Journal of ISSN: 2469 - 2786 JBMOA

Bacteriology & Mycology: Open Access
Mini Review
Volume 2 Issue 6 - 2016
Whole Genome Analysis of Fungi
Kuo David HW*
Department of Environmental Science and Engineering, Tunghai University, Taiwan
Received: June 20, 2016 | Published: November 02, 2016
*Corresponding author: Kuo David HW, Department of Environmental Science and Engineering, Tunghai University, Taiwan, Email:
Citation: David HWK (2016) Whole Genome Analysis of Fungi. J Bacteriol Mycol Open Access 2(6): 00043. DOI: 10.15406/jbmoa.2016.02.00043

Abstract

Fungi represent a ubiquitous but highly-diverse biology group of life on the earth. They are crucial players for human, ecosystems, and environments in many matters such as chemotherapy, bioremediation, pest control, food supply, biofuel production, carbon sequestration, or climate management. Current analyses of fungal genomes have significantly enhanced our understanding about fungal diversity, genome structure, genetic/proteomic functionality et cetera and improved our utilizations of these amazing organisms. This mini review is aimed to summarize some recent sequencing projects done for fungal whole genomes and briefly elucidate information been explored from these fungal genomic analyses.

Kingdom Fungi

Under the Eukaryota domain, kingdom fungi includes a group of organisms which are either unicellular (e.g., molds or yeasts) or multicellular (e.g., mushrooms). Uniquely, these organisms have chitin-containing cell walls making them different from other kingdoms (i.e., bacteria, plants, or animals). From anthropological point of views, some fungi are valuable but some are harmful with certain impacts for ecosystems as well as environments on the earth. While some fungi are pathogenic for human, many of others may have different functions such as biotrophic, symbiotic, saprotrophic, or entomopathogenic etc; thus, are essential players for human’s uses in matters of chemotherapy, bioremediation, pest control, food providing, biofuel production, carbon sequestration, or climate management.

Up to now, overall fungal types have been estimated to be around 1.5-5 million species; but currently, only some of them have been well identified and further classified into 7 phyla under the kingdom fungi (including Ascomycota, Basidiomycota, Blastocladiomyceta, Chytridiomycota, Glomeromycota, Microsporidia, and Neocallimastigomycota). In this taxonomical system, two other previously-defined phyla of Anamorphic and Zygomycota had lately been eliminated but still have been kept using by some mycology researchers. Fundamental research works for evaluating fungal diversity, genome structure, genetic/proteomic functionality et cetera are still essential developing subjects to be explored continually. Recent technique improvements of metagenomic sequencing approach have made it feasible to analyze whole genome of fungi which has truly opened another innovative door to enhancing our understanding and exploitation of fungi.

Whole Genomes of Fungi

 During the past decade, several fungal whole genomes had been completed (Table 1). For instance, some entomopathogenic fungi such as Beauveria bassiana [1], Cordyceps mulitaris [2], Metarhizium anisopliae [3] had been comparatively analyzed for their genomes (~30-40 Mbps) and found a complex set of secreted proteins has evolved in entomopathogenicity [3]. This finding may help humankind to control some agricultural insect pests or some insect-borne human diseases.

Phylum

Species

Features

Size (Mbps)

References

 

Beauveria bassiana

entomopathogenic

~33.7

Xiao et al. [1]

 

Botrytis cinerea

necrotrophic

~39.5

Amselem et al. [4]

 

Cordyceps militaris

entomopathogenic

~32.2

Zheng et al. [2]

Ascomycota

Daldinia eschscholzii

lignocellulosic

~35.5

Ng et al. [7]

 

Metarhizium anisopliae

entomopathogenic

~38.5

Staats et al. [3]

 

Neurospora crassa

Saprotrophic

~38.6

Galagan et al. [6]

 

Sclerotinia sclerotiorum

necrotrophic

~38.3

Amselem et al. [4]

 

Trichoderma reesei

lignocellulosic

~33.9

Martinez et al. [8]

 

Laccaria bicolor

ectomycorrhizal

~65.0

Martin et al. [5]

Basidomycota

Phanerochaete chrysospoeium

lignocellulosic

~29.9

Martinez et al. [11]

 

Paxillus rubicundulus

mycorrhizal

~53.0

Kohler et al. [9]

Table 1: Some examples of fungal whole genomes.

Besides, genome sequences of two necrotrophic fungi (i.e., Botrytis cinerea and Sclerotinia sclerotiorum) were determined to examine genomic features that may distinguish them from saprotrophic and other pathogenic fungi [4] but, no unique feature in their genomes was found to distinguish B. cinerea and S. sclerotiorum from other pathogenic and non-pathogenic fungi [4].

Additionally, some fungi capable of secreting lignocellulosic enzymes (e.g., Trichoderma reesei, Neurospora crassa, and Daldinia eschscholzii) had also been analyzed for their genome sequences [5-7]. These analyses explored some unexpected aspects. For example, T. reesei genome encodes fewer celluloses and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides [8].

N. crassa genome includes some genes potentially associated with red light photobiology, some genes implicated in secondary metabolism and some genes involved unique calcium ion signaling [6]. Moreover, genomes of mycorrhizal symbiotic fungi such as Laccaria bicolor and Paxillus rubicundulus also had been reported [8,9]. In L. bicolor genome, some ectomycorrhizae-specific small secreted proteins (SSPs) were found which probably have a decisive role in the establishment of the symbiosis; but, no carbohydrate-active enzymes involved in degradation of plant cell walls were found [5]. The genomic information allows deeper understanding for symbionts interactions between the mycorrhizal fungi and plants regarding carbon and nitrogen cycles.

1000 Fungal Genome (1kfg) Project

Recently, a 5-year international collaboration project, so called 1000 fungal genome (1KFG) project, has been conducted by the Joint Genome Institute (JGI) of the US Department of Energy in attempt to sequence 1000 fungal genomes from across the kingdom fungi (at least 2 reference genomes from each of more than 500 recognized families of fungi) [10]. Up to early 2016, at least 70 fungal whole genomes had been completed; and, further analyses on genome comparison had also been done to better understand genomic structures, genetic components, similarities, differences, etc [3]. For instance, genomes of 13 ectomycorrhizae (EMC) fungal species had been comparatively analyzed and came out with a finding of a unique array of plant cell wall-degrading enzymes (PCWDEs) suggesting these EMC fungi possess diverse abilities to decompose lignocelluloses [3]. Consequences of the 1KFG project would provide further information about fungal genome, diversity, functionality [11].

Future Perception

Despite of several bioinformatics challenges regarding sequence assembly, gene annotation, and genome comparison still need to be conquered for better manipulation of metagenomic sequencing results, better understanding fungal genomes has truly opened another inventive door to improving our utilization and reservation for fungi. Recent outcomes of fungal whole genomes have approved impacts of such analyses on humankind. It is essential to continually explore fungal whole genomes to full-fill some of our knowledge gaps on fungi.

References

  1. Xiao G, Ying SH, Zheng P, Wang ZL, Zhang S, et al. (2012) Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana. Sci Rep 2: 483-492.
  2. Zheng P, Xia Y, Xiao G, Xiong C, Hu X, et al. (2011) Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine. Genome Biol 12(11): R116.
  3. Staats CC, Junges A, Guedes RL, Thompson CE, de Morais GL, et al. (2014) Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins. BMC Genomics 15: 822.
  4. Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, et al. (2011) Genomic analysis of the Necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLOS Genetics 7(8): e1002230.
  5. Martin F, Aerts A, Ahren D, Brun A, Danchin EG, et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-93.
  6. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
  7. Ng KP, Ngeow YF, Yew SM, Hassan H, Soo-Hoo TS, et al. (2012) Draft genome sequence of Daldinia eschscholzii isolated from blood culture. Eukaryotic Cell 11(5): 703-704.
  8. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, et al. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology 26(5): 553-560.
  9. Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, et al. (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genetics 47(4): 410-415.
  10. US DOE (2016) 1000 Fungal Genomes Project.
  11. Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology 22(6): 695-700.
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