Table S1. Gene sequences employed for molecular evolutionary analysis

C. reinhardtii / C. incerta
Gene product description (localization) / Gene
Name / Source a, b / Source b / Number of ESTs
/Cluster
14-3-3-like protein / erb14 / 20021010.3760.1a / DQ122864 / 7
14-3-3-like protein related / 20021010.322.1a / DQ122865 / 3
16kDa membrane protein (p) / 20021010.683.1a / DQ122866 / 17
40S ribosomal protein S15 / rps15 / 20021010.8662.1a / DQ122867 / 30
40S ribosomal protein S3 / rps3a / 20021010.6021.1a / DQ122868 / 22
40S ribosomal protein S8 / rps8a / 20021010.8174.1a / DQ122869 / 110
60S ribosomal protein L11 / rpl11 / 20021010.9108.1a / DQ122870 / 39
60S ribosomal protein L31 / rpl31 / 20021010.8247.2a / DQ122871 / 15
ADP/ATP translocator (m) / Ant / 20021010.1312.4a / DQ122872 / 9
alternative oxidase 1 (m) / Aox1 / 20021010.8476.1a / DQ122873 / 1
apocytochrome c (m) / Cyc / 20021010.8047.1a / DQ122874 / 2
apoplastocyanin (p) / PetE / 20021010.5927.1a / DQ122875 / 42
apospory associated C protein / apoC / 20021010.2010.1a / DQ122876 / 6
asparagine synthetase related / 20021010.2839.1a / DQ122877 / 1
ATP synthase F0 subunit 9 (m) / Atp9 / 20021010.6793.1a / DQ122878 / 6
ATP synthase delta subunit (p) / AtpD / 20021010.6167.1a / DQ122879 / 12
ATP synthase gamma subunit (p) / AtpC / 20021010.8211.1a / DQ122880 / 4
ATP synthase subunit II (p) / AtpG / 20021010.302.1a / DQ122881 / 13
calmodulin / 20021010.7619.1a / DQ122882 / 4
carotenoid binding protein (p) / Cbr / 20021010.6282.1a / DQ122883 / 1
CR057 mitochondrial carrier protein (m) / 20021010.3328.1a / DQ122884 / 1
cytochrome b6f 4.6 kDa subunit (p) / PetM / 20021010.9358.1a / DQ122885 / 11
cytochrome b6f /Rieske Fe-S protein (p) / PetC / 20021010.5600.1a / DQ122916 / 7
cytochrome c oxidase subunit IIa (m) / Cox2a / 20021010.8491.1a / DQ122886 / 1
cytochrome c oxidase subunit IIb (m) / Cox2b / 20021010.7853.1a / DQ122887 / 5
dynein light chain outer arm 8 kDa / fla14 / 20021010.5682.1a / DQ122888 / 1
elongation factor alpha-like / efl / 20021010.7498.1a / DQ122889 / 30
extracellular polypeptide Ecp88 / 20021010.6280.1a / DQ122890 / 1
expressed protein / 20021010.2916.1a / DQ122891 / 3
ferredoxin (p) / PetF / 20021010.1713.1a / DQ122892 / 69
G-strand binding protein 1 /telomere binding / gbp1 / 20021010.7660.1a / DQ122893 / 12
glyceraldehyde-3-phosphate dehydrogenase (p) / GapA / 20021010.2014.1a / DQ122894 / 12
glyceraldehyde-3-phosphate dehydrogenase / gapC / 20021010.1974.1a / DQ122895 / 3
glycine decarboxylase complex H (m) / GcvH / 20021010.1228.1a / DQ122896 / 2
GTP-binding YPTC1 protein / yptC1 / U13168b / DQ222936 / 1
guanine nucleotide-binding beta subunit-like protein / cblP / 20021010.6103.1a / DQ122897 / 11
hydroxyproline-rich glycoprotein VSP-3 / vsp-3 / L29029b / AY795084 / -
inorganic pyrophosphatase (p) / PpaI / 20021010.8323.1a / DQ122898 / 5
light harvesting complex I protein (p) / LhcA / 20021010.2886.1a / DQ122899 / 14
light-harvesting chlorophyll-a/b binding protein (p) / LhcII-1.3 / 20021010.1951.2a / DQ122900 / 46
mago nashi-like protein / 20021010.3752.1a / DQ122901 / 1
mating type protein Mat3p/ retinoblastoma-like protein / mat3 / AY781411b / AF375824 / -
minus dominance mating type / mid / U92071b / AF002710 / -
microtubule-associated protein putative / 20021010.82.1a / DQ122902 / 3
NADH:ubiquinone oxidoreductase 13kDa-like subunit (m) / 86.14.1.0a / DQ122903 / 3
NADH:ubiquinone oxidoreductase 49kDa subunit (m) / Nad7 / 20021010.2671.1a / DQ122904 / 2
nucleic acid binding protein putative / nab1 / AY157846b / DQ122905 / 1
nucleolar RNA-binding Nop10p-like / 20021010.8625.1a / DQ122906 / 1
oxygen-evolving complex/thylakoid lumenal 25.6kDa (p) / PsbP / 20021010.3944.1a / DQ122907 / 4
oxygen-evolving enhancer protein 1/OEE1 (p) / Psb1 / 20021010.3356.2a / DQ122908 / 11
oxygen-evolving enhancer protein 3/OEE3 (p) / Psb3 / 20021010.5978.1a / DQ122909 / 8
peptidylprolyl isomerase/cyclophilin-like / 20021010.344.1a / DQ122910 / 6
pherophorin I / 20021010.8425.1a / DQ122911 / 3
phosphoenolpyruvate carboxykinase related / pepCK / 20021010.5947.2a / DQ122912 / 2
photosystem I subunit F (p) / PsaF / 20021010.1029.1a / DQ122913 / 16
photosystem I polypeptide 28 (p) / PsaH / 20021010.6118.1a / DQ122914 / 20
photosystem I subunit N (p) / PsaN / 20021010.3360.1a / DQ122915 / 13
Pr 46b / Pr46b / 20021010.3538.1a / AY825028 / -
pyruvate dehydrogenase kinase-like / pdk / AY781412b / AF387365 / -
S-adenosyl-L-homocystein hydrolase / sahH / 20021010.2773.1a / DQ122917 / 4
S-adenosyl-L-methionine synthetase / samS / 20021010.4325.1a / DQ122918 / 6
striated fiber assemblin / sfa / AJ344366b / DQ122926 / -
succinoglycan biosynthesis protein related (m) / 20021010.4076.1a / DQ122919 / 2
thioredoxin peroxidase (p) / Tpx / 20021010.9242.1a / DQ122920 / 8
translation initiation factor / eIF4A / 20021010.6321.1a / DQ122921 / 16
ubiquinol-cytochrome c oxidoreductase /Rieske Fe-S protein (m) / RisP / 20021010.3115.1a / DQ122922 / 2
unknown lumenal polypeptide (p) / 20021010.5100.1a / DQ122923 / 13

m, mitochondrial located. p, plastid located.

a C. reinhardtii EST database at http://www.chlamy.org.

b GenBank database at http://www4.ncbi.nlm.nih.gov.