Taxonomy Of Large-spored Alternaria From Solanaceae And Whole Genome Sequencing Of Strain YZU 161111

Solanaceae plants are widely distributed in temperate and tropical regions and there are 24 genera including around 105 species in China.The plants have important economic,medicinal and ornamental values.The genus Alternaria is one of the economically important fungal genera,comprising species causing many plant diseases and leading to serious economic loss,such as the early blight on Solanaceae.In this study,diseased tissues of Solanaceae plants were widely collected for Altenraria isolation and largespored strains were determined based on morphology and phylogeny.A representative strain was selected for whole-genome sequencing,combined with transcriptome sequencing data of mycelium and spores.Its systematic analysis was carried out and the results were as follows:From 2017 to 2019,a total of 78 strains of large-spored Alternaria were collected from Inner Mongolia,Jilin,Qinghai,Gansu and Hubei provinces of China.According to their colony morphology,host and sampling location,14 strains were determined for phylogenetic analyses based on the five gene sequences(Alt al,GAPDH,RPB2,ITS and TEF1)and morphological examination.A total of 5 different species were identified,of which a new species,named Alternaria physalidis sp.nov.;isolated from Physalis peruviana;a new record in China A.blumeae from Solanum tuberosum;A.solani from S.tuberosum;A.crassa from Datura stramonium and A.brassicae from Lycium chinense.In addition,it was found that there were some heterozygous sites in some protein coding genes of 7 strains.Phylogenetic tree was constructed after deleting all those bases in the combined sequences of five genes.The results showed that the seven strains were clustered together as an individual clade,however there are certain differences among them on morphology.Based on the results of taxonomy and pathogenicity tests,the strain YZU 161111(Alternaria solani)was selected as a representative strain for whole-genome sequencing.Totally 26 Scaffolds were obtained after assembly.The complete genome size is 34.38 Mb and its GC content is 51.01%.The result of genetic structure prediction on sequencing data showed that a total of 11,368 genes were included,with a total gene length of about 18.89 Mb,of which the exon length was about 16.93 Mb.The predicted genes were annotated and classified using KOG and GO databases.After the sequencing of the two transcriptomes of mycelium and spores,the Clean Reads were aligned with the genome data and the alignment efficiency was 88.66% and 88.44%,respectively.Then,the SNP analysis was performed on the two transcriptomes and both were 460 SNPs.The alternative splicing events on the two transcriptomes of mycelium and spores were predicted that the number were 17,699 and 19,757,respectively.Besides,types of TSS and TTS have the highest proportion among them.Mapped Reads of each transcriptome were aligned with the original annotation information of the genome.A total of 143 new genes were found.The amount of gene expression of Clean Reads from the two transcriptomes was calculated using FPKM method and performed the differential expression analysis.A total of 1289 differentially expressed genes were found.In the transcriptome of spores,the number of up-and down-regulated genes were 499 and 790,respectively.In addition,the obtained differentially expressed genes were annotated and classified in GO,COG and KEGG databases,and compared in the STRING database to construct a protein-protein interaction network.