| Fungi are a group of eukaryotes with huge amount of species and play indispensible roles in the matter cycle of the natural ecosystem. Fungi are tightly correlated with human health. Some fungi could supply nutrient as food for people, while fungal pathogens attack crops and could reduce or even entirely end the yield of crops. To understand fungi and make them be benificial to human is being the target of the mycology.Carbohydrate active enzyme (CAZyme), protein kinases, and tubulins are key important protein families and play essentional roles in fungal growth and development. Based on the whole genome data which are publicly available, in this study we did conparative genomic analysis and phylogenetic analysis focusing on CAZymes, tyrosines, and tubulins in fungi. Our study could be helpful for the understanding of the fungal phylogical process, and be benefit for the study on the pathogenic machansim of fungal pathogens, and also be helpful for the developing of new strategies for fungal disease control.The most important results are as follows:1. Fungi produce a variety of CAZymes for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition, and some families of CAZymes are directly involved in the fungal pathogenecity. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. We systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of94representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1family.2. Tyrosine kinase (TK) is a important group of kinses. In animals, TKs play essential roles in various cellular processes in animals. Whether the fungi have TKs is still need to be determined. Some studies on few fungi suggested that fungi lack TKs, while some other studies found candidate TKs in fungi but if they have TK activity is unclear. To better understand the origin and evolution of TKs, it is important to investigate if fungi have TK or TK-related genes. We systematically identified possible TKs across the fungal kingdom by using the profile hidden Markov Models searches and phylogenetic analyses. Our results confirmed that fungi lack the orthologs of animal TKs. We identified a fungi-specific lineage of protein kinases (FslK) which as a sister group is most closely related to TKs. Sequence analysis showed that members of the FslK lack key amino acid residues that determine TK-specific activities and therefore may not be TKs. However, they contain conserved catalytic domain of protein kinases and thus are likely enzymatically active. Phylogenetic analysis revealed that the last common ancestor of fungi have possessed numerous members of FslK. All these ancestral genes may have been lost in Ascomycota and also in Ustilaginomycotina and Pucciniomycotina of Basidiomycota during evolution. Most of these ancestral genes, however, were retained and further extensively expanded in the mushroom fungi Agaricomycetes.3. Tubulins are a group of important structural proteins in eukaryotes including fungi. Tubulins play essential role in the maintenance of cellular structure, cell division, cellular matter transportation, and so on. Most fungi contain only a single α-/β-/γ-tubulin genes, while a few fungi were found to encode two copies of α-/β-tubulin genes and functional divergence between different copies was experimentally evidenced. However, the evolution and molecular mechanisms driving functional diversification in fungal tubulins are not clear. We systematically identified tubulin genes from57representative fungi across fungal tree of life and determined their phylogenetic relationships. Results showed that α-and β-tubulin genes underwent multiple independent duplications and losses in different fungal lineages and formed distinct paralogous and orthologous clades. The last common ancestor of basidiomycetes and ascomycetes most likely possessed at least two paralogs (α1and α2; β1and β2) of each α-tubulin and β-tubulin genes, and α2was lost in ascomycetes while β2was lost in most ascomycetes. Molecular evolutionary analysis indicated α1,α2and β2but not β1underwent strong divergent selection pressure and adaptive positive selection after replication. Many of these positively selected sites are directly involved or adjacent to functional important sites such as those related to GTP binding and α/β interface, which most likely contribute to the functional diversification. Therefore, different evolutionary mechanisms for functional diversification occurred in α-tubulin paralogs in ascomycetes and β-tubulin paralogs in basidiomycetes. Moreover, we experimentally confirmed functional divergence of two β-tubulins (FgTubl and FgTub2) in F. graminearium; The Fgtubl plays major roles in sexual development, whereas the FgTub2plays key roles in vegetative growth. Furthermore, both molecular evolutionary analysis and experimental research revealed that the two tubulins may differently interact with microtubule associate proteins, and type Ⅱ variations in FgTub2may be associated with its functional variation. In addition, we found that chytridiomycetes contain members of the δ, ε, and η tubulin subfamilies, which have not been reported before but may be functionally related to zoospore movement. |
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