Comparative genomics of and section .

is an important model organism for eukaryotic biology and the reference for the section in comparative studies. In this study, we sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 species and clarifies the position of clades inside section . Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in as well as its SMGC families are generally present in the section , supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section , while there is remarkable diversity of organization of MAT- both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of as a reference species for cell biology.