Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations

Abstract

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

Keywords: Arctic biology; TE proliferation; biotrophy–saprotrophy evolution; carbon degradation; fungal genomics; fungal guild; genome size diversity; plant-fungus interactions; root-associations; saprotrophs.

Graphical abstract

Figure 1

Genomic features and statistics for 58 Agaricomycete species Fungal lifestyle in color. The median values are indicated by dotted lines. Genome, genome size; TE content, coverage of TE in the genome; genes, number of genes; secreted, number of predicted SSPs (see STAR Methods). Scaffolds, number of scaffolds; L50, N50 length; BUSCO, genome completeness. Further details are provided in Table S6.

Figure 2

Distribution of TEs in the 58 genomes LTR, long terminal repeat retrotransposons; non-LTR, non-long terminal repeat retrotransposons; DNA, DNA transposons; LINE, long interspersed nuclear element; unknown, unclassified repeated sequences. The bubble size is proportional to the coverage of each TE (shown inside the bubbles). The right bars show the total coverage per genome. Fungal ecology is indicated by color codes. See Tables S1 and S7.

Figure 3

DNA transposons near the ends and within the gene spaces (A) Short gene-repeat distances of Mycena. Mycena species were compared to non-Mycena fungi based on estimated mean distances. Cold-adapted Mycena species (n = 3, in blue), other Mycena species (n = 22, in red), and the remaining fungi (n = 33, in green). Different letters represent significantly different groups (Dunn test; FDR-adjusted p < 0.05). (B) Selected genes containing repeats among Mycena fungi. A high number of repeat elements overlapping genes present in Mycena fungi were selected. The following TE families were included in the analysis: DNA transposons (DNA), retrotransposons with long terminal repeats (LTR), retrotransposons with long interspersed nuclear elements (LINEs), retrotransposons with short interspersed nuclear elements (SINEs), rolling-circle/helitron transposons (RC), and unclassified repeats (unknown). See Table S3.

Figure 4

Patterns of gene repertoire expansion in Mycena (A) Relationship between genome size and number of genes containing known conserved protein motifs (InterPro terms). (B) Origins of novel gene families (left) across 58 species. (C) Differences in singleton genes between Mycena and non-Mycena species (Welch two-sample t test). (D) Patterns of gene duplication (right) across the 58 species.

Figure 5

Secretomic profiles of 58 fungi Bubble plots (left) show the number of secreted genes for CAZymes, lipases, proteases, and other proteins that were not present in the first three groups. SSPs are a subcategory showing the number of small secreted proteins (<300 amino acids). The size of the bubbles corresponds to the number of genes. Fungal lifestyle is indicated by colors. The first bar plots (in the middle) represent the ratio of CAZymes, lipases, and proteases to all secreted proteins (left), and the ratio of SSPs in the entire secretome (right). The second bubble plot (on the right) shows CAZymes grouped according to their functions, including PCWDEs and fungal cell-wall-degrading enzymes (FCWDEs); peptidoglycan (i.e., bacterial membrane)-degrading enzymes (BMDEs); trehalose-, starch-, glycogen-degrading enzymes (storage); lytic polysaccharide monooxygenase (LPMO); substrate-specific enzymes for cellulose, hemicellulose, lignin, and pectin (plant cell walls); and chitin, glucan, and mannan (fungal cell walls). The second bar plots (far right) show the total number of genes, including PCWDE, microbial cell wall degrading enzymes (MCWDEs) and BMDE (left), and the proportions of PCWDE, MCWDE, and BMDE (right)

Figure 6

Phylogenetic PCA of secreted CAZyme profiles All 58 species were placed according to the first and second principal components calculated by the count of secreted CAZymes, with phylogenetic distances of the species taken into account. CAZymes with high loadings are shown in red with arrows. Fungal ecology is in color, and Mycena and non-Mycena fungi are in different shapes. The blue circle shows a cluster of Mycena species.