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. 2015 Apr 2;17:8. doi: 10.1186/s12575-015-0020-z

The diversity of fungal genome

Tapan Kumar Mohanta 1,✉, Hanhong Bae 1,✉
PMCID: PMC4392786  PMID: 25866485

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

Fungi are the larger group of eukaryotic organisms that ranges from yeast and slime molds to mushrooms. These organisms are majorly classified as monophyletic Eumycota group and their diversity ranges from 500 thousand to 9.9 million spanning over 1 billion years of evolutionary history [1,2]. They are abundant at worldwide scale due to their small size and their cryptic lifestyle in soil, dead and decomposing matter, as symbionts with algae, fungi, bryophyte, pteridophyte, higher plants and animals [3-7]. These organisms dominate earth from polar to temperate and tropical habitats [8-10]. Due to their ecological dominance, 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 out nutrient cycling by decomposing organic matter [11-13]. They also produce antibiotics, enzymes, mycotoxins, alkaloids, polyketides and other chemical compounds [14-21].

The kingdom fungi are classified into several major phyla namely Ascomycota, Basidiomycota, Chytridiomycota, Monoblepharidomycota, Neocallimastigomycota, Blastocladiomycota, Glomeromycota, Entomophthoromycota, Stramenopiles and Micorsporidia and sub-phyla namely Kickxellomycotina, mucoromycotina and Zoopagomycotina [22,23]. The diverse ecological dominance of fungus makes them important from an evolutionary point of view. That is why fungi are subjected to intense phylogenetic, ecological and molecular studies. The advancement in high throughput sequencing technology progressed rapidly that led to sequencing of large numbers of fungal genomes. The evolution of biological diversity raises several questions such as how much variation can be expected among closely or related genomes. This can be answered by the comparing closely related genomes. So we carried out a global search of fungal genomes in MycoCosm and JGI database and studied the evolutionary relationships of their genome sizes and reported here [24-26].

Fungal genome size

Recently, the genome sequencing technology has emerged as one of the most efficient tools that can provide whole information of a genome in a small period of time. Since the completion of genome sequencing of the model fungus S. cerevisae in 1996, sequencing of large numbers of fungal genomes are now completed. Sequencing of large numbers of fungal genomes will allow us to understand the diversity of genes encoding enzymes, and pathways that produces several novel compounds [24]. Although the fungi are very diverse in nature, their basic cellular physiology and genetics shares some common components with plants and animal cells. These include multi-cellularity, cytoskeletal structures, cell cycle, circadian rhythm, intercellular signaling, sexual reproduction, development and differentiation [27]. It was previously thought that genomes of all fungi are derived from the genome of the model fungi Saccharomyces cerevisae [27]. However recent explosion in fungal genome sequencing greatly expanded the fungal genomics and molecular diversity of these organisms. Compared to the genome size of animals and plants, the genome sizes of fungi are small [28]. The genome size of model fungi S. cerevisae is bit more than 12 Mb (Table 1). From the studied 172 fungal species, only seven species have genome sizes larger than 100 Mb (Table 1). So, the probability of occurrence of larger genomes in fungi is very small. The genome size of Cenococcum geophilum (177.57 Mb) is the largest and the genome size of Hansenula polymorpha (8.97 Mb) is the smallest from the studied species. Both species belong to Ascomycota. In the group of Basidiomycota species, the genome size of Wallemia sebi (9.82 Mb) is the smallest one and genome of Dendrothele bispora (130.65) is the largest one (Table 1). No single species from Chytridiomycota, Glomeromycota, Oomycota, Stramenopiles, Mucoromycotina have genome size larger than 100 Mb. Although there is large variation in genome size in fungi, the average genome size of fungal species taken during this study is 42. 30 Mb (Table 1). The average genome sizes of fungal species belonging to different phyla are provided in Table 2. From the table we can observe that the average genome size of Ascomycota group of fungi is 36.91 Mb. The average genome size of Basidiomycota group is 46.48 Mb. The average genome size of Oomycota group of fungi is 74.85 Mb which is the highest among all groups (Table 2). If we consider about the coding gene sequence in fungi, in average the Acomycota, Basidiomycota, Oomycota and Mucoromycotina groups encodes for 11129.45, 15431.51, 24173.33, 13306 no. of genes respectively in their genomes (Table 2).

Table 1.

List of genome size (Mb), numbers of coding genes, and average numbers of exons present per fungal species from the different phyla of Kingdom Fungi

Sl. No Name of Fungal Species Division Genome Size Mbp No. Of Contigs No. Of Scaffolds No of Gene Models Average Exons Per Gene
1 Acidomyces richmondensis Ascomycota 29.88 3164 3164 11202 2.28
2 Acremonium alcalophilum Ascomycota 54.42 865 15 9491 4.05
3 Agaricus bisporus Basidiomycota 30.2 254 29 10438 6.05
4 Amanita muscaria Koide Basidiomycota 40.70 3814 1101 18153 4.54
5 Amorphotheca resinae Ascomycota 28.63 261 32 9642 2.97
6 Anthostoma avocetta Ascomycota 56.23 1038 786 15755 2.93
7 Antrodia sinuosa Basidiomycota 30.17 1482 1387 11327 6.09
8 Apiospora montagnei Ascomycota 47.67 706 686 16992 2.52
9 Aplanochytrium kerguelense Stramenopiles 35.77 523 207 11892 2.75
10 Aplosporella prunicola Ascomycota 32.82 763 334 12579 2.67
11 Ascobolus immersus Ascomycota 59.53 1225 706 17877 2.67
12 Ascoidea rubescens Ascomycota 17.50 101 63 6802 1.39
13 Aspergillus acidus Ascomycota 37.47 318 107 13530 3.10
14 Aspergillus niger Ascomycota 34.85 24 24 11910 3.38
15 Atractiellales sp. Basidiomycota 51.47 3076 1998 17606 5.30
16 Aulographum hederae Ascomycota 31.98 613 173 12127 2.66
17 Aurantiochytrium limacinum Stramenopiles 60.93 1118 181 14859 1.45
18 Aureobasidium pullulans Ascomycota 29.62 84 75 10809 2.51
19 Auricularia subglabra Basidiomycota 76.85 2158 761 25459 4.80
20 Babjeviella inositovora Ascomycota 15.22 210 49 6403 1.27
21 Backusella circina Mucoromycotina 48.65 2354 1095 17039 4.25
22 Baudoinia compniacensis Ascomycota 21.88 35 19 10513 2.14
23 Bjerkandera adusta Basidiomycota 42.73 1263 508 15473 5.59
24 Boletus edulis Basidiomycota 46.64 4723 1099 16933 4.88
25 Botryobasidium botryosum Basidiomycota 46.67 1446 334 16526 5.58
26 Calocera cornea Basidiomycota 33.24 1032 545 13177 4.44
27 Calocera viscosa Basidiomycota 29.10 487 214 12378 4.59
28 Candida caseinolytica Ascomycota 9.18 49 6 4657 1.20
29 Catenaria anguillulae Blastocladiomycota 36.22 2577 801 14188 2.50
30 Cenococcum geophilum Ascomycota 177.57 2893 268 27529 4.08
31 Cercospora zeae-maydis Ascomycota 46.61 2555 917 12020 2.32
32 Chalara longipes Ascomycota 52.43 175 54 19765 3.06
33 Choiromyces venosus Ascomycota 126.04 3183 1176 17986 2.84
34 Cochliobolus sativus Ascomycota 34.42 478 157 12250 2.63
35 Coemansia reversa Kickellomycotina 21.84 1063 346 7347 1.51
36 Conidiobolus coronatus Entomophthoromycota 39.90 7809 1050 10635 2.78
37 Coniophora puteana Basdiomycota 42.97 1034 210 13761 6.11
38 Coprinopsis cinerea Basdiomycota 37.5 --- --- --- ---
39 Cortinarius glaucopus Basidiomycota 63.45 2103 769 20377 5.05
40 Cronartium quercuum Basidiomycota 76.57 10431 1198 13903 4.35
41 Cryphonectria parasitica Ascomycota 43.9 33 26 11609 2.91
42 Cryptococcus vishniacii Basidiomycota 19.69 137 50 7232 6.25
43 Cucurbitaria berberidis Ascomycota 32.91 184 42 12439 2.71
44 Cyberlindnera jadinii Ascomycota 13.02 392 76 6038 1.35
45 Cylindrobasidium torrendii Basidiomycota 31.57 1222 1149 13940 5.17
46 Dacryopinax sp. Basidiomycota 29.50 878 99 10242 4.83
47 Daedalea quercina Basidiomycota 32.74 1025 357 12199 5.80
48 Daldinia eschscholzii Ascomycota 37.55 512 398 11173 2.89
49 Dekkera bruxellensis Ascomycota 13.37 1374 84 5600 1.44
50 Dendrothele bispora Basidiomycota 130.65 6351 3942 33645 5.09
51 Dichomitus squalens Basidiomycota 42.75 2852 542 12290 5.84
52 Didymella exigua Ascomycota 34.39 1010 176 12394 2.46
53 Dioszegia cryoxerica Basidiomycota 39.52 1318 865 15948 5.36
54 Dissoconium aciculare Ascomycota 26.54 232 54 10299 2.17
55 Dothidotthia symphoricarpi Ascomycota 34.43 268 59 11790 2.71
56 Eurotium rubrum Ascomycota 26.21 371 110 10076 3.07
57 Exidia glandulosa Basidiomycota 78.17 4024 1727 26765 4.83
58 Exobasidium vaccinii Basidiomycota 16.99 246 119 7453 2.79
59 Fibulorhizoctonia sp. Basidiomycota 95.13 3901 1918 32946 4.63
60 Fomitiporia mediterranea Basidiomycota 63.35 5766 1412 11333 6.06
61 Fomitopsis pinicola Basidiomycota 46.30 988 504 13885 5.56
62 Galerina marginata Basidiomycota 59.42 1272 414 21461 5.30
63 Ganoderma sp. Basidiomycota 39.52 503 156 12910 5.82
64 Gloeophyllum trabeum Basidiomycota 37.18 2289 443 11846 6.14
65 Glomerella acutata Ascomycota 50.04 378 307 15777 2.83
66 Glomerella cingulata Ascomycota 58.84 774 119 18975 2.79
67 Gonapodya prolifera Monoblepharidomycetes 48.79 1154 352 13902 5.58
68 Gymnascella aurantiaca Ascomycota 25.35 356 347 9106 3.12
69 Gymnascella citrina Ascomycota 25.16 305 272 9779 2.99
70 Gyrodon lividus Basidiomycota 43.05 1390 369 11779 5.75
71 Hanseniaspora valbyensis Ascomycota 11.46 1163 646 4800 1.20
72 Hansenula polymorpha Ascomycota 8.97 9 7 5177 1.20
73 Hebeloma cylindrosporum Basidiomycota 37.61 222 222 16841 5.05
74 Heterobasidion annosum Basidiomycota 33.7 18 15 13405 5.54
75 Hydnomerulius pinastri Basidiomycota 38.28 2315 603 13270 5.84
76 Hypholoma sublateritium Basidiomycota 48.03 1329 704 17911 5.29
77 Hyphopichia burtonii Ascomycota 12.40 105 27 6002 1.22
78 Hypoxylon sp. Ascomycota 46.59 580 505 12256 2.90
79 Jaapia argillacea Basidiomycota 45.05 1182 295 5.53 5.53
80 Laccaria amethystina Basidiomycota 52.20 4756 1299 21066 4.49
81 Laccaria bicolor Basidiomycota 60.71 584 55 23132 5.28
82 Laetiporus sulphureus Basidiomycota 39.92 1207 403 13774 5.72
83 Lentinus tigrinus Basidiomycota 39.68 571 286 15581 5.59
84 Leucogyrophana mollusca Basidiomycota 35.19 1347 1262 14619 5.89
85 Lichtheimia hyalospora Mucoromycotina 33.28 2294 2222 12062 4.99
86 Lipomyces starkeyi Ascomycota 21.27 439 117 8192 2.85
87 Lophiostoma macrostomum Ascomycota 42.58 1294 1282 16160 2.74
88 Macrolepiota fuliginosa Basidiomycota 46.40 4852 3478 15801 5.39
89 Melampsora laricis-populina Basidiomycota 101.1 --- 462 19694 ---
90 Melanconium sp. Ascomycota 58.52 465 100 16656 2.68
91 Melanomma pulvis-pyrius Ascomycota 42.09 1771 1754 15881 2.77
92 Meliniomyces bicolor Basidiomycota 82.38 301 206 18619 2.96
93 Metschnikowia bicuspidata Ascomycota 16.06 421 48 5851 1.27
94 Mixia osmundae Basidiomycota 13.63 204 156 6903 4.54
95 Monascus purpureus Ascomycota 23.44 319 296 8918 3.19
96 Monascus ruber Ascomycota 24.80 362 320 9650 3.13
97 Mortierella elongata Mucoromycotina 49.96 3314 473 14964 3.47
98 Mucor circinelloides Mucoromycotina 36.6 26 26 11719 3.8
99 Myceliophthora thermophila Ascomycota 38.74 7 7 9110 2.83
100 Mycosphaerella graminicola Ascomycota 39.7 --- 129 10952 ---
101 Myriangium duriaei Ascomycota 25.69 32 16 10685 2.37
102 Nadsonia fulvescens Ascomycota 13.75 64 20 5657 1.57
103 Neolentinus lepideus Basidiomycota 35.64 1215 331 13164 5.71
104 Neurospora discreta Ascomycota 37.3 --- 176 9948 ---
105 Neurospora tetrasperma Ascomycota 37.8 542 155 10640 2.72
106 Oidiodendron maius Ascomycota 46.43 387 100 16703 2.97
107 Pachysolen tannophilus Ascomycota 12.60 583 198 5675 1.33
108 Patellaria atrata Ascomycota 28.69 501 127 9794 2.97
109 Paxillus rubicundulus Basidiomycota 53.01 7170 6945 22065 3.81
110 Penicillium brevicompactum Ascomycota 32.11 96 35 11536 3.09
111 Penicillium canescens Ascomycota 33.26 248 62 12374 3.12
112 Penicillium janthinellum Ascomycota 35.15 273 94 12098 3.07
113 Penicillium raistrickii Ascomycota 31.44 104 76 11368 3.11
114 Phlebia brevispora Basidiomycota 49.96 3178 1645 16170 5.66
115 Phlebiopsis gigantea Basidiomycota 30.14 1195 573 11891 6.00
116 Phycomyces blakesleeanus Mucoromycotina 53.9 350 80 16528 4.5
117 Phytophthora capsici Oomycota 64 10760 917 19805 2.20
118 Phytophthora cinnamomi Oomycota 77.97 9537 1314 26131 2.10
119 Phytophthora sojae Oomycota 82.60 1643 83 26584 2.39
120 Pichia stipitis Ascomycota 15.4 --- 394 5841 ~1
121 Piedraia hortae Ascomycota 16.95 214 132 7572 1.84
122 Piloderma croceum Basidiomycota 59.33 4469 715 21583 4.75
123 Piromyces sp. Neocallimastigomycota 71.02 17217 1656 14648 3.09
124 Pisolithus microcarpus Basidiomycota 53.03 5476 1064 21064 4.04
125 Pleomassaria siparia Ascomycota 43.18 1023 193 13486 2.81
126 Pleurotus ostreatus Basidiomycota 35.6 3272 572 11603 6.1
127 Polychaeton citri Ascomycota 27.21 451 416 10582 2.12
128 Polyporus arcularius Basidiomycota 43.45 2601 2540 17525 5.27
129 Punctularia strigosozonata Basidiomycota 34.17 1327 195 11538 6.23
130 Pycnoporus sanguineus Basidiomycota 36.04 2046 657 14165 5.59
131 Ramaria rubella Basidiomycota 105.46 5927 1553 19287 5.53
132 Rhizophagus irregularis Glomeromycota 91.08 28405 28371 30282 3.46
133 Rhizopus microsporus Mucoromycotina 25.97 823 131 10905 4.03
134 Rhodotorula graminis Basidiomycota 21.01 620 26 7283 6.24
135 Rickenella mellea Basidiomycota 46.03 1236 1092 18952 4.98
136 Saccharata proteae Ascomycota 31.43 727 245 9234 3.08
137 Saccharomyces cerevisiae Ascomycota 12.07 16 16 6575 1.04
138 Saitoella complicata Ascomycota 14.14 35 35 7034 2.23
139 Schizophyllum commune Loenen D Basidiomycota 35.88 1822 1774 13827 5.55
140 Schizophyllum commune Tattone D Basidiomycota 36.46 1757 1707 15199 5.27
141 Schizopora paradoxa Basidiomycota 44.41 1342 1291 17098 5.78
142 Scleroderma citrinum Basidiomycota 56.14 3919 938 21012 4.33
143 Sebacina vermifera Basidiomycota 38.09 2457 546 15312 4.94
144 Septoria musiva Ascomycota 29.35 706 72 10233 2.44
145 Serpula lacrymans Basidiomycota 42.73 375 36 12789 5.73
146 Sistotremastrum niveocremeum Basidiomycota 35.36 699 179 13080 5.95
147 Sodiomyces alkalinus Ascomycota 43.45 290 25 9411 3.32
148 Spathaspora passalidarum Ascomycota 13.2 26 8 5983 1.2
149 Sporobolomyces roseus Basidiomycota 21.2 --- 76 5536 ---
150 Sporormia fimetaria Ascomycota 25.89 293 140 10783 2.70
151 Stereum hirsutum Basidiomycota 46.51 995 159 14072 6.52
152 Suillus brevipes Basidiomycota 51.71 4139 1550 22453 4.54
153 Talaromyces aculeatus Ascomycota 37.27 165 49 13793 3.16
154 Terfezia boudieri Ascomycota 63.23 2078 516 10200 3.61
155 Thermoascus aurantiacus Ascomycota 28.49 196 48 8798 3.33
156 Thielavia appendiculata Ascomycota 32.74 501 109 11942 2.77
157 Thielavia arenaria Ascomycota 30.99 354 69 10954 2.80
158 Thielavia hyrcaniae Ascomycota 31.18 972 251 11338 2.73
159 Trametes versicolor Basidiomycota 44.79 1443 283 14296 5.81
160 Trichaptum abietinum Basiodiomycota 40.61 1345 492 14978 5.65
161 Trichoderma citrinoviride Ascomycota 33.48 699 533 9737 3.10
162 Trypethelium eluteriae Ascomycota 32.16 747 730 11858 2.83
163 Tulasnella calospora Basidiomycota 62.39 6848 1335 19659 4.65
164 Umbelopsis ramanniana Mucoromycotina 23.08 239 198 9931 4.75
165 Wallemia sebi Basidiomycota 9.82 114 56 5284 4.03
166 Wickerhamomyces anomalus Ascomycota 14.15 207 46 6423 1.42
167 Wilcoxina mikolae Ascomycota 117.29 5591 1604 13093 3.24
168 Wolfiporia cocos Basidiomycota 50.48 2228 348 12746 6.31
169 Xanthoria parietina Ascomycota 31.90 302 39 10818 2.98
170 Xylona heveae Ascomycota 24.34 56 27 8205 3.41
171 Zasmidium cellare Ascomycota 38.25 365 267 16015 2.50
172 Zopfia rhizophila Ascomycota 152.78 1349 864 21730 2.77
Average 42.300 13437.21 3.79
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The fungal classifications (phyla/sub-phyla) are based on reports of Humber (2012) and Hibbet et al. (2007) [22,23].

Table 2.

Average genome size, and average number of coding genes and exons present in the different phyla/sub-phyla of the Kingdom Fungi

Fungal division Average Genome Size (Mb) Average No. Of Genes Average No. Of Exons
Ascomycota 36.91 11129.45 2.58
Basidiomycota 46.48 15431.51 5.28
Oomycota 74.85 24173.33 2.23
Mucoromycotina 38.777 13306.85 4.25
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The comparative analysis of fungal genomes show fungi are very divergent [27]. It was earlier thought that genomes of Magnaporthe grisea and Neurospora crassa share a common ancestor. But, comparative genomes analyses revealed only 47% amino acid sequence identity and absence of conserved synteny [27]. Only few genes are identified to be in conserved co-linearity. This shows that even members of the same genus can show remarkable divergence at the genomic level. A genomic comparison between Aspergillus nidulans, Aspergillus fumigatus and Aspergillus oryzae shows only 68% of amino acid sequence identity [27]. The genome duplication and translocation have major impact in evolution in yeast (Figure 1) [29,30]. The whole genome duplication in yeast followed by massive gene loss is confirmed by comparative experimental analysis [31,32]. This indicates that fungal genomes are very dynamic in nature. Lavergne et al. [33] reported that genome size reduction can trigger rapid phenotypic evolution in invasive plants. Their report suggests that the invasive genotypes had smaller genomes. Smaller genome sizes have phenotypic effects that increased the invasive potential [33]. But in exception, for example, the duckweeds which are smallest, fast-growing and simplest flowering plants are invasive in nature and contains increased DNA content in their genomes [34].

Figure 1.

Figure 1

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Role of different forces affecting the evolution of genome size. The major important factors are transposable elements (TEs), short sequence repeats, microsatellites, genome duplication and others. The mutational and selection pressure plays a significant role in this process. The negligible selective effects governed by genetic drift also contribute for the evolution of genome size. Overall all the forces play a role towards the increase in genome size at different levels. The photograph is adapted according to the report of Petrov [37].

Evolution in genome size

Genomes are aggregates of genes and this concept nicely fits with the prokaryotic organisms and viruses [35]. This concept is very inappropriate for eukaryotic organisms as most of the eukaryotic genomes are studded with nongenic and unconstrained repetitive DNA. This can lead to approximately 200,000 fold variation in genome size [36]. The genome size of an organism depends on the particular developmental and ecological need of the organism [37]. The genes are made up of DNA and it is a general assumption that more complex organisms requires more genes and thus contain more DNA in its genomes. The simple organisms probably contain fewer essential genes compared to more complex organisms and thus contain less DNA in its genomes. However this observation is not true. Some very simple organisms could have more DNA content than complex multi-cellular organisms. For example, some amoeba species have 200 times more DNA than humans [38]. Similarly, lilies have 200 times more DNA than that of rice [39]. But in many organisms much of the DNA content is noncoding and repetitive. But it is very important to understand which evolutionary forces produces enormous amount of noncoding DNA? What are the adaptive functions of these nongenic DNA? If these nongenic DNA don’t have any essential adaptive roles, than why natural selection favors the burden of synthesis of extra DNA? Several hypotheses are postulated since long days to address these questions. But still there is debate over it. Some of the hypotheses are discussed later. From the studied fungal genomes, the average genome sizes of Oomycota species (74.85 Mb) are higher than other. The Ascomycota and Mucoromycotina species shares more or less than same average genome size i.e. 36.91 and 37.02 Mb, respectively. In contrary, the average genome sizes of Basidiomycota species is 46.48 Mbs. The increase in genome size in Oomycota species is also directly correlated with the increase in the numbers of average coding gene sequences. The average numbers of coding genes present in Oomycota species are 24173.33 genes per genome which is almost the double number present in Ascomycota and Basidiomycota species.

The adaptive theories of genome evolution

If certain numbers of genes are responsible for the phenotype and genotypic characters of an organism, why there are extra amounts of DNA in its genome? The adaptive theory explains that this extra DNA abundance is for adaptive function and its content don’t have any significant effects in phenotype of the organism [40]. A large genome directly increases the nuclear and cellular volumes [41]. This largely helps to buffer the fluctuation in the concentration of regulatory proteins or protect coding DNA from spontaneous mutation [42]. So the variation in the genome size is due to adaptive needs or due to natural selection in different organisms [37].

Junk DNA theory of genome evolution

The junk DNA hypothesis suggests that these extra DNAs are useless, maladaptive DNAs and fixed by random drift [43]. These DNAs are carried in chromosome and don’t have any significant role in the phenotype of an organism [43]. These junk DNAs are known as parasitic DNA or transposable elements (TEs) [44]. The mutational mechanisms of DNA gain or loss can lead to minor changes in the genome of an organism, but changes in genome size may occur by the involvement of different evolutionary forces [37]. An increase in transposition rate certainly can lead to an increase in genome size [37]. Instead of thinking in genome size evolution by adaptive evolution theory or by junk DNA theory, it is very important to understand which evolutionary force is responsible for changes in genome size. The mutational and selective forces might have vast potential to affect the change in genome sizes (Figure 1) [37]. If we can get the specific clue, we can try to estimate the strength of individual force and whether the magnitude of individual force may produce changes in genome sizes. This approach can explain the quantitative sense about genetic mechanism and the selective forces that affect the genome size.

The activities of transposable elements are very fast and can able to amplify the a transposable copy number into 20-100 copies (~0.1-1 Mbp) in a single generation [45,46]. The changes in genome size through spontaneous deletion or insertion are relatively slow [47]. For example, the Drosophila melanogaster genome losses less than a single base pair per generation [47]. If there is strong selection in increasing in gnome sizes, strong mutational pressure also can not affect the evolution of genome size [37]. However, strong selection for increase in genome size can substantially slow down the impact of mutation rate. If we can get the information of time scale of genome size divergence, then we can infer the genome-size changes between two closely related organisms. If we will consider the evolutionary development of fungus, Ascomycota has higher evolutionary rate than Basidiomycota [48]. But when we compared the average genome size of Ascomycota, Basidiomycota and Mucoromycotina, we found that the genome size of Basidiomycota is larger than the genome size of Ascomycota and Mucoromycotina. This may suggests that the evolution of fungal genome size is due to addition of nucleotides/DNA contents rather than deletion of nucleotides.

Some forces act on the traits correlated with total genome size of an organism [37]. In this case, natural selection forces affect only to few genomic components. For example, the increase in rate of heterochromatin shrinkage through heterochromatic DNA should not affect the size of euchromatin [37]. Similarly, the expansion in satellite DNA should not hamper the size of satellite free sequences. Another important question is that, whether different genomic components are varying together in a correlated fashion during evolution of genome size? Although there are no significant current evidences regarding this question, there are certain cytogenetic and molecular studies available. The cytogenetic study revealed that genome size differences are scattered throughout the euchromatic portion of the genome [49-52]. Comparison of orthologous introns revealed correlation between average size of intron and genome size [53]. The changes in the intron length do not account for the changes in the genome size. Although transposable elements are largely associated with the increase in genome size, presence of increased simple repeated sequences, pseudogenes, increased size of inter-enhancer spacers and microsatellites are also associated with increase in genome size (Figure 1) [54-56]. When there are changes in genome size, they do it across all the genomic components. This suggests that a global force acts as the direct agent for change in genome size. So, from our study we can speculate that Oomycota species might harbors high densities of TEs, simple repeat sequences, microsatellites and pseudogenes. Similarly, the Basidiomycota species might have more densities of TEs, simple repeat sequences, microsatellites and pseudogenes compared to Ascomycota and other groups. Whitney et al. [57] reported about the nonadaptive process in plant genome size evolution. They hypothesized that genome expansion is maladaptive and lineages with small effective population size evolve larger genomes than those with large population size. In addition, mating systems are likely to affect genome size evolution via population size and spread of transposable elements [57].

Conclusion

The question of genome size (C-value paradox) is very puzzling. Most probably we can better understand about the evolution of fungal genome size by completely understanding the roles of noncoding DNAs. It is also equally important to understand whether the addition and deletion of additional DNA content varies between species to species and at organism level too. Although experimental approach like cytogenetic study of euchromatic region can give some lime light about this issue, still high fidelity experimental approaches are lacking till to date.

Acknowledgement

This work was carried out with the support of the Next-Generation Biogreen 21 Program (PJ011113), Rural Development Administration, Republic of Korea.

Footnotes

Competing interests

The authors declare that they have no competing interests.

Authors’ contribution

TKM: collected all the relevant publications, surveyed the fungal genome, arranged the general structure of review, and drafted the manuscript and figure. HB: given permission for publication. Both authors read and approved the final manuscript.

Contributor Information

Tapan Kumar Mohanta, Email: nostoc.tapan@gmail.com.

Hanhong Bae, Email: hanhongbae@ynu.ac.kr.

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