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The life cycle of Phomopsis liquidambari consist of two distinct phases,the saprophytic and endophytic phase,respectively.Once fungi colonize inside plant tissues and establish a symbiotic association with host plant,the genes coding for enzymes decomposing plant cell will not be expressed.With the senescence and the internal environmental change of the host plant,fungi start to express the gene for saprophytism and shift from biotrophy to saprotrophy.However,little is known about the genes involved in this progress and the in vivo environmental factors that lead to gene expression.Understanding the dynamics of the transcriptome is essential for interpreting phenotypic variation caused by combinations of genotypic and environmental factors.It was found that under different host environment,the genes related to carbohydrate metabolism play a vital role in the processes of fungal biotrophy and saprotrophy.Genes mainly performing molecular function of catalysis and transporter,and participating in metabolic processes in the cell and on the cellular membrane.Under the condition of biotrophy,in order to adapt to the host,P.liquidambari synthesize a large amount of secondary metabolites and ribosome.The genes of Citrate cycle pathway were up regulated.Under the condition of saprotrophy,P.liquidambari be forced to decompose organic matterdue to the host lack the nutrition.The genes involved in carbohydrate metabolism were up-regulated resulting enhanced the catabolism of hardly degradable organic compounds.Our results explained the interrelation of fungal endosymbiosis and saprotrophy from genetic perspective.