The Diversity of Fungal Genome Tapan Kumar Mohanta* and Hanhong Bae*
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Mohanta and Bae Biological Procedures Online (2015) 17:8 DOI 10.1186/s12575-015-0020-z Biological Procedures Online REVIEW Open Access The diversity of fungal genome Tapan Kumar Mohanta* and Hanhong Bae* Abstract The genome size of an organism varies from species to species. The C-value paradox enigma is a very complex puzzle with regards to vast diversity in genome sizes in eukaryotes. Here we reported the detailed genomic information of 172 fungal species among different fungal genomes and found that fungal genomes are very diverse in nature. In fungi, the diversity of genomes varies from 8.97 Mb to 177.57 Mb. The average genome sizes of Ascomycota and Basidiomycota fungi are 36.91 and 46.48 Mb respectively. But higher genome size is observed in Oomycota (74.85 Mb) species, a lineage of fungus-like eukaryotic microorganisms. The average coding genes of Oomycota species are almost doubled than that of Acomycota and Basidiomycota fungus. Keywords: Ascomycota, Basidiomycota, Chytridiomycota, Monoblepharidomycota, Neocallimastigomycota, Blastocladiomycota, Glomeromycota, Entomophthoromycota, Stramenopiles and micorsporidia Introduction fungus makes them important from an evolutionary point Fungi are the larger group of eukaryotic organisms that of view. That is why fungi are subjected to intense phylo- ranges from yeast and slime molds to mushrooms. These genetic, ecological and molecular studies. The advancement organisms are majorly classified as monophyletic Eumycota in high throughput sequencing technology progressed rap- group and their diversity ranges from 500 thousand to 9.9 idly that led to sequencing of large numbers of fungal ge- million spanning over 1 billion years of evolutionary his- nomes. The evolution of biological diversity raises several tory [1,2]. They are abundant at worldwide scale due to questions such as how much variation can be expected their small size and their cryptic lifestyle in soil, dead and among closely or related genomes. This can be answered decomposing matter, as symbionts with algae, fungi, bryo- by the comparing closely related genomes. So we carried phyte, pteridophyte, higher plants and animals [3-7]. These out a global search of fungal genomes in MycoCosm and organisms dominate earth from polar to temperate and JGI database and studied the evolutionary relationships of tropical habitats [8-10]. Due to their ecological dominance, their genome sizes and reported here [24-26]. they play a central role in human endeavor. The fungus (mushroom and truffle) are directly used as human food and yeasts are used in bread industry. The fungi also carry Fungal genome size out nutrient cycling by decomposing organic matter Recently, the genome sequencing technology has emerged [11-13]. They also produce antibiotics, enzymes, myco- as one of the most efficient tools that can provide whole toxins, alkaloids, polyketides and other chemical com- information of a genome in a small period of time. Since pounds [14-21]. the completion of genome sequencing of the model fun- The kingdom fungi are classified into several major gus S. cerevisae in 1996, sequencing of large numbers of phyla namely Ascomycota, Basidiomycota, Chytridio- fungal genomes are now completed. Sequencing of large mycota, Monoblepharidomycota, Neocallimastigomycota, numbers of fungal genomes will allow us to understand Blastocladiomycota, Glomeromycota, Entomophthoromy- the diversity of genes encoding enzymes, and pathways cota, Stramenopiles and Micorsporidia and sub-phyla that produces several novel compounds [24]. Although namely Kickxellomycotina, mucoromycotina and Zoopa- the fungi are very diverse in nature, their basic cellular gomycotina [22,23]. The diverse ecological dominance of physiology and genetics shares some common compo- nents with plants and animal cells. These include multi- cellularity, cytoskeletal structures, cell cycle, circadian * Correspondence: [email protected]; [email protected] Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of rhythm, intercellular signaling, sexual reproduction, devel- Korea opment and differentiation [27]. It was previously thought © 2015 Mohanta and Bae; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Mohanta and Bae Biological Procedures Online (2015) 17:8 Page 2 of 9 that genomes of all fungi are derived from the genome of potential [33]. But in exception, for example, the duck- the model fungi Saccharomyces cerevisae [27]. However weeds which are smallest, fast-growing and simplest flow- recent explosion in fungal genome sequencing greatly ex- ering plants are invasive in nature and contains increased panded the fungal genomics and molecular diversity of DNA content in their genomes [34]. these organisms. Compared to the genome size of animals and plants, the genome sizes of fungi are small [28]. The Evolution in genome size genome size of model fungi S. cerevisae is bit more than Genomes are aggregates of genes and this concept nicely 12 Mb (Table 1). From the studied 172 fungal species, only fits with the prokaryotic organisms and viruses [35]. This seven species have genome sizes larger than 100 Mb concept is very inappropriate for eukaryotic organisms (Table 1). So, the probability of occurrence of larger ge- as most of the eukaryotic genomes are studded with nomes in fungi is very small. The genome size of Cenococ- nongenic and unconstrained repetitive DNA. This can cum geophilum (177.57 Mb) is the largest and the genome lead to approximately 200,000 fold variation in genome size of Hansenula polymorpha (8.97 Mb) is the smallest size [36]. The genome size of an organism depends on from the studied species. Both species belong to Ascomy- the particular developmental and ecological need of the cota. In the group of Basidiomycota species, the genome organism [37]. The genes are made up of DNA and it is size of Wallemia sebi (9.82 Mb) is the smallest one and a general assumption that more complex organisms re- genome of Dendrothele bispora (130.65) is the largest one quires more genes and thus contain more DNA in its ge- (Table 1). No single species from Chytridiomycota, Glo- nomes. The simple organisms probably contain fewer meromycota, Oomycota, Stramenopiles, Mucoromycotina essential genes compared to more complex organisms have genome size larger than 100 Mb. Although there is and thus contain less DNA in its genomes. However this large variation in genome size in fungi, the average gen- observation is not true. Some very simple organisms ome size of fungal species taken during this study is 42. 30 could have more DNA content than complex multi- Mb (Table 1). The average genome sizes of fungal species cellular organisms. For example, some amoeba species belonging to different phyla are provided in Table 2. From have 200 times more DNA than humans [38]. Similarly, the table we can observe that the average genome size of lilies have 200 times more DNA than that of rice [39]. Ascomycota group of fungi is 36.91 Mb. The average gen- But in many organisms much of the DNA content is ome size of Basidiomycota group is 46.48 Mb. The average noncoding and repetitive. But it is very important to genome size of Oomycota group of fungi is 74.85 Mb understand which evolutionary forces produces enor- which is the highest among all groups (Table 2). If we con- mous amount of noncoding DNA? What are the adap- sider about the coding gene sequence in fungi, in average tive functions of these nongenic DNA? If these nongenic the Acomycota, Basidiomycota, Oomycota and Mucoro- DNA don’t have any essential adaptive roles, than why mycotina groups encodes for 11129.45, 15431.51, 24173.33, natural selection favors the burden of synthesis of extra 13306 no. of genes respectively in their genomes (Table 2). DNA? Several hypotheses are postulated since long days The comparative analysis of fungal genomes show fungi to address these questions. But still there is debate over are very divergent [27]. It was earlier thought that ge- it. Some of the hypotheses are discussed later. From the nomes of Magnaporthe grisea and Neurospora crassa studied fungal genomes, the average genome sizes of share a common ancestor. But, comparative genomes ana- Oomycota species (74.85 Mb) are higher than other. The lyses revealed only 47% amino acid sequence identity and Ascomycota and Mucoromycotina species shares more absence of conserved synteny [27]. Only few genes are or less than same average genome size i.e. 36.91 and identified to be in conserved co-linearity. This shows that 37.02 Mb, respectively. In contrary, the average genome even members of the same genus can show remarkable sizes of Basidiomycota species is 46.48 Mbs. The in- divergence at the genomic level. A genomic comparison crease in genome size in Oomycota species is also dir- between Aspergillus nidulans, Aspergillus fumigatus and ectly correlated with the increase in the numbers of Aspergillus oryzae shows only 68% of amino acid sequence average coding gene sequences. The average numbers of identity [27]. The genome duplication and translocation coding genes present in Oomycota species are 24173.33 have major impact in evolution in yeast (Figure 1) [29,30]. genes per genome which is almost the double number The whole genome duplication in yeast followed by present in Ascomycota and Basidiomycota species. massive gene loss is confirmed by comparative experimen- tal analysis [31,32]. This indicates that fungal genomes are The adaptive theories of genome evolution very dynamic in nature. Lavergne et al. [33] reported that If certain numbers of genes are responsible for the genome size reduction can trigger rapid phenotypic evolu- phenotype and genotypic characters of an organism, why tion in invasive plants.