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Agaricus bisporus genome sequence: A commentary
Fungal Genetics and Biology xxx (2013) xxx–xxx
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Agaricus bisporus genome sequence: A commentary Richard W. Kerrigan a, Michael P. Challen b, Kerry S. Burton c,⇑ a
Sylvan Biosciences, 198 Nolte Drive, Kittanning, PA 16201, United States Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK c East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK b
a r t i c l e
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Article history: Available online xxxx Keywords: Agaricus bisporus Cultivated mushroom Genome adaptation Physiological specialization Carbon cycling Bioremediation
a b s t r a c t The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7 bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, ‘humicolous’, for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and b-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium. Ó 2013 Elsevier Inc. All rights reserved.
1. Introduction Agaricus bisporus is a secondary decomposer fungus found growing over a wide geographical range on leaf and needle litter in temperate forests of Picea (Spruce) (Alberta, Canada; Washington, USA), Cupressus (Cypress) (California, USA, Greece, Crete, Italy, France), Juniperus (Mexico), Prosopis (Mesquites) and Tamarisk (Sonoran Desert, California), mixed Montane forest (New Mexico), Eucalyptus (Israel, Morocco, Congo), and in other settings including pastoral land use areas (UK, Russia, China, Australia, Tasmania, Argentina) (Kerrigan, 1995; Xu et al., 1997). It shares this general ‘humicolous’ ecological niche with at least 200 other species of Agaricus associated with diverse plant communities including grasslands, coastal dunes, bamboo forests and others (Kerrigan, 1986; Pilát, 1951; Cappelli, 1984). As many as 25 species of Agaricus may sympatrically share a single patch (ca. 104 m2) of Cupressus habitat (Kerrigan, 1982). Their participation in processes (including carbon mobilization) occurring in the forest floor is evident from the periodic and frequently abundant emergence of their fruitbodies, and from the persistent presence of Agaricus mycelium in
⇑ Corresponding author. E-mail addresses: [email protected] (R.W. Kerrigan), [email protected]. ac.uk (M.P. Challen), [email protected] (K.S. Burton).
samples of partially degraded leaf/needle litter (Xu et al., 2002; Kerrigan et al., 1998). A. bisporus is a poor competitor on dead but non-degraded leaves, but it is specifically adapted to grow on and derive nutrition from partially-decomposed humic-rich plant material. A. bisporus has also been cultivated for its edible fruitbodies over the last 350 years. This cultivation is a complex process compared with most crops but highly efficient with up to 9 crops per year grown at modern mushroom farms, resulting in a world-wide annual crop value of approx. $4.7 bn (Sonnenberg et al., 2011). The cultivation process illustrates the specificity of the niche required for growth and reproduction that this fungus occupies. The substrate for cultivation is produced from nitrogen-amended cereal straw which is taken through an aerobic solid-state fermentation, or composting, that replaces easily available carbon and nitrogen compounds with humic-rich complexes. This highly selective medium is then pasteurized and inoculated with A. bisporus mycelium. To stimulate fruitbody formation the colonised compost is covered with a soil layer and the environment is manipulated (reduced temperature and levels of gaseous CO2 and 1-octen-3-ol (Eastwood et al., this issue). Mushroom fruitbodies are harvested and transported via a cool-chain, to maintain quality characteristics, for retail sale. Humic material is the major component of soil organic matter, and contributes to soil properties (such as soil structure, water and nutrient holding capacity, and biodiversity) and therefore has a
1087-1845/$ - see front matter Ó 2013 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.fgb.2013.03.002
Please cite this article in press as: Kerrigan, R.W., et al. Agaricus bisporus genome sequence: A commentary. Fungal Genet. Biol. (2013), http://dx.doi.org/ 10.1016/j.fgb.2013.03.002
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critical role in food production and nutrient re-cycling (Dungait et al., 2012). Soil organic matter also has importance for carbon sequestration and has the potential to store increased amounts of carbon through changes in management systems. The total global stocks of soil organic carbon are estimated to be 1550 Pg while the total terrestrial biota contains about 560 Pg of carbon (Dungait et al., 2012). The critical component of the niche for this organism, humic material, has proved difficult to define chemically and the soil science community continues to debate and discuss its characteristics. Humic materials are a complex and heterogeneous mixture of chemicals derived from the decay of plant tissues and microbial metabolism, containing aromatic, aliphatic and alkyl components (Piccolo, 2001). Humic substances are no longer considered to be polymers but as supramolecular structures stabilised by van der Waals and hydrogen bonds (Piccolo, 2001). A further characteristic of humic substances which relates to residence time and accessibility by microbes is the physical structure; it can be occluded within aggregates or adsorbed onto minerals (Dungait et al., 2012). The Agaricus species have potential for bioremediation of substrates contaminated with heavy metals (Zurera et al., 1986; García et al., 1998; Garcia et al., 2005), as these decomposer fungi have a profound ability to tolerate and hyperaccumulate toxic metals (Hg, Pb and Cd) (Kuusi et al., 1981; Lodenius et al., 1981). Agaricus spp. also have potential to bioremediate other toxic pollutants, e.g. phenols; (Kameda et al., 2006; Semple and Fermor, 1997) and have utility as environmental biofilters (Stark and Williams, 1995). Genome sequence and a further expansion of transcriptomics should permit a more detailed analysis of the genetic mechanisms regulating these processes. Two haploid isolates of the humicolous species A. bisporus have recently been genome sequenced (Morin et al., 2012) and the analyses of, reflections upon, and hypotheses arising from the genome sequences and the associated microarray-based transcriptomic profiling are the subject of this special edition of Fungal Genetics and Biology. The isolates were deliberately chosen to be phylogenetically and physiologically distinct, were obtained from two different, isolated geographical locations, and represent populations emphasizing two different sexual life-cycles. The species is amphithallic, employing both uniparental and biparental sexual reproductive routes. In bisporic strains and populations, following the predominant pseudohomothallic route, two sexually compatible postmeiotic nuclei pair nonrandomly in basidiospores that produce offspring having a sexually fertile (competent) phenotype. In tetrasporic strains and populations, including the var. burnettii, the predominant route is heterothallic, in which each basidiospore receives a single haploid postmeiotic nucleus, and the sexually fertile phenotype is restored only after a post-dispersal mating event between two compatible offspring re-establishes the heterokaryotic condition. The two pathways are determined primarily by a locus on chromosome I, mapped by Imbernon et al. (1996). Isolate H97 is from a cultivated European strain that is bisporic, and consequently employs a predominantly pseudohomothallic (intramictic) sexual reproductive cycle, while isolate JB137-s8 was obtained from a wild strain in the Sonoran Desert, California, USA, that is tetrasporic and consequently employs a predominantly heterothallic (outcrossing) reproductive cycle. The two genomes H97 and JB137-s8 have sizes 30.4 and 32.8 Mb with 10,438 and 11,289 protein-coding genes estimated respectively. The genome/transcriptome analyses have informed our understanding of the biology and ecology of this organism, e.g. hypotheses for the molecular mechanism for niche adaptation. These analyses can also be focussed towards improved cultivation technologies, e.g. understanding the causes of tissue browning (Weijn et al., this issue). These approaches are however complementary and enhance our increased understanding of the fungus.
2. Eco-nutritional physiology The A. bisporus genome contains a full set of genes for polysaccharide-degrading enzymes similar to other fungi growing on plant wastes or wood, and two Mn-peroxidases for lignin breakdown. Yet A. bisporus grows poorly on non-degraded lignocellulosic plant tissues, e.g. straw. The organism shows adaptations to growing in a humic-rich environment on partially-decomposed plant material both in genome composition and transcriptional regulation. Compared to other lignocellulosic fungi A. bisporus has a much larger number (24) of heme-thiolate peroxidases (HTPs), 16 of which are up-regulated in mycelium growing on humic-rich compost relative to defined media. These HTPs including aromatic peroxidases and chloroperoxidases, together with an expanded number of betherases, have catalytic properties able to metabolise the derivatives of lignin (Morin et al., 2012). When the mycelial transcript levels from growth on humic-rich compost are compared with mycelia growing on non-humic media and ranked, 23 of the top 33 genes have a common promoter motif which is hypothesized to be a ‘humic-response element’. Unlike other genome-sequenced soil-inhabiting or lignocellulosic fungi this motif occurs at a higher frequency in the A. bisporus genomes than by random chance: 4.2 and 3.1 times more frequent in JB137-s8 and H97 respectively (Morin et al., 2012). A recent comparative genomics study has placed fungal evolution into geological time by estimating the time that fungi first evolved the ability to degrade lignin, 295 million years ago at the end of the carboniferous geological period (Floudas et al., 2012). It is tempting to continue this theme and speculate that adaptation to humicolous environments may have evolved subsequent to those events. It is interesting to note that sequence divergence between conserved proteins of A. bisporus and other Agaricales (e.g. L. bicolor, S. commune, C. cinerea) would estimate the split between ancestral species occurred at least 100 million years ago (Morin et al., 2012). The combination of physiology, genome composition and transcriptional regulation does not allow A. bisporus to be readily assigned into white-rot or brown-rot classifications of wood decay fungi. A new classification for adaptation to humic-rich environments is proposed, and as this is the only genome-sequenced organism with this adaptation, it is therefore the ‘type organism’ or model species for this environment so important for soil structure and biology, carbon cycling and sequestration (Morin et al., 2012).
3. Morphogenesis and sexuality In response to environmental stimuli, A. bisporus mycelium can switch growth habit from vegetative to reproductive growth. Numerous mushroom fruitbodies are then produced from below ground level simultaneously at approximately weekly intervals (‘flushes’) suggesting co-ordinated regulation and metabolism. Periodic peaks of enzymic activity have been described; mycelial endocellulase and fruitbody trehalase, glycogen phosphorylase and proteinase in phase with the flushing cycle while fruitbody glucose-6-phosphate dehydrogenase peaks out of phase with the flushing cycle (Claydon et al., 1988; Wells et al., 1987; Burton et al., 1994; Hammond, 1981). This morphogenesis starts by the formation of mycelial cords or strands in the non-nutritious casing layer followed by dense localized branching and hyphal aggregation to form hyphal knots. These then grow and differentiate to primordia and after further tissue differentiation mushroom fruitbody growth is largely due to osmotically-driven cellular expansion (Umar and van Griensven, 1997). Two of the environmental signals for this switch, 1-octen-3-ol levels and temperature, act at
Please cite this article in press as: Kerrigan, R.W., et al. Agaricus bisporus genome sequence: A commentary. Fungal Genet. Biol. (2013), http://dx.doi.org/ 10.1016/j.fgb.2013.03.002
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different points in the morphogenetic time-line, while CO2 levels act as a quantitative regulator (Eastwood et al., this issue). Conserved promoter motifs specific to morphogenetically-related gene clusters are indicative of regulation by co-ordinated transcription (Eastwood et al., this issue). Previous research has identified genes and ESTs associated with mushroom growth and development both while attached to the mycelium and harvested mushroom fruitbodies (De Groot et al., 1997; Ospina-Giraldo et al., 2000; Eastwood et al., 2001). Analysis of the A. bisporus genome suggests that some of the regulatory switches are shared with other Agaric species while others are clade specific (Morin et al., 2012). In A. bisporus, of 50 gene transcripts most highly expressed in fruiting bodies, 20 are from orphan genes not observed in other lineages within Agaricales. Genes regulating compatibility, mating-type loci, are master regulators of fruiting-body development in homobasidiomycetes (Kües, 2000; Raudaskoski and Kothe, 2010). Although genomic architecture can vary between different species, genome studies invariably reveal three different classes of genes encoding (i) homeodomain transcription factors, (ii) pheromone precursors, and (iii) cognate G protein-coupled 7-transmembrane pheromone receptors (Kües et al., 2011). The Agaricus species have bipolar (or unifactorial) breeding systems (Elliott, 1978, 1979) and within the genus, different species exhibit a range of diverse life-styles (Kerrigan et al., 1993), homothallism (e.g. Agaricus subfloccosus), pseudohomothallism (e.g. A. bisporus), and heterothallism (e.g. Agaricus bitorquis). Agaricus therefore forms a particularly interesting genus in which to study the evolution of genes controlling compatibility. Earlier efforts to characterize mating type genes in Agaricus species (Li et al., 2004) were severely constrained by the lack of genome sequence. The A. bisporus genome sequence has enabled comprehensive mapping of the genes encoding homeodomain transcription factors in this pseudohomothallic species, and revealed genes encoding conserved pheromone and pheromone receptors (Morin et al., 2012). Further functional analysis is required to fully determine the role of pheromone/receptor genes in Agaricus and indeed other bipolar species (Kües et al., 2011). Sequencing of other species from the genus Agaricus should provide insight into factors governing evolution of the diverse life-styles observed in these bipolar homobasidiomycota. In laboratory crosses between mating partners of A. bisporus, mitochondria have been observed to be inherited predominantly uniparentally (Jin et al., 1992). However when natural geographically distinct populations were examined, evidence was found of recombination in three out of the four populations (Xu et al., this issue). Possible mechanisms for the differences in mitochondrial recombination rates and ecological significance are discussed by Xu et al. (this issue).
4. Concluding remarks A. bisporus plays an ecologically significant role in the growth and degradation of partially-degraded leaf and needle litter substrates rich in humic chemicals. While it has the genes to degrade complex polymers (e.g. lignin, cellulose and hemicellulose) it has specific adaptations in gene content and transcriptional regulation to metabolise the breakdown products of lignin. Thus A. bisporus, with its adaptation to and persistence in humic-rich environments, is an important model for soil carbon sequestration studies and understanding of fungal contributions to terrestrial cycling of carbon, nitrogen, phosphorus and potassium. The cultivation of A. bisporus is also an economically important industry and genome sequencing will expedite efforts to improve agronomic traits including substrate utilization, pathogen resistance, morphogenesis and enhancing yield and quality (e.g. Weijn
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et al., this issue). Furthermore the potential of technologies such as heavy metals bioremediation can be investigated at the genetic level.
Acknowledgments The authors wish to thank the DoE JGI (Joint Genome Institute) of the USA for sequencing the A. bisporus genomes, HDC (Horticulture Development Company) of the UK for contributing transcriptomic data, Institut National de la Recherche Agronomique (INRA – France) for bioinformatics and all consortium members of the Agaricus Genome Project.
References Burton, K.S., Hammond, J.B.W., Minamide, T., 1994. Protease activity in Agaricus bisporus during periodic fruiting (flushing) and sporophore development. Current Microbiology 28, 275–278. Cappelli, A., 1984. Agaricus L.: Fr. (Psalliota Fr.). Libreria editrice Biella Giovanna, Italy, 560 pp. Claydon, N., Allan, M., Wood, D.A., 1988. Fruitbody biomass regulated production of extracellular endocellulase during periodic fruiting by Agaricus bisporus. Transactions of the British Mycological Society 90, 85–90. De Groot, P.W., Schaap, P.J., Van Griensven, L.J., Visser, J., 1997. Isolation of developmentally regulated genes from the edible mushroom Agaricus bisporus. Microbiology 143, 1993–2001. Dungait, J.A.J., Hopkins, D.W., Gregory, A.S., Whitmore, A.P., 2012. Soil organic matter turnover is governed by accessibility not recalcitrance. Global Change Biology 3, 1781–1796. http://dx.doi.org/10.1111/j.1365-2486.2012.02665.x. Eastwood, D.C., Kingsnorth, C.S., Jones, H.E., Burton, K.S., 2001. Genes with increased transcript levels following harvest of the sporophore of Agaricus bisporus have multiple physiological roles. Mycological Research 105, 1223–1230. Eastwood, D.C., Herman, B., Noble, R., Dobrovin-Pennington, A., Sreenivasaprasad, S., Burton, K.S., this issue. Environmental regulation of reproductive phase change in Agaricus bisporus by 1-octen-3-ol, temperature and CO2. Fungal Genetics and Biology. http://dx.doi.org/10.1016/j.fgb.2013.01.001. Elliott, T.J., 1978. Comparative sexuality in Agaricus species. Journal of General Microbiology 107, 113–122. Elliott, T.J., 1979. Sexuality in the genus Agaricus. Mushroom Science 10, 41–50. Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martínez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Górecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kües, U., Kumar, T.K.A., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A., Rokas, A., Ruiz-Dueñas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St. John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., Hibbett, D.S., 2012. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336 (6089), 1715–1719. http://dx.doi.org/10.1126/science.1221748. García, M.A., Alonso, J., Fernández, M.I., Melgar, M.J., 1998. Lead content in edible wild mushrooms in northwest spain as indicator of environmental contamination. Archives of Environmental Contamination and Toxicology 34, 330–335. Garcia, M.A., Alonso, J., Melgar, M.J., 2005. Agaricus macrosporus as a potential bioremediation agent for substrates contaminated with heavy metals. Journal of Chemical Technology and Biotechnology 80, 325–330. Hammond, J.B.W., 1981. Variations in enzyme activity during periodic fruiting of Agaricus bisporus. New Phytology 89, 419–428. Imbernon, M., Callac, P., Gasqui, P., Kerrigan, R.W., Velcko, A.J., 1996. BSN, the primary determinant of basidial spore number and reproductive mode in Agaricus bisporus, maps to chromosome I. Mycologia 88, 749–761. Jin, T., Sonnenberg, A.S.M., Van Griensven, L.J.L.D., Horgen, P.A., 1992. Investigation of mitochondrial transmission in selected matings between homokaryons from commercial and wild-collected isolates of Agaricus bisporus( = Agaricus brunnescens). Applied and Environmental Microbiology 58, 3553–3560. Kameda, E., Langone, M.A.P., Coelho, M.A.Z., 2006. Tyrosinase extract from Agaricus bisporus mushroom and its in natura tissue for specific phenol removal. Environmental Technology 27, 1209–1215. Kerrigan, R.W., 1982. The genus Agaricus in coastal California. Master’s thesis. San Francisco State University, San Francisco, California, 208 pp.. Kerrigan, R.W., 1986. The Agaricales (Gilled Fungi) of California, 6. Agaricaceae. Mad River Press, Eureka, California, 62 pp.. Kerrigan, R.W., 1995. Global genetic resources for Agaricus breeding and cultivation. Canadian Journal of Botany 73, S973–S979. Kerrigan, R.W., Royer, J.C., Baller, L.M., Kohli, Y., Horgen, P.A., Anderson, J.B., 1993. Meiotic behaviour and linkage relationships in the secondarily homothallic fungus Agaricus bisporus. Genetics 133 (225), 236.
Please cite this article in press as: Kerrigan, R.W., et al. Agaricus bisporus genome sequence: A commentary. Fungal Genet. Biol. (2013), http://dx.doi.org/ 10.1016/j.fgb.2013.03.002
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Kerrigan, R.W., Carvalho, D.B., Horgen, P.A., Anderson, J.B., 1998. The indigenous coastal Californian population of the mushroom Agaricus bisporus, a cultivated species, may be at risk of extinction. Molecular Ecology 7, 35–45. Kües, U., 2000. Life history and developmental processes in the basidiomycete Coprinus cinereus. Microbiology and Molecular Biology Reviews 64 (2), 316– 353. Kües, U., James, T.Y., Heitman, J., 2011. Mating type in basidiomycetes: unipolar, bipolar, and tetrapolar patterns of sexuality. In: Pöggeler, S., Wöstemeyer, J. (Eds.), Evolution of Fungi and Fungal-Like Organisms, The Mycota XIV. SpringerVerlag, Berlin Heidelberg. Kuusi, T., Laaksovirta, K., Liukkonen-Lilja, H., Lodenius, M., Piepponen, S., 1981. Lead, cadmium, and mercury contents of fungi in the Helsinki area and in unpolluted control areas. Zeitschrift für Lebensmitteluntersuchung und -Forschung A 173, 261–267. Li, Y., Challen, M.P., Elliott, T.J., Casselton, L.A., 2004. Molecular analysis of breeding behaviour in agaricus species. Mushroom Science 16, 103–109. Lodenius, M., Kuusi, T., Laaksovirta, K., Liukkonen-Lilja, H., Piepponen, S., 1981. Lead, cadmium and mercury contents of fungi in Mikkeli, SE Finland. Annales Botanici Fennici 18, 183–186. Morin, E., Kohlera, A., Baker, A.R., Foulogne-Oriol, M., Lombard, V., Nagy, L.G., Ohm, R.A., Patyshakuliyeva, A., Brun, A., Aerts, A.L., Bailey, A.M., Billette, C., Coutinho, P.M., Deakin, G., Doddapaneni, H., Floudas, D., Grimwood, J., Hildén, K., Kües, U., LaButti, K.M., Lapidus, A., Lindquist, E.A., Lucas, S.M., Murat, C., Riley, R.W., Salamov, A.A., Schmutz, J., Subramanian, V. Wösten, H.A.B., Xu, J., Eastwood, D.C., Foster, G.D., Sonnenberg, A.S.M., Cullen, D., de Vries, R.P., Lundell, T., Hibbett, D.S., Henrissat, B., Burton, K.S., Kerrigan, R.W., Challen, M.P., Grigoriev, I.V., and Martin, F., 2012. The genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. In: Proceedings of the National Academy of Sciences of the United States of America.. Ospina-Giraldo, M.D., Collopy, P.D., Chen, X., Romaine, C.P., Royse, D.J., 2000. Classification of sequences expressed during the primordial and basidiome stages of the cultivated mushroom Agaricus bisporus. Fungal Genetics and Biology 29, 81–94. Piccolo, A., 2001. The supramolecular structure of humic substances. Soil Science 166, 810–832.
Pilát, A., 1951. The Bohemian species of the genus Agaricus. Acta Musei Nationalis Pragae 7B, 1–142. Raudaskoski, M., Kothe, E., 2010. Basidiomycete mating type genes and pheromone signaling. Eukaryotic Cell 9 (6), 847–859. Semple, K.T., Fermor, T.R., 1997. Enhanced mineralization of UL-14Cpentachlorophenol by mushroom composts. Research in Microbiology 148, 795–798. Sonnenberg, A.S.M., Baars, J.J.P., Hendrickx, P.M., Lavrijssen, B., Gao, W., Weijn, A., Mes, J.J., 2011. Breeding and strain protection in the button mushroom Agaricus bisporus. In: Proceedings of the 7th International Conference on Mushroom Biology and Mushroom Products (ICMBMP7). Stark, L.R., Williams, F.M., 1995. The role of spent mushroom substrate for the mitigation of coal mine drainage. In: Environmental Agricultural and Industrial Uses for Spent Mushroom Substrates from Mushroom Farms. JG Press, Inc., Emmaus, PA, pp. 74–84. Umar, M.H., Van Griensven, L.J.L.D., 1997. Morphological studies on the life span, developmental stages, senescence and death of fruit bodies of Agaricus bisporus. Mycological Research 101, 1409–1422. Weijn, A., Bastiaan-Net, S., Wichers, H.J., Mes, J.J., this issue. Melanin biosynthesis pathway in Agaricus bisporus mushrooms. Fungal Genetics and Biology. http:// dx.doi.org/10.1016/j.fgb.2012.01.004. Wells, T.K., Hammond, J.B.W., Dickerson, A.G., 1987. Variations in activities of glycogen phosphorylase and trehalase during the periodic fruiting of the edible mushroom Agaricus bisporus (Lange) Imbach. New Phytology 105, 273–280. Xu, J., Kerrigan, R.W., Callac, P., Horgen, P.A., Anderson, J.B., 1997. Genetic structure of natural populations of Agaricus bisporus, the commercial button mushroom. Journal of Heredity 88, 482–488. Xu, J.P., Desmerger, C., Callac, P., 2002. Fine-scale genetic analyses reveal unexpected spatial-temporal heterogeneity in two natural populations of the commercial mushroom Agaricus bisporus. Microbiology-SGM 148, 1253–1262. Xu, J., Zhang, Y., Pun, N., this issue. Mitochondrial recombination in natural populations of the button mushroom Agaricus bisporus. Fungal Genetics and Biology. http://dx.doi.org/10.1016/j.fgb.2012.09.004. Zurera, G., Rincón, F., Arcos, F., Pozo-Lora, R., 1986. Mercury content in mushroom species in the Cordova area. Bulletin of Environmental Contamination and Toxicology 36, 662–667.
Please cite this article in press as: Kerrigan, R.W., et al. Agaricus bisporus genome sequence: A commentary. Fungal Genet. Biol. (2013), http://dx.doi.org/ 10.1016/j.fgb.2013.03.002
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Fungal Genetics and Biology journal homepage: www.elsevier.com/locate/yfgbi
Agaricus bisporus genome sequence: A commentary Richard W. Kerrigan a, Michael P. Challen b, Kerry S. Burton c,⇑ a
Sylvan Biosciences, 198 Nolte Drive, Kittanning, PA 16201, United States Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK c East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK b
a r t i c l e
i n f o
Article history: Available online xxxx Keywords: Agaricus bisporus Cultivated mushroom Genome adaptation Physiological specialization Carbon cycling Bioremediation
a b s t r a c t The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7 bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, ‘humicolous’, for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and b-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium. Ó 2013 Elsevier Inc. All rights reserved.
1. Introduction Agaricus bisporus is a secondary decomposer fungus found growing over a wide geographical range on leaf and needle litter in temperate forests of Picea (Spruce) (Alberta, Canada; Washington, USA), Cupressus (Cypress) (California, USA, Greece, Crete, Italy, France), Juniperus (Mexico), Prosopis (Mesquites) and Tamarisk (Sonoran Desert, California), mixed Montane forest (New Mexico), Eucalyptus (Israel, Morocco, Congo), and in other settings including pastoral land use areas (UK, Russia, China, Australia, Tasmania, Argentina) (Kerrigan, 1995; Xu et al., 1997). It shares this general ‘humicolous’ ecological niche with at least 200 other species of Agaricus associated with diverse plant communities including grasslands, coastal dunes, bamboo forests and others (Kerrigan, 1986; Pilát, 1951; Cappelli, 1984). As many as 25 species of Agaricus may sympatrically share a single patch (ca. 104 m2) of Cupressus habitat (Kerrigan, 1982). Their participation in processes (including carbon mobilization) occurring in the forest floor is evident from the periodic and frequently abundant emergence of their fruitbodies, and from the persistent presence of Agaricus mycelium in
⇑ Corresponding author. E-mail addresses: [email protected] (R.W. Kerrigan), [email protected]. ac.uk (M.P. Challen), [email protected] (K.S. Burton).
samples of partially degraded leaf/needle litter (Xu et al., 2002; Kerrigan et al., 1998). A. bisporus is a poor competitor on dead but non-degraded leaves, but it is specifically adapted to grow on and derive nutrition from partially-decomposed humic-rich plant material. A. bisporus has also been cultivated for its edible fruitbodies over the last 350 years. This cultivation is a complex process compared with most crops but highly efficient with up to 9 crops per year grown at modern mushroom farms, resulting in a world-wide annual crop value of approx. $4.7 bn (Sonnenberg et al., 2011). The cultivation process illustrates the specificity of the niche required for growth and reproduction that this fungus occupies. The substrate for cultivation is produced from nitrogen-amended cereal straw which is taken through an aerobic solid-state fermentation, or composting, that replaces easily available carbon and nitrogen compounds with humic-rich complexes. This highly selective medium is then pasteurized and inoculated with A. bisporus mycelium. To stimulate fruitbody formation the colonised compost is covered with a soil layer and the environment is manipulated (reduced temperature and levels of gaseous CO2 and 1-octen-3-ol (Eastwood et al., this issue). Mushroom fruitbodies are harvested and transported via a cool-chain, to maintain quality characteristics, for retail sale. Humic material is the major component of soil organic matter, and contributes to soil properties (such as soil structure, water and nutrient holding capacity, and biodiversity) and therefore has a
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critical role in food production and nutrient re-cycling (Dungait et al., 2012). Soil organic matter also has importance for carbon sequestration and has the potential to store increased amounts of carbon through changes in management systems. The total global stocks of soil organic carbon are estimated to be 1550 Pg while the total terrestrial biota contains about 560 Pg of carbon (Dungait et al., 2012). The critical component of the niche for this organism, humic material, has proved difficult to define chemically and the soil science community continues to debate and discuss its characteristics. Humic materials are a complex and heterogeneous mixture of chemicals derived from the decay of plant tissues and microbial metabolism, containing aromatic, aliphatic and alkyl components (Piccolo, 2001). Humic substances are no longer considered to be polymers but as supramolecular structures stabilised by van der Waals and hydrogen bonds (Piccolo, 2001). A further characteristic of humic substances which relates to residence time and accessibility by microbes is the physical structure; it can be occluded within aggregates or adsorbed onto minerals (Dungait et al., 2012). The Agaricus species have potential for bioremediation of substrates contaminated with heavy metals (Zurera et al., 1986; García et al., 1998; Garcia et al., 2005), as these decomposer fungi have a profound ability to tolerate and hyperaccumulate toxic metals (Hg, Pb and Cd) (Kuusi et al., 1981; Lodenius et al., 1981). Agaricus spp. also have potential to bioremediate other toxic pollutants, e.g. phenols; (Kameda et al., 2006; Semple and Fermor, 1997) and have utility as environmental biofilters (Stark and Williams, 1995). Genome sequence and a further expansion of transcriptomics should permit a more detailed analysis of the genetic mechanisms regulating these processes. Two haploid isolates of the humicolous species A. bisporus have recently been genome sequenced (Morin et al., 2012) and the analyses of, reflections upon, and hypotheses arising from the genome sequences and the associated microarray-based transcriptomic profiling are the subject of this special edition of Fungal Genetics and Biology. The isolates were deliberately chosen to be phylogenetically and physiologically distinct, were obtained from two different, isolated geographical locations, and represent populations emphasizing two different sexual life-cycles. The species is amphithallic, employing both uniparental and biparental sexual reproductive routes. In bisporic strains and populations, following the predominant pseudohomothallic route, two sexually compatible postmeiotic nuclei pair nonrandomly in basidiospores that produce offspring having a sexually fertile (competent) phenotype. In tetrasporic strains and populations, including the var. burnettii, the predominant route is heterothallic, in which each basidiospore receives a single haploid postmeiotic nucleus, and the sexually fertile phenotype is restored only after a post-dispersal mating event between two compatible offspring re-establishes the heterokaryotic condition. The two pathways are determined primarily by a locus on chromosome I, mapped by Imbernon et al. (1996). Isolate H97 is from a cultivated European strain that is bisporic, and consequently employs a predominantly pseudohomothallic (intramictic) sexual reproductive cycle, while isolate JB137-s8 was obtained from a wild strain in the Sonoran Desert, California, USA, that is tetrasporic and consequently employs a predominantly heterothallic (outcrossing) reproductive cycle. The two genomes H97 and JB137-s8 have sizes 30.4 and 32.8 Mb with 10,438 and 11,289 protein-coding genes estimated respectively. The genome/transcriptome analyses have informed our understanding of the biology and ecology of this organism, e.g. hypotheses for the molecular mechanism for niche adaptation. These analyses can also be focussed towards improved cultivation technologies, e.g. understanding the causes of tissue browning (Weijn et al., this issue). These approaches are however complementary and enhance our increased understanding of the fungus.
2. Eco-nutritional physiology The A. bisporus genome contains a full set of genes for polysaccharide-degrading enzymes similar to other fungi growing on plant wastes or wood, and two Mn-peroxidases for lignin breakdown. Yet A. bisporus grows poorly on non-degraded lignocellulosic plant tissues, e.g. straw. The organism shows adaptations to growing in a humic-rich environment on partially-decomposed plant material both in genome composition and transcriptional regulation. Compared to other lignocellulosic fungi A. bisporus has a much larger number (24) of heme-thiolate peroxidases (HTPs), 16 of which are up-regulated in mycelium growing on humic-rich compost relative to defined media. These HTPs including aromatic peroxidases and chloroperoxidases, together with an expanded number of betherases, have catalytic properties able to metabolise the derivatives of lignin (Morin et al., 2012). When the mycelial transcript levels from growth on humic-rich compost are compared with mycelia growing on non-humic media and ranked, 23 of the top 33 genes have a common promoter motif which is hypothesized to be a ‘humic-response element’. Unlike other genome-sequenced soil-inhabiting or lignocellulosic fungi this motif occurs at a higher frequency in the A. bisporus genomes than by random chance: 4.2 and 3.1 times more frequent in JB137-s8 and H97 respectively (Morin et al., 2012). A recent comparative genomics study has placed fungal evolution into geological time by estimating the time that fungi first evolved the ability to degrade lignin, 295 million years ago at the end of the carboniferous geological period (Floudas et al., 2012). It is tempting to continue this theme and speculate that adaptation to humicolous environments may have evolved subsequent to those events. It is interesting to note that sequence divergence between conserved proteins of A. bisporus and other Agaricales (e.g. L. bicolor, S. commune, C. cinerea) would estimate the split between ancestral species occurred at least 100 million years ago (Morin et al., 2012). The combination of physiology, genome composition and transcriptional regulation does not allow A. bisporus to be readily assigned into white-rot or brown-rot classifications of wood decay fungi. A new classification for adaptation to humic-rich environments is proposed, and as this is the only genome-sequenced organism with this adaptation, it is therefore the ‘type organism’ or model species for this environment so important for soil structure and biology, carbon cycling and sequestration (Morin et al., 2012).
3. Morphogenesis and sexuality In response to environmental stimuli, A. bisporus mycelium can switch growth habit from vegetative to reproductive growth. Numerous mushroom fruitbodies are then produced from below ground level simultaneously at approximately weekly intervals (‘flushes’) suggesting co-ordinated regulation and metabolism. Periodic peaks of enzymic activity have been described; mycelial endocellulase and fruitbody trehalase, glycogen phosphorylase and proteinase in phase with the flushing cycle while fruitbody glucose-6-phosphate dehydrogenase peaks out of phase with the flushing cycle (Claydon et al., 1988; Wells et al., 1987; Burton et al., 1994; Hammond, 1981). This morphogenesis starts by the formation of mycelial cords or strands in the non-nutritious casing layer followed by dense localized branching and hyphal aggregation to form hyphal knots. These then grow and differentiate to primordia and after further tissue differentiation mushroom fruitbody growth is largely due to osmotically-driven cellular expansion (Umar and van Griensven, 1997). Two of the environmental signals for this switch, 1-octen-3-ol levels and temperature, act at
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different points in the morphogenetic time-line, while CO2 levels act as a quantitative regulator (Eastwood et al., this issue). Conserved promoter motifs specific to morphogenetically-related gene clusters are indicative of regulation by co-ordinated transcription (Eastwood et al., this issue). Previous research has identified genes and ESTs associated with mushroom growth and development both while attached to the mycelium and harvested mushroom fruitbodies (De Groot et al., 1997; Ospina-Giraldo et al., 2000; Eastwood et al., 2001). Analysis of the A. bisporus genome suggests that some of the regulatory switches are shared with other Agaric species while others are clade specific (Morin et al., 2012). In A. bisporus, of 50 gene transcripts most highly expressed in fruiting bodies, 20 are from orphan genes not observed in other lineages within Agaricales. Genes regulating compatibility, mating-type loci, are master regulators of fruiting-body development in homobasidiomycetes (Kües, 2000; Raudaskoski and Kothe, 2010). Although genomic architecture can vary between different species, genome studies invariably reveal three different classes of genes encoding (i) homeodomain transcription factors, (ii) pheromone precursors, and (iii) cognate G protein-coupled 7-transmembrane pheromone receptors (Kües et al., 2011). The Agaricus species have bipolar (or unifactorial) breeding systems (Elliott, 1978, 1979) and within the genus, different species exhibit a range of diverse life-styles (Kerrigan et al., 1993), homothallism (e.g. Agaricus subfloccosus), pseudohomothallism (e.g. A. bisporus), and heterothallism (e.g. Agaricus bitorquis). Agaricus therefore forms a particularly interesting genus in which to study the evolution of genes controlling compatibility. Earlier efforts to characterize mating type genes in Agaricus species (Li et al., 2004) were severely constrained by the lack of genome sequence. The A. bisporus genome sequence has enabled comprehensive mapping of the genes encoding homeodomain transcription factors in this pseudohomothallic species, and revealed genes encoding conserved pheromone and pheromone receptors (Morin et al., 2012). Further functional analysis is required to fully determine the role of pheromone/receptor genes in Agaricus and indeed other bipolar species (Kües et al., 2011). Sequencing of other species from the genus Agaricus should provide insight into factors governing evolution of the diverse life-styles observed in these bipolar homobasidiomycota. In laboratory crosses between mating partners of A. bisporus, mitochondria have been observed to be inherited predominantly uniparentally (Jin et al., 1992). However when natural geographically distinct populations were examined, evidence was found of recombination in three out of the four populations (Xu et al., this issue). Possible mechanisms for the differences in mitochondrial recombination rates and ecological significance are discussed by Xu et al. (this issue).
4. Concluding remarks A. bisporus plays an ecologically significant role in the growth and degradation of partially-degraded leaf and needle litter substrates rich in humic chemicals. While it has the genes to degrade complex polymers (e.g. lignin, cellulose and hemicellulose) it has specific adaptations in gene content and transcriptional regulation to metabolise the breakdown products of lignin. Thus A. bisporus, with its adaptation to and persistence in humic-rich environments, is an important model for soil carbon sequestration studies and understanding of fungal contributions to terrestrial cycling of carbon, nitrogen, phosphorus and potassium. The cultivation of A. bisporus is also an economically important industry and genome sequencing will expedite efforts to improve agronomic traits including substrate utilization, pathogen resistance, morphogenesis and enhancing yield and quality (e.g. Weijn
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et al., this issue). Furthermore the potential of technologies such as heavy metals bioremediation can be investigated at the genetic level.
Acknowledgments The authors wish to thank the DoE JGI (Joint Genome Institute) of the USA for sequencing the A. bisporus genomes, HDC (Horticulture Development Company) of the UK for contributing transcriptomic data, Institut National de la Recherche Agronomique (INRA – France) for bioinformatics and all consortium members of the Agaricus Genome Project.
References Burton, K.S., Hammond, J.B.W., Minamide, T., 1994. Protease activity in Agaricus bisporus during periodic fruiting (flushing) and sporophore development. Current Microbiology 28, 275–278. Cappelli, A., 1984. Agaricus L.: Fr. (Psalliota Fr.). Libreria editrice Biella Giovanna, Italy, 560 pp. Claydon, N., Allan, M., Wood, D.A., 1988. Fruitbody biomass regulated production of extracellular endocellulase during periodic fruiting by Agaricus bisporus. Transactions of the British Mycological Society 90, 85–90. De Groot, P.W., Schaap, P.J., Van Griensven, L.J., Visser, J., 1997. Isolation of developmentally regulated genes from the edible mushroom Agaricus bisporus. Microbiology 143, 1993–2001. Dungait, J.A.J., Hopkins, D.W., Gregory, A.S., Whitmore, A.P., 2012. Soil organic matter turnover is governed by accessibility not recalcitrance. Global Change Biology 3, 1781–1796. http://dx.doi.org/10.1111/j.1365-2486.2012.02665.x. Eastwood, D.C., Kingsnorth, C.S., Jones, H.E., Burton, K.S., 2001. Genes with increased transcript levels following harvest of the sporophore of Agaricus bisporus have multiple physiological roles. Mycological Research 105, 1223–1230. Eastwood, D.C., Herman, B., Noble, R., Dobrovin-Pennington, A., Sreenivasaprasad, S., Burton, K.S., this issue. Environmental regulation of reproductive phase change in Agaricus bisporus by 1-octen-3-ol, temperature and CO2. Fungal Genetics and Biology. http://dx.doi.org/10.1016/j.fgb.2013.01.001. Elliott, T.J., 1978. Comparative sexuality in Agaricus species. Journal of General Microbiology 107, 113–122. Elliott, T.J., 1979. Sexuality in the genus Agaricus. Mushroom Science 10, 41–50. Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martínez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Górecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kües, U., Kumar, T.K.A., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A., Rokas, A., Ruiz-Dueñas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St. John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., Hibbett, D.S., 2012. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336 (6089), 1715–1719. http://dx.doi.org/10.1126/science.1221748. García, M.A., Alonso, J., Fernández, M.I., Melgar, M.J., 1998. Lead content in edible wild mushrooms in northwest spain as indicator of environmental contamination. Archives of Environmental Contamination and Toxicology 34, 330–335. Garcia, M.A., Alonso, J., Melgar, M.J., 2005. Agaricus macrosporus as a potential bioremediation agent for substrates contaminated with heavy metals. Journal of Chemical Technology and Biotechnology 80, 325–330. Hammond, J.B.W., 1981. Variations in enzyme activity during periodic fruiting of Agaricus bisporus. New Phytology 89, 419–428. Imbernon, M., Callac, P., Gasqui, P., Kerrigan, R.W., Velcko, A.J., 1996. BSN, the primary determinant of basidial spore number and reproductive mode in Agaricus bisporus, maps to chromosome I. Mycologia 88, 749–761. Jin, T., Sonnenberg, A.S.M., Van Griensven, L.J.L.D., Horgen, P.A., 1992. Investigation of mitochondrial transmission in selected matings between homokaryons from commercial and wild-collected isolates of Agaricus bisporus( = Agaricus brunnescens). Applied and Environmental Microbiology 58, 3553–3560. Kameda, E., Langone, M.A.P., Coelho, M.A.Z., 2006. Tyrosinase extract from Agaricus bisporus mushroom and its in natura tissue for specific phenol removal. Environmental Technology 27, 1209–1215. Kerrigan, R.W., 1982. The genus Agaricus in coastal California. Master’s thesis. San Francisco State University, San Francisco, California, 208 pp.. Kerrigan, R.W., 1986. The Agaricales (Gilled Fungi) of California, 6. Agaricaceae. Mad River Press, Eureka, California, 62 pp.. Kerrigan, R.W., 1995. Global genetic resources for Agaricus breeding and cultivation. Canadian Journal of Botany 73, S973–S979. Kerrigan, R.W., Royer, J.C., Baller, L.M., Kohli, Y., Horgen, P.A., Anderson, J.B., 1993. Meiotic behaviour and linkage relationships in the secondarily homothallic fungus Agaricus bisporus. Genetics 133 (225), 236.
Please cite this article in press as: Kerrigan, R.W., et al. Agaricus bisporus genome sequence: A commentary. Fungal Genet. Biol. (2013), http://dx.doi.org/ 10.1016/j.fgb.2013.03.002
4
R.W. Kerrigan et al. / Fungal Genetics and Biology xxx (2013) xxx–xxx
Kerrigan, R.W., Carvalho, D.B., Horgen, P.A., Anderson, J.B., 1998. The indigenous coastal Californian population of the mushroom Agaricus bisporus, a cultivated species, may be at risk of extinction. Molecular Ecology 7, 35–45. Kües, U., 2000. Life history and developmental processes in the basidiomycete Coprinus cinereus. Microbiology and Molecular Biology Reviews 64 (2), 316– 353. Kües, U., James, T.Y., Heitman, J., 2011. Mating type in basidiomycetes: unipolar, bipolar, and tetrapolar patterns of sexuality. In: Pöggeler, S., Wöstemeyer, J. (Eds.), Evolution of Fungi and Fungal-Like Organisms, The Mycota XIV. SpringerVerlag, Berlin Heidelberg. Kuusi, T., Laaksovirta, K., Liukkonen-Lilja, H., Lodenius, M., Piepponen, S., 1981. Lead, cadmium, and mercury contents of fungi in the Helsinki area and in unpolluted control areas. Zeitschrift für Lebensmitteluntersuchung und -Forschung A 173, 261–267. Li, Y., Challen, M.P., Elliott, T.J., Casselton, L.A., 2004. Molecular analysis of breeding behaviour in agaricus species. Mushroom Science 16, 103–109. Lodenius, M., Kuusi, T., Laaksovirta, K., Liukkonen-Lilja, H., Piepponen, S., 1981. Lead, cadmium and mercury contents of fungi in Mikkeli, SE Finland. Annales Botanici Fennici 18, 183–186. Morin, E., Kohlera, A., Baker, A.R., Foulogne-Oriol, M., Lombard, V., Nagy, L.G., Ohm, R.A., Patyshakuliyeva, A., Brun, A., Aerts, A.L., Bailey, A.M., Billette, C., Coutinho, P.M., Deakin, G., Doddapaneni, H., Floudas, D., Grimwood, J., Hildén, K., Kües, U., LaButti, K.M., Lapidus, A., Lindquist, E.A., Lucas, S.M., Murat, C., Riley, R.W., Salamov, A.A., Schmutz, J., Subramanian, V. Wösten, H.A.B., Xu, J., Eastwood, D.C., Foster, G.D., Sonnenberg, A.S.M., Cullen, D., de Vries, R.P., Lundell, T., Hibbett, D.S., Henrissat, B., Burton, K.S., Kerrigan, R.W., Challen, M.P., Grigoriev, I.V., and Martin, F., 2012. The genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. In: Proceedings of the National Academy of Sciences of the United States of America.
Pilát, A., 1951. The Bohemian species of the genus Agaricus. Acta Musei Nationalis Pragae 7B, 1–142. Raudaskoski, M., Kothe, E., 2010. Basidiomycete mating type genes and pheromone signaling. Eukaryotic Cell 9 (6), 847–859. Semple, K.T., Fermor, T.R., 1997. Enhanced mineralization of UL-14Cpentachlorophenol by mushroom composts. Research in Microbiology 148, 795–798. Sonnenberg, A.S.M., Baars, J.J.P., Hendrickx, P.M., Lavrijssen, B., Gao, W., Weijn, A., Mes, J.J., 2011. Breeding and strain protection in the button mushroom Agaricus bisporus. In: Proceedings of the 7th International Conference on Mushroom Biology and Mushroom Products (ICMBMP7). Stark, L.R., Williams, F.M., 1995. The role of spent mushroom substrate for the mitigation of coal mine drainage. In: Environmental Agricultural and Industrial Uses for Spent Mushroom Substrates from Mushroom Farms. JG Press, Inc., Emmaus, PA, pp. 74–84. Umar, M.H., Van Griensven, L.J.L.D., 1997. Morphological studies on the life span, developmental stages, senescence and death of fruit bodies of Agaricus bisporus. Mycological Research 101, 1409–1422. Weijn, A., Bastiaan-Net, S., Wichers, H.J., Mes, J.J., this issue. Melanin biosynthesis pathway in Agaricus bisporus mushrooms. Fungal Genetics and Biology. http:// dx.doi.org/10.1016/j.fgb.2012.01.004. Wells, T.K., Hammond, J.B.W., Dickerson, A.G., 1987. Variations in activities of glycogen phosphorylase and trehalase during the periodic fruiting of the edible mushroom Agaricus bisporus (Lange) Imbach. New Phytology 105, 273–280. Xu, J., Kerrigan, R.W., Callac, P., Horgen, P.A., Anderson, J.B., 1997. Genetic structure of natural populations of Agaricus bisporus, the commercial button mushroom. Journal of Heredity 88, 482–488. Xu, J.P., Desmerger, C., Callac, P., 2002. Fine-scale genetic analyses reveal unexpected spatial-temporal heterogeneity in two natural populations of the commercial mushroom Agaricus bisporus. Microbiology-SGM 148, 1253–1262. Xu, J., Zhang, Y., Pun, N., this issue. Mitochondrial recombination in natural populations of the button mushroom Agaricus bisporus. Fungal Genetics and Biology. http://dx.doi.org/10.1016/j.fgb.2012.09.004. Zurera, G., Rincón, F., Arcos, F., Pozo-Lora, R., 1986. Mercury content in mushroom species in the Cordova area. Bulletin of Environmental Contamination and Toxicology 36, 662–667.
Please cite this article in press as: Kerrigan, R.W., et al. Agaricus bisporus genome sequence: A commentary. Fungal Genet. Biol. (2013), http://dx.doi.org/ 10.1016/j.fgb.2013.03.002