strains are still used to produce this vitamin.

<i>Aureobasidium pullulans</i> Species of fungus

Aureobasidium pullulans is a ubiquitous and generalistic black, yeast-like fungus that can be found in different environments. It is well known as a naturally occurring epiphyte or endophyte of a wide range of plant species without causing any symptoms of disease. A. pullulans has a high importance in biotechnology for the production of different enzymes, siderophores and pullulan. Furthermore, A. pullulans is used in biological control of plant diseases, especially storage diseases.

Pathogenic fungi are fungi that cause disease in humans or other organisms. Although fungi are eukaryotic, many pathogenic fungi are microorganisms. Approximately 300 fungi are known to be pathogenic to humans; their study is called "medical mycology". Fungal infections kill more people than either tuberculosis or malaria—about 2 million people per year.

<i>Hortaea werneckii</i> Species of fungus

Hortaea werneckii is a species of yeast in the family Teratosphaeriaceae. It is a black yeast that is investigated for its remarkable halotolerance. While the addition of salt to the medium is not required for its cultivation, H. werneckii can grow in close to saturated NaCl solutions. To emphasize this unusually wide adaptability, and to distinguish H. werneckii from other halotolerant fungi, which have lower maximum salinity limits, some authors describe H. werneckii as "extremely halotolerant".

<span class="mw-page-title-main">Wallemiomycetes</span> Class of fungi

The Wallemiomycetes are a class of fungi in the division Basidiomycota. It consists of the single order Wallemiales, containing the single family Wallemiaceae, which in turn contains the single genus Wallemia. The phylogenetic origin of the lineage was placed to various parts of Basidiomycota, but according to the analysis of a larger dataset it is a sister group of Agaricomycotina. The genus contains species of xerophilic molds that are found worldwide. The seven described species are distinguished by conidial size, xerotolerance, halotolerance, chaotolerance, growth temperature regimes, extracellular enzyme activity profiles, and secondary metabolite patterns. They are typically isolated from low-moisture foods, indoor air dust, salterns and soil. W. sebi is thought to be one of the causes of the hypersensitivity pneumonitis known as the farmer's lung disease, but since the other species were recognised and separated from W. sebi only recently, their role in the disease cannot be excluded.

Saccharomyces eubayanus, a cryotolerant type of yeast, is most likely the parent of the lager brewing yeast, Saccharomyces pastorianus.

Black yeasts, sometimes also black fungi, dematiaceous fungi, microcolonial fungi or meristematic fungi is a diverse group of slow-growing microfungi which reproduce mostly asexually. Only few genera reproduce by budding cells, while in others hyphal or meristematic (isodiametric) reproduction is preponderant. Black yeasts share some distinctive characteristics, in particular a dark colouration (melanisation) of their cell wall. Morphological plasticity, incrustation of the cell wall with melanins and presence of other protective substances like carotenoids and mycosporines represent passive physiological adaptations which enable black fungi to be highly resistant against environmental stresses. The term "polyextremotolerance" has been introduced to describe this phenotype, an example of which is the species Aureobasidium pullulans. Presence of 1,8-dihydroxynaphthalene melanin in the cell wall confers to the microfungi their characteristic olivaceous to dark brown/black colour.

<i>Wallemia sebi</i> Species of fungus

Wallemia sebi is a xerophilic fungus of the phylum Basidiomycota.

<i>Wallemia ichthyophaga</i> Species of fungus

Wallemia ichthyophaga is one of the three species of fungi in the genus Wallemia, which in turn is the only genus of the class Wallemiomycetes. The phylogenetic origin of the lineage was placed to various parts of Basidiomycota, but according to the analysis of larger datasets it is a (495-million-years-old) sister group of Agaricomycotina. Although initially believed to be asexual, population genomics found evidence of recombination between strains and a mating type locus was identified in all sequenced genomes of the species.

Previously classified under the species complex Aureobasidium pullulans, Aureobasidium subglaciale is a black yeast-like, extremophile, ascomycete fungus that is found in extreme cold habitats. The species was originally isolated from subglacial ice of arctic glaciers. The first isolate of this species was obtained from subglacial ice of the Norwegian island Spitsbergen, one of the coldest places inhabited by humans. of Genomic data collected from specimens in the Aureobasidium pullulans complex justified distinction of four different species

Aureobasidium melanogenum, formerly known as Aureobasidium pullulans var. melanogenum is a ubiquitous black, yeast-like fungus that is found mainly in freshwater habitats. The species also includes strains causing human infections, which were previously classified as A. pullulans. It was named due to abundant melanin production and accumulation in the cell walls, which leads to dark green, brown or black appearance of the cells and colonies The species was established when the genomes of the four former varieties of Aureobasidium pullulans were sequenced and the large differences between them were discovered.

Aureobasidium namibiae, formerly known as Aureobasidium pullulans var. namibiae is a ubiquitous black, yeast-like fungus. It was described on the basis of only one strain isolated from dolomitic marble in Namibia. The species was established when the genomes of the four former varieties of Aureobasidium pullulans were sequenced and the large differences between them were discovered.

<span class="mw-page-title-main">Joseph Heitman</span>

Joseph Heitman is an American physician-scientist focused on research in genetics, microbiology, and infectious diseases. He is the James B. Duke Professor and Chair of the Department of Molecular Genetics and Microbiology at Duke University School of Medicine.

ERG5 or Sterol 22-desaturase is a cytochrome P450 enzyme in the ergosterol biosynthesis pathway of fungi Saccharomyces cerevisiae, with the CYP Symbol CYP61A1. CYP61A1 is one of only three P450 enzyme found in baker's yeast, the other two are CYP51F1 and CYP56A1. The ortholog in Schizosaccharomyces pombe, was named CYP61A3 for historical reasons, and is only one of two P450 enzyme found with CYP51F1. ERG5 catalyzes the C22-C23 double bond formation on the sterol side chain of ergostatrienol to convert it into ergostatetraenol, then the C24 double bond of ergostatetrenol will be hydrogenation reduced into ergosterol by ERG4.

Wallemia mellicola is a xerophilic fungus of the phylum Basidiomycota, described in 2015 upon taxonomic revision of the species Wallemia sebi. A large amount of published research referring to W. sebi was likely actually performed on W. mellicola. An example of this is the sequencing of the W. mellicola genome, which was published under the name of W. sebi.

References

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  4. ↑ Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, et al. (March 2012). "The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction". Fungal Genetics and Biology. 49 (3): 217–26. doi:10.1016/j.fgb.2012.01.007. PMID   22326418.
  5. ↑ Morand SC, Bertignac M, Iltis A, Kolder IC, Pirovano W, Jourdain R, Clavaud C (February 2019). "Malassezia restricta CBS 7877, an Opportunist Pathogen Involved in Dandruff and Seborrheic Dermatitis". Microbiology Resource Announcements. 8 (6). doi:10.1128/MRA.01543-18. PMC   6368656 . PMID   30746521.
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  12. ↑ Gostinčar C, Turk M, Zajc J, Gunde-Cimerman N (October 2019). "Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist". Environmental Microbiology. 21 (10): 3638–3652. doi:10.1111/1462-2920.14693. PMC   6852026 . PMID   31112354.
  13. ↑ Gostinčar C, Sun X, Zajc J, Fang C, Hou Y, Luo Y, et al. (2019-09-04). "Wallemia ichthyophaga". Frontiers in Microbiology. 10: 2019. doi: 10.3389/fmicb.2019.02019 . PMC   6738226 . PMID   31551960.
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