| Sugarcane smut(Sporisorium.Scitamineum),a biotrophic basidiomycete fungus causes the vast cost lost world-widely.The S.scitamineum is a dimorphic pathogen,including the haploid stage without pathogenic ability and the virulence dikaryotic mycelium stage.Previous studies have shown that the mating type(MAT)genes play key role of the stage transition and belong to the pathogenic genes.Two different MAT types of spores form pathogenic dikaryotic mycelium,which infects sugarcane.Coordination-related genes are a group of key genes that transform from haploid to dikaryotic,and are also genes related to pathogenicity.However,at present,there is only one reference geneome with annotated MAT genes.Although the genome sequences of two Ssc strains have been published or submit to the public gene information database,the genetic diversity of the pathogen is still insufficient,which limits the further investigation of mechanism leading to the pathogenic of S.scitamineum.In this study,a pair of mating compatible S.scitamineum strains(JG 35 and JG36)were sequenced with Pacbio platform.Flowing the data analysis pipeline,the genome sequences of a pair of S.scitamineum strains of highquality chromosome level were obtained.With the analysis of the genetic diversity,the genes composition of the a1b1 and a2b2 coordination loci located on chromosome 2 were identified.The genes in the a2b2 type a-loci were Lba,maf1.3,pra2,lga2,rga2,mfa2.1 and rba2 genes,the genes in the a1b1 type a-loci were Lba,mfa3.2,mfa1.3,pra1 and rba1.The fragment on chromosome 2 that is closely linked to the matching locus was about 62 Kb in the type of a1b1 and 70 Kb in the type of a2b2.Through further comparison,the variations at the a-loci over 40%,and there were significant multi-base insertion / deletion mutation sites.Beside these two Pacbio platform geneome data,another 15 S.scitamineum samples which collected from Guang Dong,Guangxi and Yunnan province were sequenced with Illumina platform.The genome of Ssc I8 strain and Australian strain are computed with our 17 S.scitamineum strains(2 Pacbio platform and 15 Illumina platform data).There were 5,507 core genes,3,142 shell genes and 3,633 cloud genes are idenfied with pan-genome analysis.Therefore,the total S.scitamineum gene numbers were 12,282 in 19 strains.The pan-genome results provide the boundary of Ssc population evolution,and also can clarify the genetic composition of different strains and the genetic basis of pathogenic differences.The RNA-seq date revealed that the alternative splicing events occurred in both haploid and diploid S.scitamineum.A total of 593 genes were detected with alternative splicing in all samples.The maxism one has 13 different type of alternative splicing.At the same time,a total number of 1,566 differentially expressed genes were identified with haploid and diploid data.Among of them,904 genes were up-regulated and 662 genes were down-regulated.The lnc RNAs were predicted with the RNA-seq data.There were 206 lnc RNA in haploid sample and 356 lnc RNA in diploid sample.To discover the pattern of lnc RNA-regulated pathogenic gene expression,the lnc RNA-m RNA binding network was constructed with haploid data.The results showed that the antioxidant activity,transcription factor binding,protein binding,symplast and detoxification genes are mayjor virulence related genes.Using a method similar to pan-genome analysis,a total of 757 effector candidate genes were predicted in all samples of this study,including 501 core effector genes,229 coat effector genes,and 45 cloud effector genes.Some effector genes also showed genetic diversity during different strains.This is the first systemic genetic diversity investigation on S.scitamineum with genomic data.The results provide fundamental knowledge for S.scitamineum infection mechanism research. |
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