TABLE 3 in A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions

TABLE 3. Comparison of 74 noncoding loci from five plastid genomes of Apiaceae (Daucus, Anthriscus, Tiedemannia, Petroselinum, and Crithmum). For the individual intergenic spacers and introns, the loci are listed as they occur on the Crithmum ptDNA map (Fig. S1), starting at JLA, proceeding counterclockwise, and excluding the two IR regions. These noncoding loci represent all intergenic spacers>150 bp and introns from both LSC and SSC regions. The trnH-psbA locus excludes Crithmum because of alignment ambiguities. LocusLength (bp)Aligned length (bp)Constant positionsUninformative positionsParsimony-informative positionsVariable positionsSequence divergence (%)Total indelsParsimony-informative indelsPercent variabilitytrnH-psbA180 – 191197165293325.5– 12.510121.3psbA-3 0 trnK204 – 259265226327395.4– 12.68017.73 0 trnK-matK221 – 283284268133161.8 – 4.4306.7matK-5 0 trnK716 – 736760709447511.4 – 3.71628.85 0 trnK-3 0 rps16508 – 751817641139371769.1– 16.222124.2rps16 intron837 – 8759028098310932.3 – 6.716312.15 0 rps16-trnQ1,087 – 1,4321,5451,307204342383.8– 11.9401018.0trnQ-psbK343 – 362363341148220.9 – 4.0607.7psbK-psbI316 – 4124343615914733.6– 12.815320.3trnS-5 0 trnG510 – 5576055286314773.8– 10.018315.7trnG intron698 – 7127266545022723.9 – 6.612211.6atpF intron721 – 741770682799881.1 – 8.419513.95 0 atpF-atpH275 – 4124203614910593.0 – 9.68116.0atpH-atpI742–11691,2091,028154271813.5 – 9.528417.3atpI-rps2264 – 290338320162181.9 – 4.31028.3rps2-rpoC2209 – 230257234185230.5 – 7.38112.1rpoC2-rpoC1211 – 214216202104141.9 – 4.3207.4rpoC1 intron742 – 7517757164712592.2 – 4.21529.5rpoB-trnC1,189 – 1,2721,3601,155178272054.3– 10.542618.2trnC-petN475 – 6907556628211933.7 – 8.825415.6petN-psbM1,073 – 1,1311,2131,031150321823.8 – 9.033617.7psbM-trnD613 – 68970460386151014.4 – 9.912116.1trnE-trnT599 – 7948505752027327513.9 – 23.942337.3trnT-psbD1,235 – 1,4651,5261,298187412283.7 – 10.035717.2psbC-trnS229 – 254262242182202.1 – 5.37210.3trnS-psbZ340 – 3944003573310433.7 – 6.612213.8psbZ-trnG276 – 299317285284322.1 – 6.412113.9trnfM-rps14159 – 1661721655270– 3.1426.4psaA-ycf3 exon3697 – 7217496835610662.1 – 5.615010.8ycf3 intron2735 – 784794730559641.3 – 5.31119.4ycf3 intron1697 – 731755695537602.1 – 4.31339.7ycf3 exon1-trnS693 – 877903759122221443.1– 11.228119.0trnS-rps4186 – 320328278455504.9 – 8.99218.0rps4-trnT353 – 3824083474318614.1– 10.516318.9trnT-5 0 trnL766 – 803863730107261333.7– 11.129318.8trnL intron496 – 518522492282300.8 – 4.8516.73 0 trnL-trnF310 – 375377334394432.9 – 7.712214.6trnF-ndhJ385 – 3994273654814623.1 – 9.912217.3ndhC-3 0 trnV830 – 1,1021,152942181292102.3– 16.743722.0trnV intron558 – 5685705273310431.4 – 4.1818.9trnV-trnM173 – 183183167124162.4 – 5.23010.4atpB-rbcL742 – 7708397428611971.3 – 8.122014.2rbcL-accD582– 6056315734513582.9 – 5.915311.6accD-psaI370– 479525443739824.2– 14.126320.6psaI-ycf4386– 422449397439523.6 – 7.118115.6ycf4-cemA682 – 8639268377514892.4 – 7.214111.1cemA-petA229 – 267275253202221.2 – 6.37010.5petA-psbJ733 – 9671049888144171615.7 – 9.441419.3psbE-petL916 –1,1601,2151,068124231473.2 – 7.527114.3trnP-psaJ378 – 384386338399483.2 – 8.24113.5psaJ-rpl33437 – 462486403758833.6– 10.318420.8rps18-rpl20202 – 230235193357421.8– 10.89421.7rpl20–5 0 rps12769 – 7858077385811692.2 – 4.713210.25 0 rps12–3 0 clpP145 – 172177157173203.4– 10.85014.1clpP intron2619 – 660670610537602.9 – 4.827313.0clpP intron1839 – 8508747897510851.6 – 6.422312.25 0 clpP-psbB432 – 495534490377442.2 – 6.614210.9psbB-psbT172 – 206213194136191.0 – 6.59013.1petB intron748 – 7567576935410641.7 – 4.9509.1petD intron747 – 7737867215411652.1 – 4.81319.9rps8-rpl14194 – 203206179234271.0– 10.95015.5rpl16 intron883 – 9521,000883100171172.4 – 7.432514.9ndhF-rpl32843 –1,0861,202945213442577.0– 15.055526.0rpl32-trnL634 – 9751,006669296413378.5– 26.252238.7ccsA-ndhD205 – 2242281724412564.9– 17.513230.3psaC-ndhE260 – 2862942493312453.3– 10.45017.0ndhE-ndhG209–230235197344382.4–10.95018.3ndhG-ndhI301–362377319508584.0– 9.414119.1ndhA intron1,055–1,1041,1421,005111261372.8– 7.630114.6rps15-ycf1289 – 4024273585811693.5–11.417020.1Combined RegionstrnD-trnY-trnE-trnT945 –1,1501,219898227943217.6–19.351630.5trnS-psbZ-trnG-trnfM1,065–1,1331,2061,09990171072.5– 5.034511.7psbB-psbT-psbN-psbH594 – 626638611198271.3– 2.71216.1rpl36-infA-rps8-rpl141,066–1,0791,0839947613892.1– 5.0809.0 (Continued)