Genome Sequencing And Comparative Genomic Analysis Of Arthrinium Phaeospermum AP-Z13

Arthrinium phaeospermum(Corda)M.B.Ellis is a pathogenic fungus with a wide host range and worldwide distribution;its hosts include not only plants,but also humans and animals,therefore,it has attracted much attention of researchers.As a pathogen of hybrid bamboo blight,A.phaeospermum AP-Z13 can cause a large number of Bambusa ervariabilis × Dendrocalamopsis daii hybrid bamboo dead in Sichuan cultivation area,huge economic lossed,and which greatly threatening the process of returning farmland to forestry and the construction of ecological barriers in the middle and upper reaches of the Yangtze River.The whole genome was obtained from mycelia of the strain AP-Z13 using a combination of a high-throughput Illumina Hi Seq 4000 system with the Pac Bio RSII longread sequencing platform.Functional annotation was accomplished by blasting protein sequences against different publicly available databases to obtain their corresponding annotations.The whole genome sequencing and comparative genomics analysis of AP-Z13 were carried out,which was to study AP-Z13 more comprehensively from the aspects of collinearity,protein family,specific genes,single copy genes,phylogenetic evolution,gene enrichment,gene content,gene function annotation and secondary metabolites.The main results are as follows:1.By genome sequencing and bioinformatics analysis,the genome size of AP-Z13 was 48,449,939 bp,Gap(N)was 0,19 scaffolds,N90 fragment length was 1,931,147 bp and GC content was 53.05%;the total length of encodes 19,836 putative predicted genes was 28,733,037 bp,accounting for 59.30% of the total genome length;there are 468 dispersed repeats,39,268 bp in length,accounted for 0.08% of the total genome length,and 11,027 tandem repeats,288 t RNA,54 r RNA.Among them,18,071,11,451,19,131,15,565,6,559,1,917,3,611 and 9,050 genes were able to annotate in NR,Swiss-Pro,KOG,KEGG,GO,CAZy,PHI and Pfam databases respectively.1,721 secreted proteins,66 secondary metabolite biosynthetic gene clusters were also obtained.The sequencing data from this article are available in the Gen Bank database(accession number QYRS00000000).The SRA accession number is SRR7881020.2.Through genome-wide comparative genomics analysis,it was found that AP-Z13 had lower collinearity with FO-v2,Aci Ta?1,UCR-El and RN-2;there were 29,549 homologous genes and 5,886 gene families between AP-Z13,FO-v2,UCR-El and RN-2species.AP-Z13 has 9,686 specific expressed genes and 8,741 gene family;Among AP-Z13,the “metabolic pathway” enriched specific genes were up to 697,accounting for53.17% of the differentially expressed genes(1,311)of the total pathway annotation.AP-Z13 has 2,513 specific genes which are significantly enriched in GO functional categories,mainly including “metabolic process”,“single-organism process”,“cellular component organization or biogenesis” in the classification of biological process and“catalytic activity” and “binding” in the classification of molecular function.The evolutionary relationship between AP-Z13 and FO-v2 was the most closest by comparing and analyzing the evolution of single copy homologous genes;through Ka/Ks analysis,there were 3,560 single-copy homologous genes in the AP-Z13 and FO-v2,of which 3,559non-synonymous mutations,1,913 synonymous mutations,2 strongly positive-selected genes,59 weakly positive-selected genes,331 negative-selected genes.SSR analysis showed that there were 425 single-copy genes with simple repeat sequences in AP-Z13,among which AGC/CTG and CCG/CGG had the highest frequency.This research was the first genome-scale assembly and annotation for A.phaeospermum,which also was the first sequenced species in Arthrinium.The aim of this study is to develop genomic resources for A.phaeospermum to provide solid data and a theoretical basis for further study of its pathogenesis,genomics,transcriptomics,proteomics,metabolomics and RNA genomics.It is helpful to the in-depth study of the fungus.