Comparative Genomics Of Five Pathogenic Species Of Genus Valsa

Fungi of ascomycetes genus Valsa are aggressive pathogens that cause the Valsa Canker on tree branches,which occur extensively in China and around the world and are hard to be controlled.Therefore,comparing the genomic information of different pathogenic species of Valsa spp.is worth on the understanding of pathogenic mechanism.Moreover,it will play important role in guiding disease resistance breeding and drug research and development.In this study,the whole genome of five pathogenic species of genus Valsa were sequenced and comparatively analyzed,and the following main results were obtained:1.Newly sequencing three genomes of Valsa spp.,and the genome-wide comparative analysis of five Valsa spp.were performed for the first time.(1)This study completed genomes of three important pathogens of Valsa spp isolated from China,including a weak pathogenic strain V.malicola isolated from apple tree,a poplar tree pathogen V.sordida and a peach tree pathogen V.persoonii.The genome size of them were 38.3 Mb,36.2 Mb and37.6 Mb,respectively.The numbers of protein coding genes were 10848,10099 and 10296,respectively.(2)We systematically clarified the evolutionary relationship between these three species and two previously sequenced species,V.mali and V.pyri: V.mali(Vm)and V.pyri(Vp)were closest,V.malicola(Vmc)and V.sordida(Vs)were closest,V.persoonii(Vps)have the farthest evolutionary relationship from others.(3)Comparison of homology between Valsa spp.indicated that they showed a high collinearity level,more than 90% of the genes were in the synteny blocks,and more than 90% of the genes had orthologous genes between these species.2.Comparative analysis revealed potential factors which may influence the virulence differences of Valsa spp.that preferring different host.(1)Secondary metabolic gene clusters tended to diverge between Valsa spp.,a lot of the clusters were location-related to highly variable AT-rich regions and enriched with orphans of Valsa spp.,this may facilitate the production of host specific toxins.(2)Host resistance-related membrane proteins,such as DHA and ABC transporter families,were divergent in sequence variation and genome location between Valsa spp..And G-protein coupled receptors(GPCRs),which play critical role in pathogen-host interaction,showed significant positive selection in Vm and Vs.These variations of membrane proteins may promote Valsa spp.to adapt to different host environments and nutritional conditions.(3)Secretory signals were differentially lost in orthologs of Valsa spp.,which including putative effectors,cell wall degrading enzymes and proteases.This indiacted that certain virulence factors may evade identification of host immunity through loss of secretory signal,and therefore it is beneficial for Valsa spp.to prefer different hosts.3.Our analysis found that repeat elements played important role in divergence of Valsa spp..(1)The insertion of repeats into genes affected the variation rate which was distinct from that of non-inserted genes,and genes duplication may be related to the insertions.(2)Repeat-rich sequcences were highly coincident with AT-rich regions,and may drive the formation and sequence variation of these regions.(3)Expansion and Contraction of repeats content happened obviously during divergence of Valsa spp..In Vm,large fragment insertion within conserved synteny blocks was a form of extending genome size that differs from other species.Based on the above analysis,this study systematically analyzed the evolutionary relationship,homology,difference and causes of the differences among the five pathogenic species of Valsa spp..It provides important clues for deeper understanding of the pathogenic mechanism and host preference.