Distribution of Substitutions per Silent Site (Ks) for Homolog Pairs in Segmental, Tandem, and Background Duplications

<p>In (A), contributions from the recent segmental duplication on Chromosomes 11 and 12 are colored in red. The tandem duplication data are shown on two different scales, one to emphasize the magnitude of the zero peak (B) and another to highlight the exponential decay (C). Background duplications are shown in (D).</p

Graphical View of All Duplicated Segments

<p>The 12 chromosomes are depicted along the perimeter of a circle, not in order but slightly rearranged so as to untangle the connections between segments. Overall, we cover 65.7% of the genome.</p

Functional Classifications from GO, Focused on Plant-Specific Categories Outlined by Gramene

<p>(A) compares predicted genes from <i>Arabidopsis</i> and Beijing <i>indica</i>. (B) compares predicted genes from Beijing <i>indica</i> with nr-KOME cDNAs. We ignore categories with less than 0.1% of the genes.</p

A View of All Duplications Found on Rice Chromosome 2

<p>In contrast to <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030038#pbio-0030038-g006" target="_blank">Figure 6</a>, where we featured those cDNAs with one and only one TBlastN homolog, here we show all detectable TBlastN homologs, up to a maximum of 1,000 per cDNA.</p

Basic Algorithm for Construction of Scaffolds and Super-Scaffolds

<p>We start with the smallest plasmids and progressively work our way up to the largest BACs. Only links with two or more pieces of supporting evidence are made. These include 34,190 “anchor points” constructed from a comparison of <i>indica</i> and <i>japonica</i>. Each anchor is a series of high-quality BlastN hits (typically 98.5% identity) put together by a dynamic programming algorithm that allows for small gaps to accommodate the polymorphic intergenic repeats. Typical anchor points contain four BlastN hits at a total size of 9 kb (including gaps). Notice how in the beginning <i>indica</i> and <i>japonica</i> are processed separately, to construct what we called scaffolds. Only at the end do we use data from one subspecies to link scaffolds in the other subspecies, and these are what we called super-scaffolds.</p

A Sample Bioverse-Predicted Interaction Network for Defense Proteins and Their Direct Neighbors

<p>The symbols are colored to indicate some of the major GO categories under “molecular function.” We draw a cross over the symbol for an NH gene. Rectangles indicate proteins that are manually classified as being R-genes. They appear on genes that are not colored as defense, because some genes have multiple functions, not because of an annotation error. The white circles with green outline are unannotated genes that might also belong to this network, at a lower confidence.</p

Overlapping FGENESH Predictions in All Three Rice Assemblies

<p>Two predictions are shared when 50% of their coding regions can be aligned. Because of imprecision in the predictions and overlap criteria, we get slightly different numbers for each assembly, and these are encoded through multiple color-coded numbers in the Venn diagram. EST confirmation requires 100 bp of exact match. Unlike the genes, we do not bother to show a different number for each assembly, because they are very similar.</p

Ka/Ks Distribution for Homolog Pairs

<p>Ka and Ks are the fraction of the available nonsynonymous and synonymous sites that are changed in the homolog pairs. Ka/Ks > 1 is an indicator of positive selection. Shown is the Ka/Ks distribution for segmental duplications (A) and for tandem duplications (B).</p

Duplicated Segments in the Beijing <i>indica</i> Assembly

<p>Depicted here are the plots for Chromosomes 2 (A) and 6 (B). Each data point represents the coordinated genomic positions in a homolog pair, consisting of one nr-KOME cDNA and its one and only TBlastN homolog in rice. Shown on the <i>x</i>-axis is the position of a gene on the indicated chromosome, and shown on the <i>y</i>-axis is the position of its homolog on any of the rice chromosomes, with chromosome number encoded by the colors indicated on the legend at the right.</p

A Region on Beijing <i>indica</i> Chromosome 2, Showing Three Gene Islands Separated by Two Intergenic Repeat Clusters of High 20-mer Copy Number

<p>Transposable elements identified by RepeatMasker are classified based on the nomenclature of <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030038#st002" target="_blank">Table S2</a>. Depicted genes include both nr-KOME cDNAs and FGENESH predictions.</p