High-yield Glucoamylase Industrial Aspergillus Niger Strains Strain Genome Assembly And Annotation And Comparative Analysis Of Functional Genes

Aspergillus niger is a filamentous fungus commonly used in industrial production.The objects of this study were Aspergillus niger SH2 and HL₁ which have the characteristics of non-spore production and strong protein secretion,and can be used for high-density fermentation in a wide range of applications.The third-genome sequencing technology,single-molecule sequencing technology without PCR amplification,eliminates the error of amplification and introduction of bases.At the same time,with its unique read-length feature,it significantly reduces subsequent gene splicing and improves the quality of functional annotations.There are significant advantages in genome sequencing.In this study,the third generation single-molecule sequencing technology was used to sequence Aspergillus niger SH2 and Aspergillus niger HL₁ Through assembly and functional gene annotation,these two strains and Aspergillus niger CBS513.88 were subjected to comparative genomics studies,respectively,from genes and functions.Protein expression and other aspects elaborated on the genetic characteristics of the two strains.The main contents and results of this study are as follows.1.Aspergillus niger SH2,HL₁ genome assembly and functional gene annotationBased on the Pac Bio platform,the whole genome sequencing of Aspergillus niger SH2 and Aspergillus niger HL₁ was performed using the third generation single molecule technique.The original reads were obtained and assembled using Celera and Falcon software to obtain optimal results.Among them,Aspergillus niger SH2 obtained 11 Scaffolds.The genome size was 34.4 Mb,11348 genes,35883 exons,11348 protein coding regions,317 t RNAs,57 r RNAs,62 s RNAs,28 sn RNAs,170 mi RNAs,and GC content of 49.74 %.Aspergillus niger HL₁ obtained 28 contigs with genome size of 34.6 Mb,10821 genes,35582 exons,10821 protein coding regions,300 t RNAs,4 s RNAs,18 sn RNAs,and GC content of 49.49 %.2.Comparative genomic analysis of Aspergillus niger SH2,HL₁ and model strain CBS513.88The genomic sequences of Aspergillus niger SH2,HL1 and Aspergillus niger model strain CBS513.88 were analyzed for homology at the nucleotide level and at the protein level,and the gene composition differences of the three strains and the missing genes of the two strains were obtained by comparison.The results of bioinformatics analysis were validated by PCR to improve the genomic information of Aspergillus niger SH2 and HL₁.Among them,the core gene associated with the spore development of Aspergillus niger strain was An18g01170?Prp A?and the model strain CBS513.88.The whole genome of Aspergillus niger SH2 and Aspergillus niger HL₁ was compared with the model strain.The result of comparison showed that Aspergillus niger SH2 lacks the gene and the gene is present in Aspergillus niger HL₁ and was 100% matched with CBS513.88,which is in contrast to the spore-free form of SH2 strain.The phenotypes of the type and HL₁ produced a small amount of spores.At the same time,the two strains have more gene enrichment in the translation and expression of proteins,and it is theoretically demonstrated that SH2 and HL₁ can become the cause of heterologous protein expression host in industrial production.Phylogenetic analysis showed that SH2 and ATCC-1015 were closely related,and HL₁ and CBS513.88 were closely related.This result provides theoretical support for the identification of the genetic relationship and evolution and evolutionary status of industrial Aspergillus niger strains.3.Annotation and analysis of key metabolic genes of Aspergillus niger SH2 and HL₁Aspergillus niger SH2 and Aspergillus niger HL₁ are industrially produced bacteria for the production of glucoamylase and heterologous expression hosts.They have important industrial value for gene cluster clustering related to protein translation,transcription and secretion.This research mainly focuses on proteolytic enzyme gene clusters.,polysaccharide degradation enzyme gene clusters,transcription factor gene clusters,secondary metabolic gene clusters,and cell wall related gene clusters were clustered,and two strains of the central metabolic network of Aspergillus niger were constructed.This information was used to perform genetic modification on strains.Remodeling,thus further increasing its protein secretion has a certain reference value.By analyzing the frequency of codon usage of the two strains of Aspergillus niger,two strains of high expression frequency codons ATG?methionine,Met?and TGG?tryptophan,Trp?were obtained as industrial strains.Codon optimization and its transformation provide a reference.This paper aims to use the third-generation single-molecule technology to sequence whole genomes of two strains of Aspergillus niger SH2 and HL₁,perform function prediction and annotation,analyze all gene functions,and fully understand the genetic characteristics,transcription,and expression of the two strains of Aspergillus niger.Such characteristics and mechanisms,through comparative genomics research,improve the genetic level information of the two strains,provide genetic information support for modern industrial production,and provide technical and data analysis reference for the research of microbial genomics.The central metabolic pathways of these two high-producing glucoamylases,Aspergillus niger,were constructed and their proteolytic enzyme gene clusters,polysaccharide degrading enzymes,secondary metabolic gene clusters,and cell wall related gene clusters were clustered,and the expression of these gene clusters and proteins was Secretion has a certain link,but also analyze the codon bias of the two strains,which has a certain guiding role in strain modification,genetic modification or codon optimization,and has important significance for further increasing protein yield.