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Abstract
Pleurotus tuoliensis (Bailinggu, designated Pt) and P. eryngii var. eryngii (Xingbaogu, designated Pe) are highly valued edible mushrooms. We report de novo assemblies of high-quality genomes for both mushrooms based on PacBio RS II sequencing and annotation of all identified genes. A comparative genomics analysis between Pt and Pe with P. ostreatus as an outgroup taxon revealed extensive genomic divergence between the two mushroom genomes primarily due to the rapid gain of taxon-specific genes and disruption of synteny in either taxon. The re-appraised phylogenetic relationship between Pt and Pe at the genome-wide level validates earlier proposals to designate Pt as an independent species. Variation of the identified wood-decay-related gene content can largely explain the variable adaptation and host specificity of the two mushrooms. On the basis of the two assembled genome sequences, methylomes and the regulatory roles of DNA methylation in gene expression were characterized and compared. The genome, methylome and transcriptome data of these two important mushrooms will provide valuable information for advancing our understanding of the evolution of Pleurotus and related genera and for facilitating genome- and epigenome-based strategies for mushroom breeding.
Highlights
The Pleurotus eryngii species complex in basidiomycetes, encompassing the largest number of species in the oyster mushroom genus (Pleurotus), constitutes many kinds of edible mushrooms such as Bailinggu (P. tuoliensis) (Pt), Xingbaogu (P. eryngii var. eryngii) (Pe), Aweigu (P. eryngii var. ferulae) and so forth[1,2,3]
It was observed that transposable element (TE) and other repetitive sequences were interspersed by condensed genic regions which were transcribed at high levels (Fig. 1)
Profiles of DNA methylomes of Pt and Pe were characterized in detail and potential factors for establishing and maintaining the DNA methylation profiles were explored
Summary
The Pleurotus eryngii species complex in basidiomycetes, encompassing the largest number of species in the oyster mushroom genus (Pleurotus), constitutes many kinds of edible mushrooms such as Bailinggu (P. tuoliensis) (Pt), Xingbaogu (P. eryngii var. eryngii) (Pe), Aweigu (P. eryngii var. ferulae) and so forth[1,2,3]. Prior studies of whole-genome profiles of DNA methylation and siRNA in fungi only focused on a few ascomycetes and basidiomycetes species[30,31,32] without involving any Pleurotus taxa. Despite the two Pleurotus genomes harboring a similar content of TEs and protein-coding genes, the extent of their sequence divergence supports the viewpoint that Pt is a separate species of the Pleurotus eryngii species complex. Our two assembled Pleurotus genomes and characterized methylomes and transcriptomes offer a collection of valuable genomic, epigenomic and gene expression resources for future research on evolution and functional genomics in Pleurotus and related genera as well as on more efficient breeding of improved edible mushroom cultivars
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