Convergent Evolution of Intron Structures INTRON LENGTH Median Table 2. Intron features for the 50 eukaryotic species included in this study. SPECIES NAME Aspergillus fumigatus Anopheles gambiae Aspergillus nidulans Arabidopsis thaliana Bigellowiella natans NM Cyanidioschyzon merolae Candida albicans Caenorhabditis elegans Candida glabrata Chlamydomonas reinhardtii Ciona intestinalis Cryptococcus neoformans Cryptosporidium parvum Dictyostelium discoideum Debaryomyces hansenii Drosophila melanogaster Danio rerio Encephalitozoon cuniculi Eremothecium gossypii Entamoeba histolytica Giardia lamblia Guillardia theta NM Gibberella zeae Homo sapiens Kluyveromyces lactis Neurospora crassa Ostreococcus lucimarinus Ostreococcus tauri Oryza sativa Paramecium tetraurelia Plasmodium chabaudi Plasmodium falciparum Phytophthora ramorum Phytophthora sojae Plasmodium yoelii Rhizopus oryzae Saccharomyces cerevisiae Schizosaccharomyces pombe Strongylocentrotus purpuratus Toxoplasma gondii Theileria parva Trichomonas vaginalis Ustilago maydis Yarrowia lipolytica Brassica oleracea Candida tropicalis Candida guilliermondii Candida lusitaniae Dicyema acuticephalum Plasmodiophora brassicae % of introns containing most common branch point motif for given number of degenerate sites 0 10.97% (actgac) 6.12% (actaat) 8.33% (ctaaca) 8.23% (tctgat) 1.16% (ctaata) 100.00% (actaac) 95.43% (actaac) 7.09% (ctaatt) 66.25% (actaac) 7.29% (ctgacc) 8.37% (ctaatt) 10.08% (ctgaca) 9.39% (ctaatt) 18.66% (actaat) 71.83% (actaac) 8.73% (actaat) 8.57% (ctgatt) 38.46% (ctaatt) 82.03% (actaac) 5.95% (actaat) 60.00% (ctaaca) 6.06% (actaac) 15.88% (ctaaca) 7.90% (ctgacc) 99.22% (actaac) 15.38% (ctaaca) 41.15% (actgac) 9.55% (actgac) 7.86% (ctaatt) 1.66% (tctaat) 5.46% (ctaatt) 3.30% (ctaatt) 5.94% (ctgacg) 5.42% (ctgacg) 5.37% (ctaata) 4.77% (actaat) 94.40% (actaac) 21.61% (actaac) 8.52% (tctaat) 4.54% (tctgac) 9.03% (ctaatt) 94.12% (ctaaca) 11.64% (actgac) 70.72% (actaac) 7.67% (tctgat) 100.00% (actaac) 76.92% (actaac) 90.00% (actaac) 4.88% (ctaatt) 8.14% (tctgac) 1 2 17.96% (ctgacw) 29.99% (ctracw) 11.12% (wctaat) 18.04% (wctaay) 15.79% (actrac) 28.32% (ctracw) 14.95% (tctrat) 23.36% (wctrat) 1.39% (ctaatm) 1.39% (wctaay) 100.00% (wctaac) 100.00% (wctrac) 96.45% (actaay) 96.95% (wctaay) 10.43% (ctratt) 15.13% (ctratw) 72.50% (actaay) 75.00% (wctaay) 13.22% (ctgacs) 19.51% (ctgays) 14.97% (ctaatw) 23.47% (ctaayw) 17.12% (ctgacw) 27.49% (ctgayw) 14.08% (ctaatw) 17.37% (ctaayw) 24.67% (wctaat) 31.89% (wctaay) 77.18% (actaay) 81.41% (wctaay) 14.68% (wctaat) 21.63% (wctaay) 15.17% (ctratt) 26.26% (wctrat) 69.23% (ctaayt) 69.23% (ctrayt) 85.71% (actrac) 87.10% (wctrac) 9.09% (wctaat) 12.16% (wctaay) 100.00% (ctraca) 100.00% (ctraya) 6.06% (wctaac) 6.06% (wctrac) 24.62% (actrac) 38.10% (ctracw) 14.06% (ctgacy) 22.80% (ctgayy) 100.00% (wctaac) 100.00% (wctrac) 26.83% (ctraca) 42.59% (ctracm) 42.97% (actrac) 44.93% (wctrac) 10.53% (actrac) 11.83% (wctgay) 14.40% (ctratt) 23.80% (wctrat) 2.72% (ctaatw) 3.12% (ctaayw) 10.18% (ctaatw) 12.73% (ctratw) 5.93% (ctaatw) 7.31% (ctratw) 10.54% (ctgack) 19.15% (ctrack) 9.87% (ctgack) 17.69% (ctrack) 10.09% (ctaatw) 12.77% (ctratw) 8.78% (wctaat) 13.62% (wctrat) 95.52% (actaay) 96.64% (actray) 35.26% (actaay) 50.46% (wctaay) 16.08% (tctrat) 26.67% (wctrat) 8.45% (tctgay) 14.06% (ctgayk) 14.38% (ctaatw) 18.13% (ctaayw) 97.06% (ctaacm) 97.06% (ctracm) 17.78% (ctgacm) 24.77% (ctgaym) 78.73% (wctaac) 80.25% (wctrac) 12.88% (tctrat) 20.27% (wctrat) 100.00% (wctaac) 100.00% (wctrac) 84.62% (actaay) 84.62% (wctaay) 90.00% (wctaac) 90.00% (wctrac) 7.32% (ctwatt) 9.76% (ctwayt) 13.95% (ctgacr) 22.09% (ctgayk) 3 43.18% (ctrayw) 24.58% (wctray) 42.78% (ctrayw) 30.99% (wctray) 1.39% (wctray) 100.00% (wctray) 96.95% (wctray) 20.34% (ctrayw) 78.75% (wctray) 25.64% (ctrays) 32.71% (ctrayw) 39.66% (ctrayr) 20.19% (wctray) 33.31% (wctray) 83.38% (wctray) 28.71% (wctray) 37.70% (ctrayw) 69.23% (ctrayw) 89.40% (wctray) 14.95% (wctray) 100.00% (ctraym) 6.06% (wctray) 50.15% (ctrayw) 34.32% (ctrayw) 100.00% (wctray) 50.83% (ctraym) 47.16% (wctray) 14.02% (wctray) 33.73% (ctrayw) 3.55% (ctrayw) 16.02% (ctrayw) 8.50% (ctrayw) 30.72% (ctrayk) 26.92% (ctrayk) 15.76% (ctrayw) 20.37% (wctray) 97.39% (wctray) 56.22% (wctray) 36.30% (wctray) 17.75% (ctrayk) 21.43% (ctrayw) 97.06% (ctraym) 29.50% (ctraym) 82.87% (wctray) 27.12% (wctray) 100.00% (wctray) 84.62% (wctray) 90.00% (wctray) 12.20% (ctwayk) 26.74% (ctrayk) *No full genome sequence available. doi:10.1371/journal.pgen.1000148.t002 Introns studied 18267 33443 25500 134535 860 27 197 102420 80 105401 48942 33059 213 17300 346 41049 200465 13 228 3053 5 17 25853 197835 130 5991 2148 6450 102728 90253 6738 7370 12829 17360 7890 40358 260 4722 120111 27085 3390 34 4859 719 1096* 34* 13* 10* 41* 86* PLoS Genetics | www.plosgenetics.org 5 August 2008 | Volume 4 | Issue 8 | e1000148 %AT 54.08 56.18 54.22 68.04 87.96 46.82 70.61 68.07 67.48 36.14 66.74 56.76 77.96 89.13 66.23 59.93 64.47 60.77 46.56 79.48 50.8 84.8 56.92 58.5 65.53 52.11 37.24 39.27 61.56 83.77 77.89 87.77 49.8 48.09 79.73 71.06 66.46 71.47 64.37 50.8 76.05 71.94 49.67 51.48 67.97 72.19 63.51 63.17 69.89 49.87 61 91 63 98 19 234 100 65 467 238 337 55 61 103 89 71 984 32 63 58 32 46 56 1507 266 83 111 52 171 25 121 144 74 78 133 57 148 56 748 490 63 104 95 204 93 81 65 98 25 55 Aver 100.06 1044.3 101.52 157.66 19.1 247.89 196.28 303.49 462.65 371.60 540.56 67.36 82.08 142.85 171.86 892.93 2864.33 35.77 113.3 97.5 85 46.27 92.84 5429.85 344.69 130.57 168.4 83.39 406.55 25.14 152.82 176.73 132.37 131.22 207.25 79.08 241.53 82.27 1628.48 578.26 91.42 101.27 126.88 268.75 165.67 199.26 100.54 110.7 24.93 55.66 Std Dev 297.62 3533.97 99.94 163.99 0.57 229.06 174.31 677.7 295.64 527.54 1117.91 55.1 72.97 158.36 166.52 3802.06 11125.47 8.48 96.77 179 70.35 2.67 94.09 19221.6 252.34 122.29 274.23 85.39 594.32 3.06 135.06 136.85 371.64 444.38 277.27 56.89 175.93 68.21 4405.72 468.81 102.53 27.13 109.79 225.59 316.9 175.43 94.49 58.67 2.51 7.01