Additional file 1: of Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

Table S1. List of switchgrass accessions used in the study with their ID and name, number of genotypes, ecotype identification, ploidy level, state of origin, and GPS coordinates [114–116]. Table S2. Sequences and annealing temperatures of the 33 primer pairs used for PCR amplification of the selected 12 genes. Conserved regions in orthologous exons in Oryza sativa (rice), Sorghum bicolor (sorghum), Zea mays (maize) and Setaria italica (foxtail millet) were used for primer design. Table S3. Sequences of 56 regions of AP13 extracted from the Phytozome database ( http://www.phytozome.net/ ), and used as reference for read mapping and SNP identification. Table S4. Number of amplicon reads mapped to each of the 56 reference switchgrass contigs. Table S5. Summary statistics for the non-synonymous SNPs analyzed in 12 biomass genes. Table S6. Genic regions for which the SNP distribution is different in the K and N subgenomes. The percentage of SNPs and the region in which they are located are given for each subgenome. Table S7. Tajima’s, and Fu and Li’s tests on a per gene basis within each subpopulation. Figure S1. Distance between SNPs. Figure S2. Log probability of data as a function of K. STRUCTURE was run for K ranging from 1 to 10, and 10 repetitions were performed with 100,000 burn-ins and 100,000 runs. K = 3 clusters were retained as the most likely number of genetic clusters in the switchgrass panel analyzed. Figure S3. UPGMA tree performed on the 251 SNPs across the 372 genotypes with a 500 replicates bootstrap test using Mega 6 [60] based on the maximum composite likelihood method. C1, C2 and C3 clusters are colored in blue, green and red respectively; admixed individuals are in gray. Figure S4. Local Indicator of Spatial Autocorrelation Analysis (2D-LSA) on 372 genotypes. Individuals that are consistently significantly more related to their 7 to 14 nearest neighbors than to random individuals are represented as plain blue dots. The number of genotypes is given in parenthesis. Accessions with significant P values for more than 90% of the genotypes are listed; their subpopulation and number of genotypes are indicated. USA Map source: https://upload.wikimedia.org/wikipedia/commons/c/ca/Blank_US_map_borders.svg . Figure S5. Regression analysis of the percentage of polymorphic loci and latitude bins across the switchgrass accessions. Figure S6. Protein structure modeling of an amino acid substitution in the PAS domain of 1D06, a protein with similar PAS domain as PHYB (A) Original structure of protein 1D06; (B) modified structure after two amino-acid changes in the PAS domain (in yellow): one conservative substitution (Val - > Ile; in green) and one non-conservative substitution (Asp - > Tyr; in pink). Swiss-Pdb Viewer 4.1.0 [70] was used to visualize the crystal structure. (PDF 1034 kb

B73_Mo17_extreme_allele_freq_matrix_3301371_SNPs_bias_correct_100bp_0.25_0.75_control_with_header

Genotype counts and frequencies for the filtered SNP set from pooled sequencing data from control plants and selected extremes for flowering time and plant height

Additional file 3: Figure S1. of Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Snapshot of synteny dot plot between C. olivacea and C. puteana. (TIFF 582 kb

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

27 juin 19371937/06/27 (A38,N13339)

A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism

<div><p>In <i>Neurospora crassa</i>, the transcription factor COL-26 functions as a regulator of glucose signaling and metabolism. Its loss leads to resistance to carbon catabolite repression. Here, we report that COL-26 is necessary for the expression of amylolytic genes in <i>N</i>. <i>crassa</i> and is required for the utilization of maltose and starch. Additionally, the Δ<i>col-26</i> mutant shows growth defects on preferred carbon sources, such as glucose, an effect that was alleviated if glutamine replaced ammonium as the primary nitrogen source. This rescue did not occur when maltose was used as a sole carbon source. Transcriptome and metabolic analyses of the Δ<i>col-26</i> mutant relative to its wild type parental strain revealed that amino acid and nitrogen metabolism, the TCA cycle and GABA shunt were adversely affected. Phylogenetic analysis showed a single <i>col-26</i> homolog in Sordariales, Ophilostomatales, and the Magnaporthales, but an expanded number of <i>col-26</i> homologs in other filamentous fungal species. Deletion of the closest homolog of <i>col-26</i> in <i>Trichoderma reesei</i>, <i>bglR</i>, resulted in a mutant with similar preferred carbon source growth deficiency, and which was alleviated if glutamine was the sole nitrogen source, suggesting conservation of COL-26 and BglR function. Our finding provides novel insight into the role of COL-26 for utilization of starch and in integrating carbon and nitrogen metabolism for balanced metabolic activities for optimal carbon and nitrogen distribution.</p></div

Additional file 2: Table S1. of Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Comparison of TE content estimation from REPET and Repeatexplorer. (XLSX 9 kb

POInT’s inferences regarding the loss of genes post-WGD.

<p>The At-α duplication produced two sets of homoeologous regions, one from the parental subgenome with more surviving genes (“Less fractionated subgenome,” upper track) and one with fewer (“More fractionated subgenome,” lower track). Genes in these tracks may have surviving duplicates in at least some taxa (orange/tan), or they may be single-copy in all species (blue if derived from the less fractionated subgenome and green if from the more fractionated one). Under each taxon name is the number of single-copy genes predicted to have been retained from that parental subgenome in that taxon. The branch length (numbers under the branches of the <u><i>upper</i></u> tree) gives the value of α×time in the model of <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007267#pgen.1007267.g002" target="_blank">Fig 2B</a>: larger values correspond to a relatively higher chance that a position with a ohnolog pair present at the start of a branch will be single-copy by its end. Numbers above the branches give POInT’s estimate of the number of genes returned to single copy deriving from the less fractionated (upper panel) and more fractioned (lower panel) subgenomes, respectively. Under the branches of the lower tree are the branch-specific ratio of genes retained from subgenome #2 relative to subgenome #1: these values can be compared to the overall estimate of this parameter, which is 0.64, shown in the upper left. POInT’s estimates of the other global parameters for this model are also given here. Above each pillar of genes is POInT’s estimate of the posterior probability of the set of subgenome assignments depicted, relative to the other <i>2</i>^<i>n</i><i>-1</i> possible assignments (where <i>n</i> is the number of genomes). The two root branches are shown in red: these correspond to branches where the biased fractionation parameter ε was allowed to differ from the rest of the tree in our analyses of temporal patterns of biased fractionation (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007267#sec002" target="_blank">Methods</a>). Similar trees depicting loss events for the grass and yeast WGDs are given as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007267#pgen.1007267.s001" target="_blank">S1 Fig</a>.</p

Protein interactions between single-copy genes from alternative subgenomes are rarer than expected.

<p>We extracted single-copy genes for a range of values of POInT’s overall confidence in pillar assignments to subgenomes (<i>x</i>-axis) and computed the <i>P</i>-value for the test of the null hypothesis of no fewer protein-protein interactions between products of genes from alternative subgenomes than expected (<i>y</i>-axis; panel <b>A</b>: see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007267#sec002" target="_blank">Methods</a>). We also computed the frequency of such “crossing” interactions relative to interactions between products of the same subgenome (<i>y</i>-axis, panel <b>B</b>).</p

POInT estimates for different datasets and ancestral orders.

<p>POInT estimates for different datasets and ancestral orders.</p

Consistency across the ancestral genome of POInT’s estimates of the subparental genome of origin.

<p><b>A)</b> In the six panels, we illustrate how often POInT’s assignment of parental subgenome of origin for At-α changes between two successive pillars when considering the “high synteny” dataset. A red tick at position <i>i</i> corresponds to a situation where POInT assigned parents-of-origin to two chromosomal regions at position <i>i-1</i> with probability of ≥85% and either the <i>opposite</i> combination of parents at position <i>i</i> or with the same assignment but with confidence less than 85%. Gray ticks, in turn, correspond to those positions immediately after a red tick where the confidence in the parental assignments is less than 85%. The blue ticks in the lower half of each block indicate positions where there is a double synteny break after position <i>i-1</i> (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007267#sec002" target="_blank">Methods</a><i>)</i>. At these positions, the parental inferences at position <i>i</i> are independent of those at <i>i-1</i>. Locations where all 6 genomes have such breaks are shown with the pink dotted lines. <b>B)</b> Estimates of shared parental blocks across genomes. With very few exceptions, locations where POInT finds a change in subgenome assignments correspond to these six-fold synteny breaks from <b>A</b>. Each blue/green colored block corresponds to a situation where at least 5, 4, or 3 genomes (top, middle and bottom, respectively) agree between every neighbor as to the subgenome assignment at a confidence of 85% or more. Narrower black regions are regions where there is no position-to-position agreement in assignment for any number of genomes (e.g., these are regions where our confidence in subgenome assignments is low overall). Any shared loss of synteny can induce a new block: such synteny breaks might, for instance, reflect a shift to new ancestral chromosome. For reference, we also show the set of blocks inferred with the WGD-<i>f</i> model as the smaller set of red/purple blocks. This model does not include BF, making it degenerate, so that subgenome 1 and 2 can be swapped. We therefore define one region of one genome as being subgenome #1 and make the block assignments correspondingly. Almost all of the phasing of blocks can be done without the assumption of BF, as is seen with the similarity between the blue/green and red/purple blocks. The implication of this fact is that the blocks are defined by the pattern of shared gene losses and that including BF in the model serves only to allow us to assign unlinked blocks to the same subgenomes based on their BF patterns. <b>C)</b> For the 16 blocks with more than 100 pillars, we show the estimates of the strength of BF (maximum likelihood estimate of ε; <i>y</i>-axis) judged solely from that block (block mid-point on the <i>x</i>-axis). These values indicate strong BF in all but three cases: in most of the larger blocks the estimated strength of BF is nearly identical to that for the full dataset (blue line). For the three blocks with weak evidence for BF (ε≈1.0), we further interrogated the patterns of gene loss (tables at bottom). In two of three cases, the signal of BF is relatively strong along the shared root branch where most losses occurred, with conflicting patterns on other branches. We attribute these differences to sampling effects among the relatively small number of losses along each branch. For the final block, with coordinates from pillars 2113 to 2318, the inferred pattern of losses contradicts the subgenome assignment, with more inferred losses from subgenome 1. When we examined the pattern of synteny breaks in this region, we discovered an anomaly: all of the genomes except <i>Eutrema salsugineum</i> had a synteny break at the end of this block: <i>E</i>. <i>salsugineum</i> instead had a break six pillars later (the pink shaded region). Hence, this synteny pattern caused the block to be linked to the next, larger, block, giving rise to the incongruous gene loss inferences. Equivalent figures for the full At-α dataset, the yeasts and the grasses are given as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007267#pgen.1007267.s002" target="_blank">S2 Fig</a>.</p