TABLE 1

Estimates of dS and dN between C. incerta (Ci) and C. reinhardtii (Cr) and other evolutionary parameters

Ci/Cr
Gene product descriptionGene nameLcdSdNdN/dSGC%GC3%NcCAI
Guanine nucleotide-binding β-subunit-like proteincblP2770.0250.0010.05665.0/65.094.6/94.924.2/24.10.90/0.89
60S ribosomal protein L11rpl11169a0.0830.0050.05464.3/64.593.5/94.725.1/24.80.87/0.88
Cytochrome b6f /Rieske Fe-S protein (p)PetC1780.0990.0200.19866.2/66.783.7/84.827.3/27.50.79/0.78
Photosystem I subunit F (p)PsaF2150.1090.0160.14266.4/67.187.4/87.027.0/27.40.79/0.79
40S ribosomal protein S15rps15129a0.1100.0060.05762.5/62.589.9/89.926.3/26.10.89/0.88
Cytochrome b6f/4.6-kDa subunit (p)PetM98a0.1330.0040.03371.4/69.487.8/81.626.9/29.50.79/0.72
Ferredoxin (p)PetF125a0.136067.5/67.586.4/86.426.4/26.50.84/0.84
ATP synthase subunit II (p)AtpG208a0.1360.0100.07165.7/65.490.9/88.926.4/27.00.80/0.80
Translation initiation factorEif4A1480.139064.0/63.395.3/93.224.9/25.80.85/0.83
Apoplastocyanin (p)PetE144a0.1390.0150.10666.0/66.483.3/84.026.6/25.70.80/0.82
Glyceraldehyde-3-phosphate dehydrogenase (p)GapA3690.1440.0090.06564.5/65.191.1/93.224.9/24.10.87/0.89
NADH:ubiquinone oxidoreductase 49-kDa subunit (m)Nad72760.1490.0130.08667.8/67.493.1/92.827.4/28.60.72/0.71
Unknown lumenal polypeptide (p)116a0.1550.0160.10569.3/67.689.3/86.424.2/25.20.82/0.83
60S ribosomal protein L31rpl31115a0.1680.0100.05861.7/61.593.0/93.027.6/28.20.73/0.76
Dynein light chain outer arm 8-kDafla1490a0.170058.1/57.590.0/87.841.7/46.80.73/0.70
16-kDa membrane protein (p)125a0.1700.0060.03768.0/68.392.0/92.825.0/24.00.86/0.88
Apocytochrome c (m)Cyc111a0.1710.0070.04363.1/62.882.9/81.132.5/31.10.72/0.71
14-3-3-like proteinerb141970.1770.0060.03461.4/61.189.8/88.330.4/32.70.70/0.66
ATP synthase F0 subunit 9 (m)Atp9158a0.178068.1/67.186.8/83.625.6/28.40.75/0.73
40S ribosomal protein S3rps3a229a0.1800.0070.04064.6/63.587.3/85.628.8/29.30.80/0.77
Oxygen-evolving enhancer protein 1/OEE1 (p)Psb1291a0.1810.0060.03165.1/64.990.0/89.325.4/26.60.86/0.85
ATP synthase Δ-subunit (p)AtpD218a0.1900.0210.11262.5/62.287.6/86.728.3/28.60.77/0.76
Cytochrome c oxidase subunit II (m)Cox2a1370.1930.0100.05167.9/68.181.8/81.028.9/29.40.68/0.67
Elongation factor α-likeefl462a0.1940.0080.04362.2/62.190.5/89.825.0/25.00.87/0.87
Light-harvesting complex I protein (p)LhcA240a0.1960.0250.12865.8/66.487.9/88.727.3/26.00.80/0.84
Thioredoxin peroxidase (p)Tpx2360.2060.0100.04965.4/64.892.0/87.725.7/27.80.87/0.81
Light-harvesting chlorophyll-a/b binding protein (p)LhcII-1.3256a0.2110.0100.05368.3/67.595.3/93.422.6/23.90.93/0.90
14-3-3-like protein related258a0.2180.0030.01462.7/62.089.2/86.829.9/30.60.74/0.72
Cytochrome c oxidase subunit II (m)Cox2b152a0.2200.0110.04862.3/62.188.8/88.233.8/31.10.68/0.68
40S ribosomal protein S8rps8a207a0.2210.0190.08563.6/63.593.2/93.230.0/29.60.77/0.79
Nucleic acid binding protein putativenab12250.2300.0110.04970.8/71.685.8/88.035.1/32.90.61/0.62
Ubiquinol-cytochrome c oxidoreductase/Rieske Fe-S protein (m)RisP2110.2410.0040.01665.6/65.787.2/88.231.1/30.70.66/0.67
ATP synthase γ-subunit (p)AtpC2320.2480.0200.08064.5/63.296.6/93.523.5/23.10.91/0.90
G-strand binding protein 1/telomere bindinggbp1219a0.2510.0080.03169.3/69.484.0/83.132.2/32.50.71/0.71
S-adenosyl-l-homocystein hydrolasesahH2560.2740.0140.05065.9/65.593.0/91.224.9/24.70.88/0.87
Photosystem I subunit N (p)PsaN138a0.2800.0060.02166.4/66.491.3/89.926.1/26.10.87/0.86
GTP-binding YPTC1 proteinyptC1202a0.2890.00058.0/58.884.1/86.637.3/36.30.63/0.65
Oxygen-evolving enhancer protein 3/OEE3 (p)Psb3198a0.3120.0200.06569.4/69.291.9/90.425.4/24.40.83/0.85
CR057 mitochondrial carrier protein (m)350a0.3150.0110.03664.9/63.691.4/87.727.8/29.20.80/0.77
Glyceraldehyde-3-phosphate dehydrogenasegapC1950.3400.0140.04066.3/66.099.0/98.023.0/23.70.88/0.87
ADP/ATP translocator (m)Ant307a0.3670.0040.01063.1/63.190.2/89.627.5/26.50.83/0.81
Glycine decarboxylase complex H (m)GcvH158a0.3670.0130.03662.9/63.384.2/85.432.3/31.30.71/0.74
NADH:ubiquinone oxidoreductase 13-kDa-like subunit (m)153a0.3700.0160.04463.4/61.783.7/78.443.1/44.80.61/0.61
Photosystem I polypeptide 28 (p)PsaH129a0.3760.0160.04365.6/66.984.5/86.827.8/28.50.81/0.79
Oxygen-evolving complex/thylakoid Lumenal 25.6-kDa (p)PsbP2040.3950.0140.03664.9/65.485.8/86.334.5/31.60.65/0.69
Inorganic pyrophosphatase (p)PpaI2070.3980.0130.03466.3/66.290.8/89.826.8/28.00.81/0.80
Calmodulin162a0.3980.0020.00660.5/60.587.7/87.036.2/35.60.71/0.73
Mago nashi-like protein147a0.4550.0050.01256.5/55.185.0/82.334.2/38.90.68/0.66
Carotenoid binding protein (p)Cbr161a0.5080.0220.04264.6/64.682.0/81.433.0/32.20.62/0.62
Nucleolar RNA-binding Nop10p-like63a0.5130.0270.05259.8/60.876.2/81.044.5/36.30.55/0.54
Minus dominance mating typemid143a0.5200.1130.21750.0/48.757.0/55.461.0/60.00.36/0.38
Microtubule-associated protein putative132a0.5400.0320.05958.1/56.681.8/77.245.6/49.60.56/0.57
Succinoglycan biosynthesis protein related (m)2000.5490.0540.09967.5/64.284.2/76.640.0/42.00.56/0.51
Hydroxyproline-rich glycoprotein VSP-3vsp-32590.5750.0400.07063.6/63.183.4/83.036.3/37.90.58/0.56
Apospory-associated C proteinapoC3100.5790.0150.02567.0/66.395.5/93.523.5/29.90.84/0.81
Peptidylprolyl isomerase/cyclophilin-like199a0.5900.0210.03668.5/68.295.0/93.525.8/25.20.81/0.84
PR46b proteinpr46b265a0.6240.0530.08562.0/65.270.6/79.246.9/40.50.45/0.52
Expressed protein107a0.6470.0350.05568.5/66.791.6/86.930.2/28.70.67/0.72
S-adenosyl-l-methionine synthetasesamS2410.6490.0110.01765.0/63.394.2/90.523.8/26.40.89/0.84
Pyruvate dehydrogenase kinase-like (m)Pdk487a0.6950.0320.04666.7/65.089.7/84.432.1/34.50.60/0.57
Mating-type protein Mat3p/retinoblastoma-like proteinmat31194a0.7130.0610.08567.9/68.085.0/84.836.2/35.90.54/0.54
Alternative oxidase 1 (m)Aox12600.7340.0170.02369.9/68.196.9/92.726.1/31.00.74/0.67
Phosphoenolpyruvate carboxykinase relatedpck2170.7930.0200.02565.0/63.991.2/86.630.0/31.00.76/0.72
Extracellular polypeptide Ecp882290.8050.0330.04165.6/65.591.3/90.825.6/28.40.74/0.71
Asparagine synthetase related2191.1610.0240.02165.3/64.587.7/84.934.1/42.20.60/0.57
Striated fiber assemblinsfa2031.194b0.008b0.007b62.9/64.783.7/88.238.0/31.80.64/0.64
Pherophorin I2311.6820.1200.07166.1/66.892.3/92.227.0/26.00.85/0.82
Average2200.3700.0180.05664.7/64.4*88.2/87.2*30.1/30.20.75/0.75
Coefficient of variation %6579122715/57/723/2215/15
  • Lc, length of codons analyzed. dS and dN, numbers of synonymous and nonsynonymous substitutions per site, respectively. GC%, percentage of G + C. GC3%, percentage of G + C in the third codon position. m, mitochondrial targeted. p, plastid targeted. * Significantly different at P < 0.01.

  • a Full-length coding sequence.

  • b dS and dN estimated by using the counting method (Yang and Nielsen 2000), because the maximum-likelihood method failed to converge.