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Fungi play important roles in nature and in our daily life. In nature, fungal species serve as decomposers of biomass, which is critical for carbon and nutrient cycling. In our daily life, edible mushrooms are well-known examples of fungi. Saccharomyces cerevisiae, known as a baker's yeast, is widely used in winemaking, baking and brewing. Some fungi are also known as producers for drugs, such as antibiotics. Fungal species are also important pathogens in insects, animals, human and plants.
Fungi belong to one of the four kingdoms of eukaryotic organisms. Fungal cells contain multiple subcellular compartments for performing different subcellular activities. For example, a mitochondrion, which is a membrane-enclosed structure, is mainly used to provide cellular energy; and a nucleus is a place for storing genetic materials and a site for controlling gene transcription. In this work, we define a secretome as all proteins secreted outside the plasma membrane in a species. These proteins include cell wall proteins, extracellular matrix proteins, and secreted soluble proteins that may serve as a hormone or signal molecule or an enzyme. However, the proteins in the secretory pathway machinery were not included, which is slightly different form the original definition of a secretome (Tjalsma et al., 2000; Lum and Min, 2011a). Secreted proteins in biotrophic fungi are identified as the main effectors responsible for pathogenic or symbiotic interactions between plants and fungi (Girard et al., 2013). Saprophytic fungi secrete a large number of families of hydrolytic enzymes such as glycoside hydrolases for breaking down complex biomaterials like lignin and cellulose (Martinez et al., 2004; Martinez et al., 2009; Murphy et al., 2011). Recently, along with complete genome sequencing of many fungi, identification and analysis of secretomes in fungi has been an important subject of research, using both computational and experimental approaches (Bouws et al., 2008). For example, the secretomes have been reported in following fungi including Aspergillus niger (Tsang et al., 2009; Braaksma et al., 2010), Aspergillus fumigatus (Powers-Fletcher et al., 2011), Candida albicans (Lee et al., 2003; Ene et al., 2012), Doratomyces stemonitis C8 (Peterson et al., 2011), Fusarium graminearum (Paper et al., 2007; Brown et al., 2012), Irpex lacteus (Salvachúa et al., 2013), Magnaporthe oryzae (Jung et al., 2012), Mycosphaerella graminicola (Morais et al., 2012), Paracoccidioides (a complex...