Alignment of genes from twenty-five fungi

Alignment of genes used to generate phylogenetic tree of twenty-five fungal taxa for modelling genome and chromosome evolution

Chromosome counts from fungi

Chromosome counts for the twenty-five fungi from the sequence alignment, for use with ChromEvol software

Partitioning scheme for alignment file

A RAxML formatted partition file for the sequence alignment file

An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns

<div><p>Polyploidy, a state in which the chromosome complement has undergone an increase, is a major force in evolution. Understanding the consequences of polyploidy has received much attention, and allopolyploids, which result from the union of two different parental genomes, are of particular interest because they must overcome a suite of biological responses to this merger, known as “genome shock.” A key question is what happens to gene expression of the two gene copies following allopolyploidization, but until recently the tools to answer this question on a genome-wide basis were lacking. Here we utilize high throughput transcriptome sequencing to produce the first genome-wide picture of gene expression response to allopolyploidy in fungi. A novel pipeline for assigning sequence reads to the gene copies was used to quantify their expression in a fungal allopolyploid. We find that the transcriptional response to allopolyploidy is predominantly conservative: both copies of most genes are retained; over half the genes inherit parental gene expression patterns; and parental differential expression is often lost in the allopolyploid. Strikingly, the patterns of gene expression change are highly concordant with the genome-wide expression results of a cotton allopolyploid. The very different nature of these two allopolyploids implies a conserved, eukaryote-wide transcriptional response to genome merger. We provide evidence that the transcriptional responses we observe are mostly driven by intrinsic differences between the regulatory systems in the parent species, and from this propose a mechanistic model in which the cross-kingdom conservation in transcriptional response reflects conservation of the mutational processes underlying eukaryotic gene regulatory evolution. This work provides a platform to develop a universal understanding of gene expression response to allopolyploidy and suggests that allopolyploids are an exceptional system to investigate gene regulatory changes that have evolved in the parental species prior to allopolyploidization.</p></div

Parental and allopolyploid expression patterns from extreme differentially expressed genes.

<p>Plots show the relative expression level between the two homeologs in Lp1 (“Lp1”), between AR5 and E8 orthologs (“Parents”), between the AR5 ortholog and the AR5-like Lp1 homeolog (“AR5 copy”), and between the E8 ortholog and the E8-like Lp1 homeolog (“E8 copy”). (A) Genes with zero expression for one Lp1 homeolog, but non-zero expression for the other; (B) genes with >50-fold difference in expression between the Lp1 homeologs; (C) genes with >50-fold difference in expression between AR5 and E8 orthologs. Heat spectrum (bottom) varies between similar expression (white) and different expression (black). Vertical bars to the right indicate where genes are physically clustered; these are labeled by supercontig number. Genes on supercontig 148, present in (A) and (B), are physically contiguous in the genome. Genes 049470 and 049490, despite their numbering, are not physically adjacent.</p

SNP counts by diagnostic class.

<p>* Lp1-unique incorporates classes Lp1-AR5, Lp1-E8 and Lp1-unclassified.</p

Intrinsic gene regulatory features underlie transcriptional response patterns in the allopolyploid.

<p>Change in expression of a gene (in blue) from the two parents (circles) to the allopolyploid (ellipse) is shown symbolically where a modulon (orange star; see text for details) positively regulates gene expression (green interaction). (A) Expression is high in one parent, with the modulon not active in the other. In the allopolyploid, this modulon only acts on its own homeolog, resulting in simple inheritance of biased gene expression. Failure of the modulon to recognize the other homeolog can result from a <i>cis</i>-acting change (purple cross) in one ortholog (B). The parental situation is the same as in (A), but the modulon acts on both homeologs, yielding homeolog expression blending in the allopolyploid. (C) Expression of the two orthologs is similar in the parents, but the modulon preferentially stimulates transcription of one homeolog in the allopolyploid, generating homeolog expression bias as a result of a <i>cis</i>-acting difference (purple cross) that does not change expression in the parent. Analogous outcomes will be achieved in all cases if the modulon is repressive rather than stimulatory (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180.s004" target="_blank">Figure S4</a>). The promoter is indicated by a transcription arrow, and transcript levels by the number of thin wavy lines.</p

Phylogeny and culture morphology of <i>Epichloë</i> and <i>Neotyphodium</i> species.

<p>(A) Phylogeny of <i>Epichloë</i> and <i>Neotyphodium</i> fungi. Haploid species are indicated in black, while some of the many natural allopolyploid species in these genera are shown to the right. Colored lines indicate the parents of these allopolyploids, including the ancestors of the allopolyploid investigated in this study, Lp1 (solid red line). Phylogeny modified from published sources <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180-Schardl1" target="_blank">[49]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180-Schardl3" target="_blank">[51]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180-Charlton1" target="_blank">[82]</a>. Culture morphology of (B) <i>N. lolii</i> AR5, (C) allopolyploid <i>N. lolii</i>×<i>E. typhina</i> Lp1 and (D) <i>E. typhina</i> E8. All culture panels 30 mm square.</p

Fate of gene expression in the allopolyploid compared to the parents.

<p>Relative expression of the AR5-derived and E8-derived gene copies was calculated for Lp1 and its parents; ‘biased’ is 2-fold or greater expression difference. The right indicates numbers of genes in each of the nine possible combinations of biased/non-biased expression <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180-Yoo1" target="_blank">[46]</a>. Box-graphs represent relative expression ratios, with the position of the line within the box indicating the E8:AR5 expression ratio. Specifically, red lines high in the box indicate E8 homeolog/ortholog expression bias, black lines mid-way in the box indicate equal expression, and blue lines low in the box indicate AR5 bias. These are grouped into four expression response categories: maintenance of the parental expression pattern in Lp1; homeolog expression blending; homeolog expression bias; and homeolog expression reversal, indicated by the colored boxes on the right. On the left are proportions of genes showing bias towards AR5 or E8 expression or no bias for the parents (top) and Lp1 (bottom). The colored half-circle tabs link the nine expression combinations to the plots on the left.</p

Similarities in the transcriptional response to allopolyploidy in Lp1 and natural cotton allopolyploids.

a<p>Categories as presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen-1004180-g001" target="_blank">Figures 1</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen-1004180-g006" target="_blank">6</a>, and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen-1004180-g007" target="_blank">7</a><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180-Yoo1" target="_blank">[46]</a>.</p>b<p>Ranges reported are those of the two natural allopolyploid cotton varieties analyzed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180-Yoo1" target="_blank">[46]</a>.</p>c<p>Expressed as a percentage of all genes showing differential expression in the parents, including those with transgressive expression in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004180#pgen.1004180-Yoo1" target="_blank">[46]</a>.</p>d<p>Expressed as a percentage of all genes showing expression-level dominance.</p