(A) Maximum likelihood tree of LUC7-like protein. Red

A

B Aquilegia coerulea.Aquca 058 00048.1 Mimulus guttatus.mgv1a007359m Glycine max.Glyma09g38430.1 Vitis vinifera.GI.225430908 Physcomitrella patens patens.GI.168064814 Selaginella moellendorffii.GI.302788961 Gloeochaete witrockiana.SAG46.84.MMETSP0308 182511_1

94 100 82 100 96

91

98

94 65

96 59

92

100 99 92 99 100

84 98

100 71

97

61 100 49 100

Galdieria sulphuraria.stig 0.Gs00410.1 Galdieria phlegrea.ctg 2451.g627 Rhodosorus marinus.MMETSP0315.3464_1 Compsopogon coeruleus.MMETSP0312 1243_1 Chattonella subsalsa.CCMP2191.20439_1 Saccharina japonica.SJ16754 Hyaloperonospora arabidopsidis.HpaP800193 Pythium ultimum.G001005 Vitrella brassicaformis.Vbra19439 Togula jolla.CCCM725.19959_1 Magnaporthe oryzae 70-15.GI.389644996 Uncinocarpus.GI.258575139 Pyrenophora tritici-repentis Pt-1C-BFP.GI.189201213 Schizosaccharomyces pombe 972h-.GI.19075500 Daphnia pulex.jgiDappu1 222176 Tribolium castaneum.GI.91088003 Homo sapiens.GI.41393554 Saccoglossus kowalevskii.GI.291239634 Hydra magnipapillata.GI.449671597 Trichoplax adhaerens.GI.195999904 Amphimedon queenslandica.GI.340373897

99 39

60

97 98 56

Chondrus crispus T00001783001 Gracilariopsis chorda.GRC0002RA01050_1 Porphyridium purpureum contig 2020.13

100 54

98

56

Physcomitrella patens.GI.168010281 Selaginella moellendorffii.GI.302787324 Arabidopsis thaliana.GI.15227373 Klebsormidium flaccidum.kfl00002 0700 Coccomyxa subellipsoidea 6950 Micromonas pusilla CCMP1545.GI.303289240 Gloeochaete witrockiana.SAG46.84.MMETSP0308 184526 1 Bigelowiella natans 54244 Lotharella globosa LEX01.27957 Guillardia theta.jgiGuith1.166652 Hemiselmis andersenii.CCMP439.2575

67 88 100

Gracilariopsis chorda.GRC0075RA00050_1 Chondrus crispus T00007119001 Porphyridium purpureum contig 4508.1

100

83 100

100

98

Timspurckia oligopyrenoides.MMETSP1172.43428_1 Rhodosorus marinus.MMETSP0011 2.6770_1 Galdieria sulphuraria.stig 7.Gs11920.1 Galdieria phlegrea.ctg 823.g202 Chrysochromulina polylepis.CCMP1757.23728 Calcidiscus leptoporus.RCC1130.33455 Pediculus humanus corporis.GI.242023811 Lottia gigantea.jgiLotgi1 216477 Homo sapiens.GI.24431950 Ciona intestinalis.GI.198422965 Strongylocentrotus purpuratus.GI.72110055 Trichoplax adhaerens.GI.195999906 Nematostella vectensis.GI.156390600 Schizophyllum commune H4-8.GI.302687498 Ustilago.GI.71022699 Tuber melanosporum Mel28.GI.296412031

100 100

48 100 82 68 100 98 57 100 83 100 100

0.2

0.4

C Gsul vs Cmer 2nd hit

Gsul vs Banguacea

Gsul

2nd hit

human 1st hit

Gsul vs Porphyridium

Gsul 2nd hit

human

Cmer

1st hit

1st hit

Gsul

1st hit

human 2nd hit

1st hit

Cmer

2nd hit

Gsul vs Gcho 2nd hit

Gsul

1st hit

1st hit

Bangiacea

Gcho

1st hit

1st hit

Gsul

2nd hit

(95)

1st hit

2nd hit

Ppur

Gsul

Gsul Ccri

Gsul vs Rhom

2nd hit

human

(53)

(94)

human

(64)

(71)

1st hit

Gcho

Gsul

Gsul Gphl

Ccri

(24)

human

(23)

human

2nd hit

Gsul vs Gphl 2nd hit

(92)

(89)

human

Gsul

human

1st hit

Ppur

(75)

human

Gsul

human

(15)

(12)

(46)

2nd hit

human

Bangiacea

(4)

Gsul vs Ccri

Gsul

1st hit

Gsul

1st hit

Gsul

human

Rhom

2nd hit

Rhom

human 2nd hit

Gphl

Figure S3. Sequence conservation in Galdieria sulphuraria genes. (A) Maximum likelihood tree of LUC7-like protein. Red algal taxa connected with exceedingly long branched are shown in bigger font and bold face. Node supports values are calculated using the ultrafast bootstrap (UFboot) approximation approach with 1500 bootstrap replicates. (B) Maximum likelihood tree of PRPF4 protein. (C) Pairwise compassion in sequence conservation using BLASTp bit-score as measure. Protein databases are constructed for proteins found in both red algal species that are compared (e.g., G. sulphuraria and C. merolae). The distribution of BLASTp top hits among the two red algal species is shown in pie charts. Abbreviation: Gsul (Galdieria sulphuraria), Cmer (Cyanidiochyzon merolae), Ccri (Chondrus crispus), Gcho (Gracilariopsis chorda), Gphl (Galdieria phlegrea), Rhom (Rhodosorus marinus).

1