Groups of enriched gene ontology (GO) terms for differentially expressed genes common to both trisomy 2 and tertiary trisomy 2.

<p>The gene ontology was analyzed by use of AgriGO <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Du1" target="_blank">[33]</a>.</p>a<p>Biological process (P); molecular function (F).</p>b<p>Chi-square statistical test; FDR, false discovery rate.</p><p>Groups of enriched gene ontology (GO) terms for differentially expressed genes common to both trisomy 2 and tertiary trisomy 2.</p

The <i>aur2-1</i>/+ mutant is trisomy 2.

<p>(<b>A</b>) Rosette phenotype of wild type (Col-0) and progeny from self-fertilized <i>aur2-1</i>/+. W, wild-type rosette leaves; R, round-shaped rosette leaves; T, tiny rosette leaves. (<b>B</b>) Metaphase spreads of the mitotic cells from Col-0 and <i>aur2-1</i>/+. (<b>C</b>) Meiosis in pollen mother cells of Col-0 and <i>aur2-1</i>/+. DAPI-stained chromosomes in different meiotic stages. Yellow arrows, extra univalents; red arrow, pentavalent; yellow stars, extra sister chromatids. (<b>D</b>) Fluorescence <i>in situ</i> hybridization analysis of <i>aur2-1</i>/+. Metaphase spreads of the <i>aur2-1</i>/+ mitotic cells probed with FITC-labeled 45S rDNA (green) and rhodamine-labeled 5S rDNA (red). Dashed lines, outline of DAPI-stained chromosome. Scale bar in (<b>A</b>) 2 cm; (<b>B</b>) 5 µm; (<b>C</b>) 10 µm; (<b>D</b>) 2 µm.</p

Gene ontology (GO) terms enriched among the misregulated genes in three trisomic plants.

<p>The specific enriched GO terms for up- and downregulated genes in <i>AAA</i> (white), <i>AAa</i> (black) and trisomy 5 (gray) were derived by use of agriGO <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Du1" target="_blank">[33]</a>. The <i>p</i> values for GO terms are shown in –logarithmic scale. Data for trisomy 5 are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Huettel1" target="_blank">[5]</a>. Complete lists are presented in Tables S3 and S4 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617.s001" target="_blank">S1 File</a>.</p

The <i>aur2-1</i>/+ is tertiary trisomy 2 revealed by array comparative genome hybridization (array CGH).

<p>(<b>A</b>) The log₂ ratios of signal intensity of <i>Arabidopsis</i> chromosomes in trisomics (<i>AAA</i> or <i>AAa</i>) to wild-type diploids (Col-0). Each dot indicates one set of probes corresponding to a unique position on the chromosomes (Chr.). Locations of centromeres are the area with fewer dots. Shaded area in chromosome 2 indicates the region containing the translocation breakpoint. (<b>B</b>) A schematic representation of chromosome 2 in <i>aur2-1</i>/+. S, short; L, long arm of chromosomes. (<b>C</b>) The log₂ ratios of signal intensity of chloroplast and mitochondria genomes in trisomy (<i>AAA</i> or <i>Aaa</i>) to wild-type diploid (Col-0). Genome duplication is identified by the ratio shifting above the baseline at 0. The moving average is a series of averages of 10 probe sets.</p

Whole-genome transcriptome analysis in trisomic plants.

<p>(<b>A</b>) The log₂ ratios of the expression of all genes in trisomics (<i>AAA</i> or <i>AAa</i>) relative to wild-type diploids (Col-0). Each dot indicates one set of probes corresponding to a unique position on the chromosomes (Chr.). Positive and negative values indicate upregulated and downregulated expression, respectively. Locations of centromeres are the area with no gene expression. (<b>B</b>) Venn diagram shows the specific and overlapping genes with significant misregulated expression compared to wild-type diploid (Col-0) between trisomy 2 (<i>AAa</i>) and tertiary trisomy 2 (<i>AAA</i>) (<i>p</i><0.05). (<b>C</b>) Clustering and heat map of the 325 misregulated genes common to the two trisomics (<i>AAA</i> and <i>AAa</i>). Four groups of genes based on expression patterns are shown on the right.</p

Genetic analysis of <i>aur2-1</i>/+ inheritance.

a<p>HZ, heterozygous.</p>b<p>HM, homozygous.</p><p>Genetic analysis of <i>aur2-1</i>/+ inheritance.</p

A Model of the genomic constitution of <i>aur2-1</i>/+ <i>qrt2-1</i>/<i>qrt2-1</i> tetrads.

<p>Meiosis without (<b>A</b>) or with crossing over (<b>B</b>). Left panel shows pollen mother cells and right panel, tetrads after meiosis. Chromosome 2 carrying the wild-type <i>AUR2</i> (<i>A</i>) is shown in a blue line or the <i>aur2-1</i> allele (<i>a</i>) with a translocation is indicated in a bold red line. M I, meiosis I; M II, meiosis II; shaded cells, aborted pollen grains.</p

The number of organelle-related genes that are significantly misregulated to different degrees in trisomic genomes.

a<p>The probes matching multiple chromosomal locations are excluded.</p>b<p>Misregulated genes (<i>p</i><0.05) on Chr.1, 3 (3’ end; behind the translocation breakpoint), 4, and 5.</p>c<p>Misregulated genes (<i>p</i><0.05) on Chr.1, 2, 3, and 4; raw data from Huettel et al. (2008) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Huettel1" target="_blank">[5]</a>.</p>d<p>The genes related to plastids, mitochondria, and peroxisomes are from Law et al. (2012) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Law1" target="_blank">[70]</a>.</p>e<p>Chi-square test with Yates’ correction; two-tailed <i>P</i> value; ^*, <i>p</i><0.05; ^**, <i>p</i><0.01.</p><p>The number of organelle-related genes that are significantly misregulated to different degrees in trisomic genomes.</p

Genotype and rosette leaf phenotype in the progeny of self-fertilized and backcrossed <i>aur2-1</i>/+.

a<p>W, plants with wild-type rosette leaves.</p>b<p>R, plants with round rosette leaves.</p>c<p>T, plants with tiny stature and round rosette leaves.</p>d<p>Predicted genotype.</p><p>Genotype and rosette leaf phenotype in the progeny of self-fertilized and backcrossed <i>aur2-1</i>/+.</p