Aspergillus oryzae is an industrially useful species, of which various strains have been identified; however, their genetic relationships remain unclear. A. oryzae was previously thought to be asexual and unable to undergo crossbreeding. However, recent studies revealed the sexual reproduction of Aspergillus flavus, a species closely related to A. oryzae. To investigate potential sexual reproduction in A. oryzae and evolutionary history among A. oryzae and A. flavus strains, we assembled 82 draft genomes of A. oryzae strains used practically. The phylogenetic tree of concatenated genes confirmed that A. oryzae was monophyletic and nested in one of the clades of A. flavus but formed several clades with different genomic structures. Our results suggest that A. oryzae strains have undergone multiple inter-genomic recombination events between A. oryzae ancestors, although sexual recombination among domesticated species did not appear to have occurred during the domestication process, at least in the past few decades. Through inter- and intra-cladal comparative analysis, we found that evolutionary pressure induced by the domestication of A. oryzae appears to selectively cause non-synonymous and gap mutations in genes involved in fermentation characteristics, as well as intra-genomic rearrangements, with the conservation of industrially useful catalytic enzyme-encoding genes.

中文翻译：

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大规模比较基因组分析推断，米曲霉在驯化前后的进化。

米曲霉是一种工业上有用的物种，已经鉴定出各种菌株。但是，它们的遗传关系仍然不清楚。以前认为米曲霉是无性的，不能进行杂交。然而，最近的研究表明，米曲霉是一种与米曲霉密切相关的物种。为了调查米曲霉潜在的有性繁殖以及米曲霉和黄曲霉菌株之间的进化历史，我们组装了82个实际使用的米曲霉菌株的基因组草图。连锁基因的系统进化树证实米曲霉是单系的，并嵌套在黄曲霉的一个进化枝中，但形成了几个具有不同基因组结构的进化枝。我们的结果表明，米曲霉菌株已经在米曲霉之间经历了多个基因组重组事件。至少在过去的几十年中，尽管在驯化过程中似乎没有发生过被驯化物种之间的性重组，但是稻草的祖先。通过包间内和包间内比较分析，我们发现米曲霉驯化诱导的进化压力似乎选择性地导致参与发酵特性以及基因组内部重排的基因的非同义和空位突变。保留工业上有用的催化酶编码基因。