AUTHOR=Dai Yueting , Li Xiao , Song Bing , Sun Lei , Yang Chentao , Zhang Xin , Wang Yanfeng , Zhang Zhiwu , Fu Yongping , Li Yu 

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

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.02255

DOI=10.3389/fmicb.2019.02255

ISSN=1664-302X

ABSTRACT=<p>Species in the genus <italic>Auricularia</italic> play important roles for people’s food and nutrition especially <italic>Auricularia cornea</italic> and <italic>A. heimuer</italic>. To understand their evolutionary history, genome structure, and population-level genetic variation, we performed a high-quality genome sequencing of <italic>Auricularia cornea</italic> and the corresponding comparative genomic analysis. The genome size of <italic>A. cornea</italic> was similar to <italic>Auricularia subglabra</italic>, but 1.5 times larger than that of <italic>A. heimuer</italic>. 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 <italic>A. heimuer</italic> and other <italic>Auricularia</italic> is ∼79.1 million years ago (Mya), while the divergence between <italic>A. cornea</italic> and <italic>A. subglabra</italic> occurred in ∼54.8 Mya. Population genomic analysis also provided insight into the demographic history of <italic>A. cornea</italic> and <italic>A. heimuer</italic>, 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 <italic>A. cornea</italic> and <italic>A. heimuer</italic>, their genomic properties were remarkably different. The <italic>A. cornea</italic> genome only shared 14% homologous syntenic blocks with <italic>A. heimuer</italic> 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 <italic>Auricularia</italic> 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 <italic>Auricularia</italic> species. Consequently, our study provides new insights into the genomic evolution and genetic differentiation of <italic>Auricularia</italic> species that will facilitate future genetic breeding.</p>