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Species in the genus  Auricularia  play important roles for people’s food and nutrition especially  Auricularia cornea  and  A. heimuer . To understand their evolutionary history, genome structure, and population-level genetic variation, we performed a high-quality genome sequencing of  Auricularia cornea  and the corresponding comparative genomic analysis. The genome size of  A. cornea  was similar to  Auricularia subglabra , but 1.5 times larger than that of  A. heimuer . Several factors were responsible for genome size variation including gene numbers, repetitive elements, and gene lengths. Phylogenomic analysis revealed that the estimated divergence time between  A. heimuer  and other  Auricularia  is ∼79.1 million years ago (Mya), while the divergence between  A. cornea  and  A. subglabra  occurred in ∼54.8 Mya. Population genomic analysis also provided insight into the demographic history of  A. cornea  and  A. heimuer , indicating that their populations fluctuated over time with global climate change during Marine Isotope Stage 5-2. Moreover, despite the highly similar external morphologies of  A. cornea  and  A. heimuer , their genomic properties were remarkably different. The  A. cornea  genome only shared 14% homologous syntenic blocks with  A. heimuer  and possessed more genes encoding carbohydrate-active enzymes and secondary metabolite biosynthesis proteins. The cross-taxa transferability rates of simple sequence repeat (SSR) and insertion or deletion (InDel) markers within the genus  Auricularia  were also lower than that previously observed for species within the same genus. Taken together, these results indicate a high level of genetic differentiation between these two  Auricularia  species. Consequently, our study provides new insights into the genomic evolution and genetic differentiation of  Auricularia  species that will facilitate future genetic breeding.

Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species