Lengths of Orthologous Introns within a Quartet Are More Correlated than Those of Paralogous Introns

<p>(A) Quartet orthologous intron pairs. <i>x</i>-axis, length (log₁₀) of introns in human members of each quartet; <i>y</i>-axis, length (log₁₀) of corresponding orthologous introns in the mouse member of the same quartet. Spearman correlation coefficient: 0.903; <i>p</i> < 0.001.</p> <p>(B) Paralogous introns. <i>x</i>-axis, length (log₁₀) of introns in human members of each quartet; <i>y</i>-axis, length (log₁₀) of corresponding paralogous introns in the other human member of the same quartet. Spearman correlation coefficient: 0.140; <i>p</i> < 0.001. The mouse distributions are essentially identical to their human counterparts.</p

Cumulative Distribution Functions Illustrating Proteome-Wide Trends in Protein Similarity

<p><i>x</i>-axis, bits/aligned position; <i>y</i>-axis, cumulative fraction of HSPs having that number of bits/aligned amino acid pair or less. To facilitate display, only a subset of the 21 possible pair-wise combinations is shown. Data are based upon all reciprocal best BLASTP hits identified in all versus all BLASTP searches of the proteomes. Similarity calculations were restricted to the high-scoring HSP for each BLAST hit, in order to avoid data duplication due to overlapping alignments.</p> <p>There were 13,339 <i>M. musculus–H. sapiens</i> reciprocal best hits; 6,435 between D. melanogaster and <i>A. gambiae;</i> 5,828 between C. intestinalis and <i>H. sapiens;</i> 5,542 between D. melanogaster and <i>H. sapiens;</i> 4,669 between C. elegans and <i>H. sapiens;</i> 4,588 between C. elegans and <i>D. melanogaster;</i> 3,361 between H. sapiens and <i>A. thaliana;</i> and 2,835 between C. elegans and A. thaliana.</p> <p>atha, <i>A. thaliana;</i> cele, <i>C. elegans;</i> cint, <i>C. intestinalis;</i> dmel, <i>D. melanogaster;</i> hsap, <i>H. sapiens;</i> mmus, <i>M. musculus.</i></p

D. melanogaster Intron Lengths Are Highly Correlated with Their Inferred D. pseudoobscura Orthologs; D. melanogaster Paralogous Introns Show No Such Correlation

<p>(A) <i>x</i>-axis, length (log₁₀) of annotated D. melanogaster introns; <i>y</i>-axis, length (log₁₀) of their inferred orthologs in the D. pseudoobscura genome. Red circles indicate those introns containing a transposon in <i>D. melanogaster;</i> blue circles indicate those introns containing a transposon in <i>D. pseudoobscura;</i> gold circles indicate introns without identifiable transposons in either species. Spearman correlation coefficient: 0.637; <i>p</i> < 0.001.</p> <p>(B) Intron lengths of paralogs having the same intron–exon structure as judged by the positions of their splice junctions relative to the protein alignments of their reciprocal best-hit best HSPs. <i>x</i>-axis, length (log₁₀) of introns in an annotated D. melanogaster gene; <i>y</i>-axis, length (log₁₀) of corresponding paralogous introns. Spearman correlation coefficient: 0.448; <i>p</i> < 0.001.</p

Controlling for the Impact of Unequal Rates of Protein Evolution on the Evolution of Intron–Exon Structures

<p>(A) Unrooted neighbor-joining tree based upon amino acid similarities for reciprocal best-hit best HSPs having 1.25 bits/aligned amino acid pair.</p> <p>(B) Unrooted neighbor-joining tree based upon similarities in the intron–exon structures of those same HSPs.</p

Neighbor-Joining Trees Summarizing Proteome-Wide Trends in Protein Similarity and Genome-Wide Trends in Intron–Exon Structural Similarity

<p>Proteome-wide trends in protein similarity (A), and genome-wide trends in intron–exon structural similarity (B). Numbers beneath tree nodes are bootstrap values.</p

Intron Lengths Can Be Used as a Molecular Clock

<p><i>y</i>-axis, magnitude of the Spearman correlation coefficient for the five <i>Drosophila</i> distributions shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-g008" target="_blank">Figure 8</a>. <i>x</i>-axis, time (millions of years) since last common ancestor based on protein similarities as calculated in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-b030" target="_blank">30</a>]. Black bars above and below each data point denote observed variance in the data and were obtained by randomly resampling 1,000 orthologous intron pairs 100 times. Best-fitting curve (shown in black) y = −0.0057x + 0.9266; R² = 0.9875.</p

Global Overview of Gene Structure in Six Annotated Animal Genomes

<p>(A) Intron length. Annotated intron length (log₁₀) is plotted on the <i>x</i>-axis; the frequency at which introns of that length occur in an organism's genome is plotted on the <i>y</i>-axis.</p> <p>(B) Exon length. <i>x</i>-axis, coding-exon length in nucleotides; <i>y</i>-axis, frequency.</p> <p>(C) Intron density. A transcript's intron density is equal to its number of coding introns divided by the length of the protein it encodes. <i>y</i>-axis, frequency of annotated transcripts with a particular intron density. <i>x</i>-axis, intron density binned in increments of 0.5 introns/100 amino acid (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#s4" target="_blank">Materials and Methods</a>). Deuterostomes are shown in shades of blue; protostomes in shades of red.</p

Correlation in Orthologous Intron Lengths Is Proportional to Time since Last Common Ancestor

<p>From left to right, and top to bottom: Annotated D. melanogaster lengths (<i>x</i>-axis) versus inferred orthologous intron lengths (<i>y</i>-axis) for D. simulans (strain 6), <i>D. yakuba, D. ananassae, D. pseudoobscura,</i> and D. virilis.</p> <p>Bottom right-hand panel: Annotated D. melanogaster lengths (<i>x</i>-axis) versus inferred A. gambiae intron lengths (<i>y</i>-axis). Approximate time since last common ancestor is shown in red in the lower left-hand corner in each panel; these are approximate estimates based upon protein data [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-b030" target="_blank">30</a>]. Spearman correlation coefficients: 0.886, 0.863, 0.670, 0.637, 0.550, and 0.410 for <i>D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis,</i> and A. gambiae distributions, respectively. <i>p</i> < 0.001 for each correlation coefficient. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#s4" target="_blank">Materials and Methods</a> for analysis details.</p

Intron–Exon Structures Evolve Largely Independently of Protein Sequences

<p><i>x</i>-axis, human reciprocal best-hit best HSPs for four representative proteomes binned by percent identity in 5% increments. <i>y</i>-axis, percent of aligned introns among the HSPs in each bin.</p> <p>cele, <i>C. elegans;</i> cint, <i>C. intestinalis;</i> dmel, <i>D. melanogaster;</i> hsap, <i>H. sapiens;</i> mmus, M. musculus.</p