Genomic analysis of the aconidial and high-performance protein producer, industrially relevant Aspergillus niger SH2 strain

• We assemble a high-quality genome sequence of aconidial A. niger SH2.
• FunCat analysis verifies the efficient protein production of A. niger SH2.
• The lack of PrpA gene leads to the distinct aconidial phenotype of A. niger SH2.
• Frame shift mutation and non-synonymous SNP influence cell wall development of SH2.

Aspergillus niger is usually regarded as a beneficial species widely used in biotechnological industry. Obtaining the genome sequence of the widely used aconidial A. niger SH2 strain is of great importance to understand its unusual production capability. In this study we assembled a high-quality genome sequence of A. niger SH2 with approximately 11,517 ORFs. Relatively high proportion of genes enriched for protein expression related FunCat items verify its efficient capacity in protein production. Furthermore, genome-wide comparative analysis between A. niger SH2 and CBS513.88 reveals insights into unique properties of A. niger SH2. A. niger SH2 lacks the gene related with the initiation of asexual sporulation (PrpA), leading to its distinct aconidial phenotype. Frame shift mutations and non-synonymous SNPs in genes of cell wall integrity signaling, β-1,3-glucan synthesis and chitin synthesis influence its cell wall development which is important for its hyphal fragmentation during industrial high-efficiency protein production.