Whole Genome Sequencing Analysis With Comparative Genome Analysis Of Valsa Mali

The Valsa Canker caused by the pathogenic fungus Valsa mali has been one of the most destructive diseases of apples in China.The widespread spread of Valsa Canker has caused very serious economic losses to the domestic apple planting industry.In order to study the special mechanism of infection,colonization and pathogenicity of V.mali.In this study,a more complete genome-wide fine map was constructed by the third-generation sequencing of the whole genome of V.mali.Genome-wide analysis and comparative genomics analysis were used to search for genes that may be related to infection and colonization of host bark and drug resistance.Exploring the differences in the genomes causing Valsa canker from the genomic level,analyzing the genes related to host infection or colonization and gene families related to virulence,and exploring the basic metabolic targets of pathogenic fungi from the metabolic level.It will help us find the target metabolic pathways or key genes that inhibit its infection or growth,thus providing valuable information for studying the evolution and pathogenesis of Valsa pathogens.The main results of this study are as follows:1.We isolated and cultivated a pathogenic fungus of Valsa canker disease,identified as V.mali CCNW1,and analyzed the r DNA-ITS gene sequence to construct a phylogenetic tree of pathogenic fungi and its relatives.Using high-throughput sequencing,a high-quality V.mali genome was obtained.The genome size was 42.35 Mb and the genome integrity of V.mali was 99.2%,including 90 Scaffolds with 1.12 Mb N50,13 L50 and 120 x sequencing depth.2.The Whole genome sequencing analysis of V.mali CCNW1 showed that 490 carbohydrases were identified in V.mali,among which the most 254 were Glycoside Hydrolases(GHs)families related to cellulose degradation.In terms of pathogenic genes,V.mali has 17 plant avirulence determin-ant genes and 95 increased pathogenicity genes.In terms of antibiotic resistance,only 6 antibiotic resistance genes were identified in V.mali.Among the 61 secondary metabolic core genes,a total of 15 secondary metabolites that can secrete phytotoxins are encoded.3.The comparative genomics analysis of four Valsa pathogens including V.mali CCNW1 indicate that,The distribution of its 38,537 orthologous genes showed that 30,742 genes were shared by the four Valsa pathogens.Among them,there are only 61 specific genes of V.mali,and their gene functions are mainly related to oxidoreductase activity,acyltransferase activity,phosphopantamide binding,plant systemic acquired resistance and stress response.By analyzing the core genes related to the synthesis of secondary metabolites,it was found that V.mali contains 4 unique secondary metabolic genes,which are mainly involved in encoding pathogenic toxins such as cyclochloroquine,destruxin A,ilicicolin H and naphthpyrone.The distribution of transporter proteins in the genome showed that the genomes of these four Valsa pathogens contained DHA1(Drug: H+ Antiporter-1),especially in V.mali.Comparing the carbohydrate-active enzymes of four Valsa pathogens,it was found that there were 274 specific genes in V.mali,and V.mali shared the most CAZymes with V.pyri(112).The number of GT2 families related to cellulose degradation in the four decaying fungi was relatively close,the AA3 and AA7 families related to lignin degradation were significantly expanded in V.mali and V.pyri,and the GH28 family associated with pectin degradation was also significantly expanded in V.mali,V.pyri,V.malicola.4.A genome-wide metabolic network model i VM854 of V.mali CCNW1 was constructed.The model contains 854 genes,1504 reactions and 1098 metabolites.The carbon utilization of the i VM854 model was simulated and the gene knockout simulation of the i VM854 model was further performed to predict the growth and metabolic targets of V.mali.214 essential genes were obtained by single-gene deletion,and 90 essential gene pairs were obtained by double-gene deletion.The functions of these genes are mainly concentrated in the coenzyme transport and biosynthesis process and valine,bright Amino acid and isoleucine degradation.375 essential reactions were obtained by the reaction deletion.The functions of the essential reactions were mainly concentrated in the cellular amino acid metabolism process,the nucleotide catabolism process and the coenzyme biosynthesis process,Fatty acid biosynthesis,terpenoid backbone biosynthesis,etc.,there are functions related to cellulose degradation in non-essential reactions.In conclusion,V.mali CCNW1 not only has abundant plant cell wall degradation ability,which helps it infect the host and obtain nutrients,but also has complex pathogen-host interaction phenotype gene functions,It secretes AKT7 phytotoxin and participates in nitrogen response.virulence regulation functional mechanism to influence its pathogenicity.V.mali CCNW1 also exerts toxicity through secondary metabolites encoded by its specific secondary metabolic core genes.In addition,the transporter of Valsa spp.is also related to pathogen infection,growth and pathogenicity.The DHA1 family,which is very abundant in V.mali CCNW1,can specifically transport drug-resistant substances,helping V.mali CCNW1 to expand in the host.The simulated deletion results of the genome-scale metabolic network model also predicted essential genes and essential responses that have severe effects on V.mali CCNW1 growth.In the absence of these genes and responses,V.mali cannot perform normal biological functions.This study provides new insights into the genome-level analysis of V.mali,and provides a basic theoretical basis for the development of effective control strategies for Valsa canker disease...