| Wheat stripe rust,leaf rust and stem rust are caused by Puccinia striiformis f.sp.tritici,Puccinia recondite f.sp.tritici and Puccinia graminis f.sp.tritici respectively.Rust disease prevalence can lead to wheat production,loass and even crops,which is a serious threat to global grain production security.Virulence variety of the wheat rust fungi is the main cause of resistance to rust fungi.However,wheat rust fungal pathogenic mutation mechanism is unclear,research about rust pathogenic mechanism is main barrier.Research of genome information is one effective way for understanding growth and pathogenic mechanism of the wheat rust fungi.We have completed genome assembly update of Puccinia striiformis f.sp.tritici CY32 with Pac Bio and Illumina data.Using published genome information of leaf rust and stem rust,we finished systemic annotation and comparative analysis of Carbohydrate-active enzymes(CAZymes)and protein kinases of the wheat rust fungi.Puccinia striiformis CY32 sequencing data was used to obtain whole mitochondrial genome sequence by bioinformatics separation and assembly.The main research includes:(1)The result indicated that wheat rust contained 1,232 CAZymes coding gene(including 1,279 modules of which),the stripe rust had larger CAZymes than the others,and these three wheat rust pathogens shared 136 homologous genes of CAZymes.In comparison with the leaf rust and stem rust,the GH,GT and AA families were significantly expanded in the strip rust.There was no difference in PL family between them,but the CBM family displayed increasingly expanded from stem rust,leaf rust to stripe rust.Comparative analysis of annotations about CAZymes,cell wall degradation enzyme,secretory protein,PHI and conserved motif indicated that the strip rust mostly preferred to expansion,and the leaf rust and stem rust showed different contraction levels.CAZymes family of the wheat rusts presents expansion or contraction in different forms that may reflect the parasitic adaptation and coevolution process of the wheat rusts and the host.The results of this study willbenefit the understanding of the evolution of CAZymes families in wheat rusts,and future investigation of CAZymes in rust pathogenesis processes.(2)Stripe rust,leaf rust and stem rust had 221,159 and 159 protein kinase genes identified respectively and there is similarity and difference in the subfamily distribution.By the pan gene set of protein kinase and single copy gene set analysis,the evolutionary relationship of the wheat rust and potential pathogenic mechanism of evolution direction were identified.KEGG and GO analysis showed that protein kinase family may be an important regulatory role in pathogenic growth and development,and play the same important role in the host-pathogen interaction,including signal molecules,pathogenic factors.And MAPK protein kinase family had catalytic structure sequences,which are similar and conserved.In addition,protein-protein interaction analysis showed that MAPK protein-protein interaction was uneven in the wheat rust fungi distribution,which suggested complexity and characteristics of diversity and pathogenic mechanism of wheat rust fungi.(3)Mitochondrial genome analysis revealed that the stripe rust mitochondrial genome assembly included 31.40% in GC content and 101,520 bp.Combined with Blasr,Blat,SOAP softwares,Kmer analysis predicted genome size,to help obtain effective sequencing data including 500 Mb long reads for Pac Bio 20 Kb library and1.4 Mb short reads for Illumina 500 bp library.Miniasm software first was used to assemble the genome,in inorder to ensure genome integrity.Next GATK and SOAP softwares were used to corrrect genome sequences by Illumina data.Genome coverage and depth demonstrated the validity of assembly,laying foundation for next analysis.Using the latest genome of Puccinia striiformis f.sp.tritici CY32,this study reveald CAZymes and protein kinase annotation and evolutionary analysis,providing data for pathogenicity research of wheat rust fungi.Hybrid assembly of the third generation and second generation sequencing data,which was a high quality hybrid assembly method,made mitochondrial genome assembly level of Puccinia striiformis f.sp.Tritici increase significantly. |
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