Supplementary Figure legends:
Figure S1 – Genotypes and pairwise linkage disequilibrium between all pairs of sexlinked SNPs in reference genome v2.2. A) VG2 plot generated at the SeattleSNPs
Variation Resource website (http://pga.gs.washington.edu/VG2.html) for the T52
mapping population. B) VG2 plot for the BT68 mapping population. In A and B,
accessions are represented in rows and SNPs in columns. Correspondence between SNP
numbers in the figure and SNP location can be found in Table S2. MT indicates male P.
trichocarpa accessions, FT female P. trichocarpa accessions, MB male P. balsamifera
accessions and FB female P. balsamifera accessions. Text on top of the figure indicates
the genomic region where each group of SNPs is mapped. C) Histograms of pairwise
linkage disequilibrium (r2) in T52 between all 623 SNPs significant associated with sex
in the top panel, only significant SNPs in the same region (as defined in Table 2) in the
middle panel and only significant SNPs in different regions (as defined in Table 2) in the
bottom panel. Pairwise LD was calculated in the SeattleSNPs Variation Resource website
(http://pga.gs.washington.edu/VG2.html). Pairwise LD estimates are available at Dryad.
Figure S2 - Phylogenies of regions significantly associated with gender. For each
phylogeny, only male accessions were used. X and Y alleles were PCR amplified, cloned
and one random clone was Sanger sequenced with allele specific primers. For P.
tremuloides, the primers did not produce allele specific amplification. PCR products were
cloned and several clones were Sanger sequenced. Y chromosome alleles are indicated
with a Y and X chromosome alleles with an X at the beginning of the sequence name.
These are followed with Trich, for P. trichocarpa accessions, Balsam for P. balsamifera
accessions, Delt, for P. deltoides accessions, Nigra, for P. nigra accessions and
Trem_Clone for P. tremuloides. Maximum Likelihood phylogenies were estimated in
MEGA5, with Tamura-Nei distance and complete deletion of all positions with missing
data and alignment gaps. For each phylogeny we also included the P. trichocarpa
reference sequence from genome assembly v2.2 (indicated as POPTR_0009s08410 and
POPTR_00019s00240) and the reference sequence from genome assembly v2.2 of the
paralogue arising from the Salicoid whole genome duplication (indicated as
POPTR_0001s29310 and POPTR_0004s14140. Only bootstrap support values higher
than 80 (from 500 replicates of each tree) are shown. a) Phylogeny of Chr9 region
(Amplicon1:Chr9:7690067, SI) with a total of 358 positions, b) Schematic representation
of gene POPTR_009s08419 (v2.2 of the genome assembly), detailing the position of
Amplicon1:Chr09:7690067. Exons are indicated as blue boxes and introns as blue lines,
start codon with a green triangle and stop codon with a red triangle. c) Phylogeny of
Chr19 Amplicon1:Chr19:40024 (SI) with a total of 1231 positions, d) Phylogeny of
Chr19 Amplicon2:Chr19:41515 (SI) with a total of 1291 positions, e) Phylogeny of
Chr19 Amplicon3:Chr19:44107 (SI) with a total of 1165 positions. f) Schematic
representation of gene POPTR_019s00240 (v2.2 of the genome assembly), detailing the
position of the three amplicons. Exons are indicated as blue boxes and introns as blue
lines, start codon with a green triangle and stop codon with a red triangle.
Figure S3- Manhattan plots all SNPs mapped to the 19 chromosomes in v3.0 (a) and v1.1
(b) of the P. trichocarpa reference genome. The horizontal red line indicates the –log10(p
value) corresponding to <0.05 after Bonferroni correction for multiple testing. From top
to bottom, population T52, 34 female and 18 male P. trichocarpa accessions, population
B34, 18 female and 16 male P. balsamifera accessions and population BT68, 36 female
and 32 male accessions, where half the samples of each gender are P. trichocarpa and the
other half are P. balsamifera
Figure S1 (A)
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Figure S1 (B)
B
FT
FB
MT
MB
1
9
19 proximal
19 distal
2
6
1
Figure S1 (C)
60000
20000
0
Frequency
All significant SNPs
0.4
0.5
0.6
0.7
0.8
0.9
1.0
40000
20000
0
Frequency
Significant SNPs in the same region
0.4
0.5
0.6
0.7
0.8
0.9
1.0
30000
0 10000
Frequency
Significant SNPs not in the same region
0.4
0.5
0.6
0.7
r2
0.8
0.9
1.0
Figure S2
Figure S3
a)
b)
Genome assembly v3.0
Genome assembly v1.0
T52
T52
12
10
10
8
-log10(p)
-log10(p)
12
6
4
8
6
4
2
2
0
0
1
2
3
4
5
6
8
7
9
10
11
12
13
14
15 16
17
18
1
19
2
3
4
5
6
7
8
9
10
11
12
13
14
15 16
1718
19
9
10
11
12
13
14
15 16
1718
19
9
10
11
12
13
14
15 16
1718
19
B34
B34
12
12
10
-log10(p)
-log10(p)
10
8
6
4
8
6
4
2
2
0
0
1
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15 16
17
18
2
3
4
5
6
7
BT68
BT68
-log10(p)
12
10
-log10(p)
12
10
8
6
4
8
6
4
2
2
0
0
1
2
3
4
5
6
7
8
8
19
9
10
Chromosome
11
12
13
14
15 16
17
18
19
1
2
3
4
5
6
7
8
Chromosome