Fungal genome explained

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. 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] __TOC__

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. Major chromosomal rearrangements in fungi were found to be more frequent than in other eukaryotes, thus macrosynteny in fungi is rare. 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]

Notes and References

  1. Mohanta TK, Bae H . The diversity of fungal genome . Biological Procedures Online . 17 . 8 . 2015 . 25866485 . 4392786 . 10.1186/s12575-015-0020-z . free .
  2. Stajich JE . Fungal Genomes and Insights into the Evolution of the Kingdom . Microbiology Spectrum . 5 . 4 . July 2017 . 619–633 . 28820125 . 6078396 . 10.1128/microbiolspec.FUNK-0055-2016 . 9781555819576 .
  3. Zajc J, Liu Y, Dai W, Yang Z, Hu J, Gostinčar C, Gunde-Cimerman N . Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent . BMC Genomics . 14 . 617 . September 2013 . 24034603 . 3849046 . 10.1186/1471-2164-14-617 . free .
  4. Padamsee M, Kumar TK, Riley R, Binder M, Boyd A, Calvo AM, Furukawa K, Hesse C, Hohmann S, James TY, LaButti K, Lapidus A, Lindquist E, Lucas S, Miller K, Shantappa S, Grigoriev IV, Hibbett DS, McLaughlin DJ, Spatafora JW, Aime MC . 6 . 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 . March 2012 . 22326418 . 10.1016/j.fgb.2012.01.007 .
  5. Morand SC, Bertignac M, Iltis A, Kolder IC, Pirovano W, Jourdain R, Clavaud C . Malassezia restricta CBS 7877, an Opportunist Pathogen Involved in Dandruff and Seborrheic Dermatitis . Microbiology Resource Announcements . 8 . 6 . February 2019 . 30746521 . 6368656 . 10.1128/MRA.01543-18 .
  6. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG . 6 . Life with 6000 genes . Science . 274 . 5287 . 546, 563–7 . October 1996 . 8849441 . 10.1126/science.274.5287.546 . 1996Sci...274..546G . 16763139 .
  7. Galagan JE, Henn MR, Ma LJ, Cuomo CA, Birren B . Genomics of the fungal kingdom: insights into eukaryotic biology . Genome Research . 15 . 12 . 1620–31 . December 2005 . 16339359 . 10.1101/gr.3767105 . free .
  8. Todd RT, Forche A, Selmecki A . Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution . Microbiology Spectrum . 5 . 4 . July 2017 . 599–618 . 28752816 . 5656283 . 10.1128/microbiolspec.FUNK-0051-2016 . 9781555819576 .
  9. Hane JK, Rouxel T, Howlett BJ, Kema GH, Goodwin SB, Oliver RP . A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi . Genome Biology . 12 . 5 . R45 . 2011-05-24 . 21605470 . 3219968 . 10.1186/gb-2011-12-5-r45 . free .
  10. Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ . 6 . Rhodotorula taiwanensis MD1149 . English . Frontiers in Microbiology . 8 . 2528 . 2018 . 29375494 . 5766836 . 10.3389/fmicb.2017.02528 . free .
  11. Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G, Schacherer J . 6 . Genome evolution across 1,011 Saccharomyces cerevisiae isolates . Nature . 556 . 7701 . 339–344 . April 2018 . 29643504 . 6784862 . 10.1038/s41586-018-0030-5 . 2018Natur.556..339P .
  12. Gostinčar C, Turk M, Zajc J, Gunde-Cimerman N . Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist . Environmental Microbiology . 21 . 10 . 3638–3652 . October 2019 . 31112354 . 6852026 . 10.1111/1462-2920.14693 .
  13. Gostinčar C, Sun X, Zajc J, Fang C, Hou Y, Luo Y, Gunde-Cimerman N, Song Z . 6 . Wallemia ichthyophaga . Frontiers in Microbiology . 10 . 2019 . 2019-09-04 . 31551960 . 6738226 . 10.3389/fmicb.2019.02019 . free .
  14. Sun X, Gostinčar C, Fang C, Zajc J, Hou Y, Song Z, Gunde-Cimerman N . Wallemia mellicola . Genes . 10 . 6 . 427 . June 2019 . 31167502 . 6628117 . 10.3390/genes10060427 . free .
  15. Gostinčar C, Stajich JE, Zupančič J, Zalar P, Gunde-Cimerman N . Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast . BMC Genomics . 19 . 1 . 364 . May 2018 . 29764372 . 5952469 . 10.1186/s12864-018-4751-5 . free .
  16. Robbertse B, Strope PK, Chaverri P, Gazis R, Ciufo S, Domrachev M, Schoch CL . Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case . Database . 2017 . January 2017 . 29220466 . 5641268 . 10.1093/database/bax072 .
  17. Libkind. D.. Čadež. N.. Opulente. D. A.. Langdon. Q. K.. Rosa. C. A.. Sampaio. J. P.. Gonçalves. P.. Hittinger. C. T.. Lachance. M. A.. 2020-09-01. Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences. FEMS Yeast Research. 20. 6. 10.1093/femsyr/foaa042. 1567-1364. 32710773. free.
  18. Magain N, Miadlikowska J, Mueller O, Gajdeczka M, Truong C, Salamov AA, Dubchak I, Grigoriev IV, Goffinet B, Sérusiaux E, Lutzoni F . 6 . Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon . Molecular Phylogenetics and Evolution . 117 . 10–29 . December 2017 . 28860010 . 10.1016/j.ympev.2017.08.013 . 2268/214605 . free . free .
  19. Gostinčar C, Ohm RA, Kogej T, Sonjak S, Turk M, Zajc J, Zalar P, Grube M, Sun H, Han J, Sharma A, Chiniquy J, Ngan CY, Lipzen A, Barry K, Grigoriev IV, Gunde-Cimerman N . 6 . Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species . BMC Genomics . 15 . 1 . 549 . July 2014 . 24984952 . 4227064 . 10.1186/1471-2164-15-549 . free .
  20. Nguyen HD, Sultana T, Kesanakurti P, Hambleton S . Tilletia species to identify candidate genes for the detection of regulated species infecting wheat . IMA Fungus . 10 . 1 . 11 . 2019-07-24 . 32355611 . 10.1186/s43008-019-0011-9 . 7184893 . free .
  21. Gostinčar C . Towards Genomic Criteria for Delineating Fungal Species . Journal of Fungi . 6 . 4 . 246 . October 2020 . 33114441 . 10.3390/jof6040246. 7711752 . free .

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