Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light
Filiault et al. 10.1073/pnas.0712174105.
Supporting Information
Files in this Data Supplement:
SI Table 1SI Figure 6
SI Table 2
SI Text
SI Table 3
SI Table 4
SI Table 5
SI Table 6
SI Table 7
SI Figure 6
Fig. 6. Phylogenetic shadowing. Percent variation by amino acid position for 16 dicot PHYB sequences. Regions determined to be slow-evolving are indicated by orange bars (HMMI) or green bars (Divergence Threshold). Functional domains are marked with red bars.
Table 1. McDonald-Kreitman test for phyB, using 34 A. thaliana and 2 A. lyrata sequences
|
Source |
Polymorphisms, no. |
|
|
Synonymous |
Nonsynonymous |
|
|
Between species |
63 |
23 |
|
Within species |
66 |
16 |
P = 0.28, Fisher's exact test.
Table 2. Comparison of different association models
|
Model 1 |
Model 2 |
Preferred model |
P |
|
y » site 1 |
y » site 1 + site 3 |
Model 2 |
0.009 |
|
y » site 3 |
y » site 1 + site 3 |
No preference |
0.120 |
|
y » site 12 |
y » site 3 + site 12 |
Model 2 |
0.042 |
|
y » site 3 |
y » site 3 + site 12 |
No preference |
0.494 |
|
y » site 1 |
y » site 1 + site 12 |
No preference |
0.063 |
|
y » site 12 |
y » site 1 + site 12 |
No preference |
0.095 |
Table 3. Genbank sequences downloaded and used in this paper
|
Sequences for A. thaliana PHYB phylogenetic analysis |
Sequences for phylogenetic shadowing |
|||
|
Strain |
GenBank accession no. |
Species |
GenBank accession no. |
Phytochrome |
|
A. lyrata |
57791645 |
Arabidopsis lyrata |
57791646 |
|
|
Aua/Rhon |
57791625 |
Arabidopsis thaliana |
130189 |
|
|
Bensheim |
57791629 |
Brassica rapa |
110797028 |
|
|
Br-0 |
57791631 |
Cleome hassleriana |
57791679 |
|
|
Col-0 |
42569140 |
Glycine max |
1172496 |
|
|
Dijon-G |
57791617 |
Lotus japonicus |
121309520 |
|
|
Ita-0 |
57791635 |
Medicago truncatula |
124359940 |
|
|
Kin-0 |
57791637 |
Nicotiana plumbaginifolia |
2370331 |
|
|
Kondara |
57791643 |
Nicotiana tabacum |
464387 |
|
|
Mh-0 |
57791627 |
Pisum sativum |
6502525 |
|
|
Niederzenz |
57791633 |
Populus balsamifera subsp. trichocarpa |
10954091 |
B1 |
|
No-0 |
57791615 |
Populus balsamifera subsp. trichocarpa |
10954093 |
B2 |
|
Tsu-0 |
57791623 |
Populus tremula |
78643912 |
|
|
Wassilewskija |
57791639 |
Solanum lycopersicum |
59798480 |
B1 |
|
Solanum lycopersicum |
5757903 |
B2 |
||
|
Solanum tuberosum |
33302622 |
|||
Table 4. Genotyping assays for PHYB polymorphisms
|
Polymorphism |
Primer 1 |
Primer 2 |
Enzyme |
Ler size |
Cvi size |
|
Site 1 |
oJM79 |
PhyB-C2 |
N/A (SSLP) |
172 |
160 |
|
Site 3 |
oJM33 |
oJM32-2 |
AseI |
26, 79 |
105 |
|
Site 4 |
PB+3 |
PB24 |
BsmA1 |
392 |
122, 270 |
|
Site 7 |
oJM197 |
oJM188 |
DdeI |
23, 273 |
296 |
|
Site 12 |
oJM31 |
oJM30 |
HincII |
26, 88 |
114 |
See SI Table 7 for primer sequences.
Table 5. Genotypes of accessions used for association studies
|
Accession |
Source |
Ref., no. |
Site 1 |
Site 3 |
Site 4 |
Site 7 |
Site 12 |
|
Aa-0 |
ABRC |
CS900 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Abd-0 |
ABRC |
CS932 |
Cvi |
Ler |
NA |
Ler |
Cvi |
|
Ag-0 |
ABRC |
CS901 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Ak-1 |
ABRC |
CS6602 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
An-1 |
ABRC |
CS6603 |
Cvi |
Ler |
Ler |
Ler |
Cvi |
|
Ba-1 |
ABRC |
CS6607 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Bch-3 |
ABRC |
CS6610 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Be-0 |
ABRC |
CS6613 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Ber-0 |
ABRC |
CS8068 |
Ler |
Ler |
Ler |
Cvi |
Cvi |
|
Bl-1 |
ABRC |
CS6615 |
Cvi |
Cvi |
Ler |
NA |
Cvi |
|
Bla-10 |
ABRC |
CSC6622 |
Cvi |
Cvi |
Cvi |
Cvi |
Cvi |
|
Blh-1 |
ABRC |
CS6645 |
Cvi |
Cvi |
Cvi |
Cvi |
Cvi |
|
Br-0 |
ABRC |
CS6626 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Bs-1 |
ABRC |
CS6627 |
NA |
Cvi |
NA |
NA |
Cvi |
|
Bur-0 |
ABRC |
CS6643 |
NA |
Cvi |
NA |
NA |
Cvi |
|
C24 |
ABRC |
CS906 |
Ler |
Ler |
Ler |
Ler |
Ler |
|
Ca-0 |
ABRC |
CS6658 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Cal-0 |
ABRC |
CS6659 |
Cvi |
Cvi |
Cvi |
Cvi |
Cvi |
|
Cha-0 |
ABRC |
CS6662 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Chi-0 |
ABRC |
CS6669 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Cnt-1 |
ABRC |
CS6921 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Co-1 |
ABRC |
CS6669 |
Cvi |
NA |
Cvi |
Ler |
Cvi |
|
Col-0 |
Lehle |
WT-O2-21 |
Ler |
Ler |
Ler |
Ler |
Ler |
|
CS6188 |
ABRC |
CS6188 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Ct-1 |
ABRC |
CS6674 |
Cvi |
Ler |
Ler |
Ler |
Cvi |
|
Cvi-0 |
ABRC |
CS6675 |
NA |
Cvi |
NA |
NA |
NA |
|
Cvi-1 |
ABRC |
CS8580 |
NA |
Cvi |
NA |
NA |
NA |
|
Cvi-L |
Lehle |
WT-18-1 |
NA |
Cvi |
NA |
NA |
NA |
|
Da(1)-12 |
ABRC |
CS917 |
Cvi |
Ler |
Ler |
Ler |
Ler |
|
Da-0 |
ABRC |
CS6676 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Db-1 |
ABRC |
CS6678 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Di-g |
ABRC |
CS910 |
Cvi |
Ler |
Ler |
Ler |
Ler |
|
Dra-0 |
ABRC |
CS6685 |
Cvi |
Ler |
Ler |
Ler |
Ler |
|
Edi-0 |
ABRC |
CS6688 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Ei-2 |
ABRC |
CS6689 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Ema-1 |
ABRC |
CS1637 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
En-2+ |
ABRC |
CS327 |
Cvi |
Cvi |
Cvi |
Ler |
Cvi |
|
En-T |
ABRC |
CS6176 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Ep-0 |
ABRC |
CS6697 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
ER-0 |
ABRC |
CS6698 |
Cvi |
Ler |
Ler |
Ler |
Ler |
|
Es-0 |
ABRC |
CS6699 |
Cvi |
Ler |
Ler |
Ler |
Ler |
|
Est |
ABRC |
CS6173 |
Cvi |
Ler |
Ler |
Ler |
Ler |
|
Et-0 |
ABRC |
CS6702 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Flo-0 |
ABRC |
CS6044 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Fr-2 |
ABRC |
CS6708 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Ga-0 |
ABRC |
CS6714 |
Ler |
Ler |
Ler |
Ler |
Ler |
|
Gd-1 |
ABRC |
CS6716 |
Cvi |
Ler |
Ler |
Ler |
Cvi |
|
Ge-0 |
ABRC |
CS6717 |
Cvi |
Cvi |
Cvi |
Cvi |
Cvi |
|
Gie-0 |
ABRC |
CS6720 |
Cvi |
Cvi |
Cvi |
Cvi |
Cvi |
|
Gr-1 |
ABRC |
CS6723 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Gre-0 |
ABRC |
CS6729 |
Cvi |
Cvi |
Ler |
Ler |
Cvi |
|
Gy-0 |
ABRC |
CS6732 |