| Arthrinium rasikravindrae AQZ-20 is a devastating fungus and responsible for severe infections in a large number of host plants all over the world discovered by the author of this paper for the first time,which can cause diseases of Sichuan bamboo branches,so it has attracted widespread attention from researchers.In the present study,The author used Pacbio RSII,Illumina Hi Seq 4000 Technology to perform the whole genome sequence of devastating fungus Arthrinium rasikravindrae strain AQZ-20.Furthermore,to identify associated annotation results,various corresponding functional annotations and metabolic pathway analyses were utilized on databases.Secondary metabolite gene clusters were predicted in anti SMASH,MUMmer software was used for genome comparison.Arthrinium rasikravindrae AQZ-20 has been comprehensively studied in terms of collinearity,single nucleotide polymorphism,common genes,gene families and species evolution between Arthrinium rasikravindrae AQZ-20 and other common branch pathogens.Based on the determination of the Arthrinium rasikravindrae AQZ-20 transcriptome,the pathogenic genes were screened and validated;the relevant genes were verified by q RT-PCR.Additionally The author have investigated the metabolic profile of Arthrinium rasikravindrae AQZ-20 and the association between the transcriptome and metabolome studies has also been evaluated.The main findings are as follows:1.Through whole-genome sequencing and assembly,the fungal genome size was48.24 MB with an N90(scaffolds)length of 2,184,859 bp and encoded putative genes were11,101,respectively.32 Contigs,the length of N50 Contig is 2,356,085 bp,and the GC content is 52.66%.The genomic data predicted a total of 11,101 coding genes with an entire length of 45,874,955 bp,accounting for 31.73% of the total genome length.The coding genes mean length was noticed as 1311 bp;6442 tandem repeats;t RNA(268),sn RNA(15),s RNA(2),and mi RNA(1),respectively.The various functional annotations were assigned to the genes using functional databases,including KOG,GO,KEGG,NR,P450,Pfam,Swiss-Prot,TCDB,PHI,DFVF,and CAZy databases,2085,6793,1004,2526,98,6792,3241,197,1415,2058,and 309 genes were obtained were also used for functional annotation results.In addition,1081 secreted proteins and 82 secondary metabolite gene clusters were predicted.2.In addition,The author evaluated the comparative genomic analyses with 4 fungal strains of Ascomycota,comparing Arthrinium rasikravindrae AQZ-20 genomic data with two related species of the same genus,the remaining two of which are non related other genus species.While,two related species viz;Arthrinium phaeospermum and Arthrinium malaysianum STlab-iicb,showed a strong correlation while others Fusarium oxysporum FO2 and Fusarium proliferatum ET1 exhibited a weak correlation with the Arthrinium rasikravindrae AQZ-20 fungus.Based on the phylogenetic relationship results of species analysis,inter specific phylogenetic tree and as per the phylogenetic similarity results of species analysis,only duplicate genes are recognized by a gene family.Arthrinium phaeospermum,Arthrinium malysianum,and Arthrinium rasikravindrae AQZ-20 have shown the same phylogeny branch and have no greater evolutionary distance.Fusarium oxysporum Fo2 and Fusarium proiferatum ET1 have a different evolutionary branch from Arthrinium rasikravindrae AQZ-20 and has greater evolutionary distance.these belong to Xylariales,so,these are very closely related to Arthrinium rasikravindrae AQZ-20.3.Column rot,caused by Arthrinium rasikravindrae AQZ-20,is an overwhelming disease responsible for huge economic losses in bamboo worldwide.In order to explore the molecular mechanisms of Arthrinium rasikravindrae AQZ-20,The author performed the transcriptome analysis of Arthrinium rasikravindrae AQZ-20.Herein,the statistical analysis of expression demonstrated that,a total of 5014 differentially expressed genes(DEGs)were mapped,2354 of which were up regulated and 2660 were down regulated.Functional annotation of DEGs revealed high enrichment of transcripts associated with plant-pathogen interaction,defense signaling,secondary plant metabolism,cell wall synthesis,and other biological processes.Rapid induction of pathogen responsive genes encoding,glucanases,peroxidases,receptor kinases,and ethylene signaling suggest that Lingnania intermedia adopts multiple strategies to combat Arthrinium rasikravindrae AQZ-20.Furthermore,the GO analysis of DEPs showed that all identified DEPs could be classified to 13 different cellular Component,10 in Molecular Function and 17 in Biological Process.The highest number of expressed genes 3000 and 2800 were found in cataylic activity and Binding of Molecular Function followed by 2500,2200 and 200 number of expressed genes was found in metabolic process,single organism process and cellular process of Biological process.Overall,the present study represents related genes involved in pathogenesis of Arthrinium rasikravindrae AQZ-20,and is a valuable resource for future functional genomics studies to unravel the molecular mechanisms of Lingnania intermedia and Arthrinium rasikravindrae AQZ-20 interaction.4.Additionally,The author have done screening and validation of disease causing genes randomly selected the top ten up regulated genes with the transcriptome data based on the highest value,The author have done blast and designed the possible primers and sent to the company for getting the primers,compared with reference GAPDH gene and validate the genes using Qrt-pcr.The total 19 DEGs were selected randomly based on their Log Fc value,description of the genes and verified the expression by quantitative q RT-PCR.The results showed that all the selected genes showed similar direction value which shown in the transcriptome analysis data.5.In this study transcriptomic and metabolic analysis were performed to explore the differentially expressed genes(DEGs)and differentially expressed metabolites(DEMs)in A.raiksravindrae AQZ-20.Using liquid chromatography–mass spectrometry(LC–MS)technology combined with the data dependent acquisition,the full spectrum analysis of pathogen mycelium samples was carried out.Partial least squares discriminant analysis(PLS-DA)was used to reveal the differences in metabolic patterns among different groups.Hierarchical clustering analysis(HCA)and PLS-DA were used to reveal the relationship between samples and metabolites,which reflected the metabolic changes in Arthrinium rasikravindrae AQZ-20 with two groups(ARB and ARW).The transcritpme and metabolome findings also showed that a total of 2660 or 2354 genes were downregulated or upregulated.In addition,27 or 24 metabolites were down regulated and up regulated in negative ion mode,while 92 or 50 metabolites were down regulated and up regulated in positive ion mode in ARB And ARW samples respectively.Twenty five DEGs were detected in ARB when compared to ARW.Finally,association analysis was performed for transcriptome and metabolome between ARB and ARW,which focused on the Steroid biosynthesis,Steroid biosynthesis.,Biosynthesis of unsaturated fatty acids,Biosynthesis of unsaturated fatty acids,Glutathione metabolism,which produce pathogenic genes just like2-enoyl thioester reductase,and 3-ketosphinganine reductase,which are responsible for causing disease in different host plants.These findings will provide deep insight for further studies of differential metabolites and theoretical reference for the prevention and treatment of Arthrinium rasikravindrae AQZ-20.In summary,Arthrinium rasikravindrae AQZ-20 took the lead in discovering a dangerous pathogenic fungus on the stem of bamboo,and based on the first whole genome sequencing and genome scale assembly and annotation of the fungus,transciptomic and metabolic analysis,the group was determined and its related genes were verified,and the research results will have important guiding significance for Arthrinium rasikravindrae AQZ-20 pathogenic factor and molecular interaction between pathogen and bamboo. |
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