Genome Sequencing And Bioinformatic Analysis Of Plasmodiophora Brassicae

Clubroot is a soil-borne disease caused by Plasmodiophora brassicae,which has caused serious economic losses to Brassica oil and vegetable crops worldwide.P.brassicae is a Plasmodiophorid,obligate biotrophic protist in the eukaryotic kingdom of Rhizaria.In order to fully understand the genomic characteristics of P.brassicae,Pac Bio three-generation sequencing of strains from Liaoning Province Xinmin(LNXM-1)was carried out in this study.Combining with bioinformatics analysis,the genome of P.brassicae was analyzed,so that people could understand the P.brassicae more deeply and provide accurate basis for the control of clubroot.The main results are as follows:The isolate LNXM-1 from Xinmin of Liaoning Province was identified by Williams race identification system.It was found that isolate LNXM-1 was pathotype 4.Three methods were used to extract DNA from LNXM-1 P.brassicae in Liaoning Province.It was found that the DNA extracted by CTAB method was easy to degrade and the DNA extracted by kit method was not degradable,but the concentration could not reach the third generation sequencing standard.Finally,the DNA was extracted by urea method and the third generation genome was sequenced.The assembled genome size of LNXM-1 was 25.25 Mb and 28 scaffold.The percentage of GC content was 59.38%.A total of 13,036 coding genes were predicted.There are 234 repetitive sequences in the whole genome of P.brassicae,accounting for 0.08% of the total genome sequence;68 short interspersed nuclear elements,129 long interspersed nuclear elements and 37 DNA elements.Meanwhile,154 t RNA,318 sr RNA and 128 sr RNA and 218 sr RNA were predicted.In this sequencing,66 CRISPR were predicted,of which 3 were known CRISPR and 63 were unknown CRISPRs.A total of 815 SSRs were detected by SSR analysis.The average distance between SSRs was 30.97 kb.The number of SSRs containing the total number of SSRs was 624,accounting for 76.44% of the total number of SSRs.There were 131 SSRs with more than one SSR.There were 804 SSRs(98.7%)with 2 and 3 nucleotide repeats.The highest number of SSRs was found in three nucleotides,746 of which accounted for 91.53% of the total number of SSRs.There are 20 duplicate elements in the genome of P.brassicae.There are 58,746,4,2 and 5 nucleotide repeats in 2-6 nucleotide repeats.GC/CG,AC/GT repeats were dominant in the two nucleotide repeats,while ACG/CGT,AGC/CTG and CG/CGG repeats were dominant in the three nucleotide repeats,accounting for 49.33%,22.52% and 17.29% of the repeat types respectively.According to the whole genome sequence of LNXM-1,the gene function was annotated.There are 1371 genes involved in biological processes,917 genes with molecular functions and 900 genes involved in cell component synthesis.From KEGG,we can find 407 genes related to metabolic pathway,accounting for 27.33% of the total annotated genes;149 genes related to secondary metabolites,accounting for 10.01% of the total annotated genes;44 genes related to amino acid biosynthesis,accounting for 2.96% of the total annotated genes.There are related genes encoding lysine,arginine,phenylalanine,tyrosine,tryptophan,lysine,leucine and isoleucine in P.brassicae.Genes participate in the metabolism of glycine,serine,methionine,arginine,proline,alanine,aspartic acid,glutamic acid,tyrosine,tryptophan,phenylalanine and histidine.Genes also participate in the metabolism of valine.Degradation of amino acid,leucine,isoleucine and lysine.It was predicted that there were 13,036 proteins and 754 secreted proteins.We found that 26 genes encode chitin synthase,11 genes are related to effector pathway,11 genes are related to heat shock protein,1 gene is related to trehalose synthesis,13 genes are related to toxicity,3 genes are related to regulating pathogenic factors,and 28 genes are related to nutrition synthesis.