Genome Sequencing And Comparative Genomic Of Phomopsis(Diaporthe) Capsici

Phomopsis capsici(syn.Diaporthe capsici)is a phytopathogenic fungus that is rarely studied in the world,and mainly causes diseases of Solanaceae plants.The team of Professor Zhu from the Forestry Pathology Laboratory of Sichuan Agricultural University successfully isolated and identified P.capsici,from walnut branches infected with branch blight in Guangyuan,Sichuan,and proved that it can cause forest tree disease walnut branch blight.In China,the occurrence of walnut branch blight has caused huge economic losses.Especially,walnut is an important pillar industry and a special industry poverty alleviation project for rural development and construction.Diseases on walnuts should be paid more attention.This study used Pacbio RSII,the three-generation sequencing platform of Beijing Novogene Bioinformatics Technology Co.,to perform genome-wide sequencing on P.capsici,and annotated genes after assembly to obtain basic annotation information including the database of fungal virulence factors,P.capsici has been comprehensively studied in terms of collinearity,single nucleotide polymorphism,common genes,gene families,and species evolution between P.capsici and other common branch pathogens.The main research results are as follows:1.Through whole-genome sequencing and assembly,the fungal genome size is57585510 bp,20 Contigs,the length of N50 Contig is 5171887 bp,and the GC content is51.26%.It is predicted that 14425 coding genes,with a total length of 23205508 bp,the total length of the coding region accounted for 40.32% of the entire genome length;2117interspersed repeats;23212 tandem repeats;151 t RNA,37 r RNA,2 s RNA,16 sn RNA.Using GO,KEGG,KOG,NR,TCDB,Pfam,Swiss Prot,CAZy,CYP450,PHI,DFVF databases,9318,11022,2094,13113,495,9318,3649,843,368,1618,555 genes were obtained Notes.In addition,1488 secreted proteins and 105 secondary metabolite gene clusters are predicted.The whole genome data has been submitted to Gen Bank with the accession number WNXA00000000 and the accession number of the original data SRR10692909.2.Through comparative genomics analysis,it was found that P.capsici had good collinearity with D.helianthi and J.oblonga,and lower collinearity with N.parvum UCRNP2 and B.dothidea.The sequences of D.helianthi,J.oblonga,N.parvum UCRNP2,and B.dothidea were compared with the reference sequence P.capsici,and 1863,3710,4969,and 5196 SNPs were found,including 1765,3528,4767,and 4973.SNP occurs in the protein coding region;the number of Core genes are 8091,4702,2373,and 2426;the Pan gene are 18791,18576,21629,and 21641 respectively.The total number of genes of the five fungi is 496,40 and 117 are annotated in the DFVF and PHI databases,respectively.Gene family clustering results show that there are 7954 gene families and 7465 homologous genes in the P.capsici genome,including 2679 single-copy homologous genes and 4786 multicopy homologous genes.The phylogenetic tree was constructed through SNP and gene family.The results showed that P.capsici and D.helianthi had the closest relationship,followed by J.oblonga,and J.oblonga had the longest evolutionary distance,and was related to B.dothidea and N.parvum UCRNP2.The relationship is far away,and the results are in line with expectations.