After the completion of the project of the backer’s yeast Saccharomyces cerevisiae genome sequencing in 1996, genomes of some fungi have been decrypted. Many reasons drive the decision to sequence one genome and not the other one: some fungi being for a long time scientific models, others displaying industrial relevance, and others acting as saprophytes or pathogens. Backer et al. (2008) propose an interesting concept: let’s change our way of thinking and let’s consider microorganisms (especially fungi) as reservoirs for sustainable answers to environmental concerns. This point of view fits well with the directing idea of this chapter. To improve the "biomass to ethanol" process, we have to consider many options and enlarge the fields to be prospected rather than being focalized on a single system. As an example for biomass degradation, many efforts have been directed though Trichoderma reesei due to historical reasons (discovered during World War II because it degraded uniforms and cotton tents) and to its capacity to produce cell wall degrading enzymes, specially cellulases. But, as it will be described later in this section, this fungus is not — by far for some categories of enzymes — the most equipped in CWDE. Other fungi have to be considered then.

Genome sequence availability offers the scientific community the opportunity to analyze them, deciphering their metabolism, in order to find response to fundamental or applied questions. As valorization of plant biomass arise as an important question to be addressed, several studies attempt to describe the fungal polysaccharide degradation potential. An extensive and complete work leads to a comparison of the genome of 13 fungi (Martinez et al., 2008). The first observation is that the yeast model Saccharomyces cerevisiae is poorer in CWDE than filamentous fungi (Fig. 2). This is not surprising regarding their respective lifestyles; all the filamentous fungi shown in Fig. 2 are saprotrophs or pathogens in the opposite of S. cerevisiae. This is a first argument for considering the natural habitat of a fungus when examining it for a peculiar application. Here, clearly, fungi living in plant environment displayed many more genes encoding CWDE or associated activities. Note that the model for plant polysaccharide degradation, Trichoderma reesei, displays fewer putative glycosyl hydrolases (200) than the pathogens Magnaporthe grisea (231) and Fusarium graminearum (243). Perhaps even more important is the number of cellulose binding modules (CBM), allowing a better enzyme-substrate binding and then a better efficiency in natural cellulose hydrolysis. T. reesei was predicted to have half CBM than the two pathogens (Fig. 2). In the same study, T. reesei is shown to be poorer than M. grisea and F. graminearum in cellulases, hemicellulases and pectinases (Martinez et al., 2008).

The main idea driving genome study is that evolution leads to genomes remodeling: i. e. leading to CWDE diversity for fungi dealing with plants. But through the example of T. reesei, it could be concluded that genome study — if available — is useful but not sufficient. Furthermore, obviously, a gene is not a protein; it has to be transcribed and mRNA has to be translated and modified to yield to mature and functional proteins.