Study On Genome And Transcriptome Expression Of Aspergillus Niger AS3.350

The development and application of high-throughout sequencing technologies make a great progress of microbial molecular biology and systems biology research. Traditional studies on the analysis of the genetic markers have been changed into in-depth analysis of whole genome and transcripome information. With a better understanding of the genome and transcripome, we could find the internal genetic expression mechanism in microorganisms, understand the difference between phenotype, provide a fully basic information base for creating and improving microbial industrial strains.Aspergillus niger is a important industrial microorganism, which is commonly used in organic acids, enzymes, and heterologous protein production. A.niger AS3.350 is a typical representative of A.niger. It has a strong secrete ability of acid protease and is widely used in the acid protease production and soy sauce fermentation. In addition, A. niger AS3.350 was also often used as a host for heterologous protein expression. A.niger AS3.350 has an important status in the microbial industrial production.In this study, we used the high-throughout sequencing method to analysis the genome and transcriptome expression information of A.niger AS3.350. The main contents and results are as follows: 1.Genome assembly and annotation of A.niger AS3.350Using the Illumina high-throughout sequencing technical means sequencing the genome of A.niger AS3.350. The average sequencing depth is 100 fold. The sequence data reached a size of 3.41 Gb. A 35.98 Mb genome has been presented after assembly. There are 167 contigs with a length longer than 400 bp. The GC content of genome is 49.44%. 11832 gene was predicted in the genome, 841 of which encodes secreting proteins. The genome of A.niger AS3.350 also contains 296 t RNAs. 2.Comparative genome study between A.niger AS3.350 and A.niger CBS513.88We used A.niger CBS513.88 as the reference strain, which has a rich annotation information of genome, to compare with A.niger AS3.350 genome. The synteny analysis showed that the synteny area account for 96% in two genomes. According to the structure variation result, there are 22 deletion fragments in A.niger AS3.350 compared to the reference genome, which contained 8 transcription factor genes. Many genes involved in biological metabolism and protein synthesis are found only in A.niger AS3.350. SNP and Indel analysis found that the two genomes have a large number of mutations in gene upstream and downstream areas, suggesting that these variations in regulatory regions of Aspergillus niger have an important influence on phenotypic difference. 3.Analysis of gene transcription level in A.niger AS3.350We extracted A.niger AS3.350 RNA from soybean and wheatbrean medium. 5.6 Gb and 6.0 Gb RNA-seq data were obtained for A.niger AS3.350, with the average sequencing depth of 135 folds and 141 folds in coding area. Cufflinks software was used to analyze the gene expression level of A.niger AS3.350. Results revealed that gene involved in cell metabolism and protein synthesis have high expression level, while those genes involved in DNA replication, recombination and secondary metabolites synthesis have the lower transcriptional expression level. There is no distince differences between the transcription level of secretory protein gene between the two kinds of culture condition. These findings provided a reference data for optimizing A.niger AS3.350 industrial fermentation process.This study used the high-throughout sequencing tools to analyze the full genome and transcriptional expression of A.niger AS3.350. Got a full information about the genetic, transcription, expression and metabolic characteristics and mechanism of A.niger AS3.350. These data provided a genetic and transcriptional information basis for improving the industrial strains A.niger AS3.350. And also laied a foundation for the genome and transcriptome analysis of other industrial microorganisms.