Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

Abstract

The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.

Fig. 1.

Summary plots of chromosome II of C. cinerea. The plot shows the location of (Top panel) telomeres in red and centromere as black oval; (Second panel) the density of transposable elements (brown); (Third panel) tRNA genes (light green); (Fourth panel) recombination rates (the position of the SSR markers is indicated by vertical black bars, white is unmapped, red is high recombination, gray is average recombination, blue is low recombination); (Fifth panel) the density of all genes (orange); (Sixth panel), the density of orphan genes (light orange); (Seventh panel), the density of orthologous genes (blue); (Eighth panel) the density of paralogous genes (red); (Ninth panel) similarity of paralog families represented as 1/dS; (10th panel) syntenic regions (all regions of synteny between C. cinerea and L. bicolor are indicated in green, and blocks with >15 anchors are indicated in dark green). Vertical scales are defined for each bar in the bar title. Horizontal scale is Mb.

Fig. 2.

HMM logos of protein kinase active site regions. (A) Conventional protein kinases. (B) FunK1 protein kinases. Conserved residues positions in both conventional and FunK1 kinases are indicated with blue circles. Residue positions that are nearly universally conserved in conventional ePK domains but are altered in FunK1 kinases are indicated with red circles.

Fig. 3.

Photograph and micrographs of C. cinerea. (A) Mature C. cinerea fruiting body that is shedding spores. The upper surface of the cap has loosely adhering “veil cells.” The lower surface of the cap is composed of “gills” which support the basidia (meiotic cells). The cap is elevated several centimeters above the Petri dish by the “stipe” (stalk). (B) Simple septum between two cells in a monokaryotic hypha. (C) “False clamp” between two cells in an “A-on” hypha. (D) True clamp connection between two cells in a dikaryotic hypha (“A-on B-on”). Magnification in B–D is the same.