Pleurotus eryngii Genomes Reveal Evolution and Adaptation to the Gobi Desert Environment

Abstract

Pleurotus eryngii (King Oyster) is one of the most highly prized edible mushrooms. Among the diverse varieties within P. eryngii, P. eryngii var. eryngii is the commonest one, with a worldwide distribution, while P. eryngii var. ferulae is only distributed in Europe and China, and is especially adapted to the Gobi Desert in Xinjiang Autonomous Region of China. However, little is known about the genome-wide pattern of evolution and adaptation to the divergent environments of P. eryngii. Here, we present the high-quality genome sequences of P. eryngii var. eryngii strain PEE81 originating from Europe and P. eryngii var. ferulae strain PEF12 originating from the Gobi Desert of China. The assembled genome sizes of PEE81 and PEF12 were 53.6 and 48.0 Mbp, respectively, which are larger than other reported genomes in the genus Pleurotus. We propose that the selective amplification of long terminal repeat (LTR) retrotransposons increases the genome size of the genus Pleurotus, and may play a key role in driving their rapid species diversification. Molecular clock analyses of five Pleurotus species, namely PEE81, PEF12, P. tuoliensis, P. ostreatus and P. cf. floridanus suggest that the divergence estimates of the genus Pleurotus over time scales ranged from ∼4 to ∼38 million years ago (Mya), and PEE81 and PEF12 diverged at ∼13 Mya. The whole genome resequencing of 33 geographically diverse strains of P. eryngii var. eryngii and var. ferulae was then performed and the genome variation among and within these two populations were investigated. Comparative analyses of these two populations detected several candidate genes related to stress responses and DNA repair that are putatively involved in adaptation to the Gobi Desert environment. These findings offer insights into genome evolution of the genus Pleurotus and provide valuable genomic resources for King Oyster mushroom breeding.

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

“…We constructed 20-kb libraries for C. dendroides, and the genome was sequenced with a PacBio Sequel long-read sequencing platform [17,18,23,57]. To redress mismatch rate and increase sequencing read lengths, we performed next generation sequencing.…”

“…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].…”

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

“…It is of note that the two populations from the northwestern China and Mediterranean regions inhabited distinct climatic environments, dominated by temperate steppe with a temperate grassy climate, and by garigue, wasteland and pasture with a subtropical Mediterranean climate, respectively (Chen 1986;Zervakis et al 2014). The differences in climatic traits would be conducive to promote divergence in the individual populations, such as some candidate genes related to stress responses and DNA repair revealing adaptation to the different environments, and the long-term environmental heterogeneity could promote ongoing allopatric divergence in different populations (Dai et al 2019;Pildain et al 2009). However, the distribution pattern of P. eryngii var.…”

Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation

“…ex Fr.) P.Kumm 20 , 26 , 27 . In light of these prior studies, we believe that genomic resources can lead to breakthroughs in conservation efforts for LM, but genomic resources are currently largely unavailable for this species.…”