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

Abstract

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.

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

“… 9–11 Scarce studies at the intra-genus level have shown that functional diversity between species may arise from diversity in gene content. 12 , 13 …”

Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism

“…To date, several pathogenic genomes have been sequenced using Pacific Biosciences (PacBio) Sequel or the RSII platform [17,18,20]. With these available genomic sequences, it is possible to determine the evolutionary relationships among fungi [21][22][23][24], as well as to explore the evolution of nutritional mode. In addition, numerous gene clusters associated with pathogenicity have been identified, including secretory proteins, membrane transport proteins, pathogen-host interaction (PHI) genes, fungal virulence factors, and fungal G proteins [17,18].…”

“…In addition, numerous gene clusters associated with pathogenicity have been identified, including secretory proteins, membrane transport proteins, pathogen-host interaction (PHI) genes, fungal virulence factors, and fungal G proteins [17,18]. In addition, some expanded or contracted orthologous, species-specific genes and positive selective genes, including protein kinases, serine peptidases, cell-wall proteins, carbohydrate-active enzymes (CAZymes), secondary metabolites (SMs), and P450, were shown to be involved in biological control activity, pathogenesis, and mycoparasitism [21,22,24].…”

Effects of Biogas Slurry Combined With Chemical Fertilizer on Soil Bacterial and Fungal Community Composition in a Paddy Field

“…Pseudeurotium have been reported to have an impact on crop growth promotion and pathogen inhibition ( Zhou et al, 2018 ), and members of Archaeorhizomyces are considered to have the potential to promote the growth of grasslands ( Zhang et al, 2018 ). The genus Auricularia (10 positive and 2 negative links) usually grows on wood and plays an important role in human food supply and nutrition ( Dai et al, 2019 ), which was also significantly promoted by BS75. BS75 demonstrated prominent positive influences of crop growth and pathogen inhibition in the network association analysis.…”