Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

Abstract

In this study, we aim to identify genomic traits of the transitions to the ectomycorrhizal ecology within the Boletales, one of the most diverse lineages of symbiotrophic fungi. We sequenced the genomes and compared the gene repertoires of symbiotrophic Boletales species to their saprotrophic brown-rot relatives. We also reconstructed gene duplication/loss histories along a time-calibrated phylogeny. We showed that the rate of gene duplication is constant along the backbone of Boletales phylogeny with large loss events in lineages leading to several families. The rate of gene family expansion sharply increased in the late Miocene and mostly took place in Boletaceae. Most of the ectomycorrhizal Boletales are characterized by a large genome size due to transposable element (TE) expansions and a reduction in the diversity of plant cell wall degrading enzymes (PCWDEs) compared to their brown-rot relatives. However, several species in the Boletaceae, Paxillaceae and Boletinellaceae have kept a substantial set of endoglucanases and LPMOs acting on cellulose/hemicellulose and fungal polysaccharides suggesting that they may partly decompose organic matter by a combined activity of oxidative and hydrolytic enzymes. The present study provides novel insights on our understanding of the mechanisms that influence the evolutionary diversification of boletes and symbiosis evolution.

The genome and transcriptome of Sarocladium terricola provide insight into ergosterol biosynthesis

“…With the advent of genome and transcriptome sequencing, omics technology has been increasingly utilized to investigate various biological processes, discover novel natural products, and reconstruct phylogenomic relationships (Hittalmani et al, 2016;Ren et al, 2021;Tian et al, 2022;Wu et al, 2022;Zhao et al, 2022b;Zhao et al, 2022a). Although the Sarocladium genus encompasses 30 species (http://www.indexfungorum.org, accessed on 13 The ergosterol content in two types of media.…”

“…For example, the NCBI database contains more than 2,770 genomes from Ascomycota (https://www.ncbi.nlm.nih.gov/genome/, accessed on November 13, 2022). Genome and transcriptome sequences have provided novel insights into fungal phylogenomics, biosynthesis of metabolites, mechanisms of symbiosis, and others (Zhao et al, 2010;Ren et al, 2021;Sun et al, 2022;Wu et al, 2022;Zhao et al, 2022b;Zhao et al, 2022a). Although genome and mitochondrial genome sequences in the genus Sarocladium have been published (Hittalmani et al, 2016;Yao et al, 2016;Tian et al, 2022), phylogenomic relationships, transcriptome sequences, and characterization of the ergosterol biosynthesis pathway have not been studied.…”