Telomere-to-telomere assembled and centromere annotated genomes of the two main subspecies of the button mushroom Agaricus bisporus reveal especially polymorphic chromosome ends

Abstract

Agaricus bisporus, the most cultivated edible mushroom worldwide, is represented mainly by the subspecies var. bisporus and var. burnettii. var. bisporus has a secondarily homothallic life cycle with recombination restricted to chromosome ends, while var. burnettii is heterothallic with recombination seemingly equally distributed over the chromosomes. To better understand the relationship between genomic make-up and different lifestyles, we have de novo sequenced a burnettii homokaryon and synchronised gene annotations with updated versions of the published genomes of var. bisporus. The genomes were assembled into telomere-to-telomere chromosomes and a consistent set of gene predictions was generated. The genomes of both subspecies were largely co-linear, and especially the chromosome ends differed in gene model content between the two subspecies. A single large cluster of repeats was found on each chromosome at the same respective position in all strains, harbouring nearly 50% of all repeats and likely representing centromeres. Repeats were all heavily methylated. Finally, a mapping population of var. burnettii confirmed an even distribution of crossovers in meiosis, contrasting the recombination landscape of var. bisporus. The new findings using the exceptionally complete and well annotated genomes of this basidiomycete demonstrate the importance for unravelling genetic components underlying the different life cycles.

Figure 1

Dot-plot comparison between the genomes of the var. bisporus homokaryons H39 and H97 against var. burnettii H119p4. (A,D) Mummer 3.23 (nucmer) plots of whole genomes (13 chromosomes) of H39 (A) and H97 (D) against homokaryon H119p4. (B,E) plots of chromosome 4 of H39 (B) and H97 (E) against H119p4; an inversion (blue) is seen in H97 compared to H119p4. (C,F) plots of chromosome 10 of H39 (C) and H97 (F) against H119p4; An inversion is seen in H39 and H97 compared to H119p4. The figure was drawn using D-Gernies (https://dgenies.toulouse.inra.fr/).

Figure 2

Comparative analysis of predicted proteins of three strains of A. bisporus. The predicted proteins were clustered into gene families using Orthofinder. The VENN diagram displays the number of gene families shared between or unique to strains. The total number of predicted proteins in these gene families are indicated between parentheses. Note that the predicted genes were not filtered for repetitive elements.

Figure 3

Genetic linkage map of a 119/9 population. Four linkage groups, 1 (consists of two scaffolds), 3 (consists of two scaffolds), 10 and 11 are presented. The SNP markers were labelled as scaffold number followed by their physical positions on that particular chromosome at the right side of each chromosome. The Centimorgan (cM) distance is given per marker pair at the left side of each chromosome. The position of the mating type locus is located as a black bar next to chromosome 1. The map was drawn using R 2.5.1

Figure 4

Plots of mapping position (X-axis) of markers against the physical position (Y-axis) for chromosomes 1, 3, 10 and 11 in populations derived from a var. bisporus offspring (left column) and the var. burnettii offspring (heterokaryon 119; right column). The putative location of the centromere (LRC) on each chromosome is indicated as a blue bar. The plots were generated using Excel (Microsoft Office 2016).

Figure 5

Mummer plots of chromosome 1 and 13 of homokaryons H39, H97 and H119_p4. Chromosomes were plotted against themselves using D-Genius, revealing clusters of repetitive elements in each chromosome. The plots clearly show that each homologous chromosome has a large repeat cluster (LRC) on an almost identical position, likely representing the centromere. The figure was generated with MAFFT version 7 (https://mafft.cbrc.jp/alignment/server/large.html).

Figure 6

Genomic profiles of gene models, annotated transposable elements (TE) and CpG methylation (C^meth) of the 13 chromosomes (Chr) of homokaryon H97. Each chromosome has a clear large repeat cluster shown as the largest annotated TE peak in each chromosome. The pattern of the annotated repeats coincides well with the CpG methylation profile. The figure was generated using Integrative Genomics Viewer version 2.5.2.