Genomic Sequencing of Provides Insight Into Its Conservation and Diversification With Two Closely Related Species Associated With Citrus.

, , and are three very important species associated with citrus. is an endophyte fungus of citrus while can cause black spot of citrus (e.g., oranges and mandarins). was identified recently which is the causal agent of the pomelo tan spot. Here, we present the ∼34 Mb genome of . The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with two other species ( and ) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pair-wise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. The three species investigated shared a core set of 7261 protein families. had the largest set of orphan genes (1991), in complete contrast to that of (364) and (262). Most of the orphan genes are functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites biosynthesis clusters were identified in the three species, 21 of them being highly conserved among these species while the remaining two showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of three species of associated with citrus and paves the way to identify effectors that function in infection of citrus plants.