Supplementary Figure 14. Maximum-likelihood ...

TPM 15% 30%

. . . . . . . . . m.27316

100 100

7.2

12.2

0.10

1.4

m.14436 20.2

38.3

0.52

1.5

m.82938

38.3

1.00

7.1

4.2

DESeq2 VOOM-LIMMA p-val. log2FC p-val. log2FC

0.32

0.4

0.15

0.6

1.4E-09 2.7

0.34

0.4

0.18

0.6

0.0086

2.8

CCI44533.1 [Albugo candida]

100

100

EBSeq PPDE PostFC

CCA14050.1 [Albugo laibachii] 100

XP_008913756.1 [Phytophthora parasitica]

85

XP_002900354.1 [Phytophthora infestans]

100 72

XP_009532349.1 [Phytophthora sojae] ESA00502.1 [Rhizophagus irregularis] 100

GAN04155.1 [Mucor ambiguus] 78

100

CEI90320.1 [Rhizopus microsporus] CEG75698.1 [Rhizopus microsporus]

98 100

EPB92946.1 [Mucor circinelloides] GAN09712.1 [Mucor ambiguus]

XP_001758436.1 [Physcomitrella patens] 98

XP_011621943.1 [Amborella trichopoda] 97

XP_006400041.1 [Eutrema salsugineum] 100

KFK25768.1 [Arabis alpina] 78

NP_197028.1 [Arabidopsis thaliana]

72 XP_006287705.1 [Capsella rubella] 82

XP_006403529.1 [Eutrema salsugineum]

75

100

XP_010492352.1 [Capsella sativa]

XP_006436472.1 [Citrus clementina]

100

XP_010683905.1 [Beta vulgaris] XP_010471796.1 [Camelina sativa] 100

64

XP_006300079.1 [Capsella rubella] 71 XP_006407687.1 [Eutrema salsugineum]

57

62

XP_002884729.1 [Arabidopsis lyrata]

76

AAF14030.1 [Arabidopsis thaliana]

100 NP_187544.2 [Arabidopsis thaliana]

XP_011094890.1 [Sesamum indicum]

99 100

XP_009621095.1 [Nicotiana tomentosiformis] XP_009621094.1 [Nicotiana tomentosiformis]

XP_010673018.1 [Beta vulgaris] 0.1

Supplementary Figure 14. Maximum-likelihood phylogenetic tree for gene duplication cluster encoding amino acid permeases. For H. seosinensis sequences (in bold), expression values are indicated: TPM = averaged transcript per million at 15% or 30% salt, PPDE = Posterior Probability of being Differentially Expressed and PostFC = Posterior Fold Change calculated by EBSeq, p-val. = adjusted p-value and log2FC = log2 fold change calculated either by DESeq2 or voom-limma. Bootstrap values (>50%) are indicated at branch nodes. The scale bar indicates the expected substitutions/site.