S3 Table. Description of differentially methylated regions (DMRs) occurring in annotated
coding regions of the Populus trichocarpa genome.
DMR gene IDs
POPTR_0001s01660g
POPTR_0001s017003g
POPTR_0001s03710g
POPTR_0001s06110g
POPTR_0001s11520g
POPTR_0001s11530g
POPTR_0001s11770g
POPTR_0001s14470g
higher
methylation
site
NBS-LRR resistance gene-like gene body + Wallstawe
protein ARGH35
promoter
leucine-rich repeat (LRR)
gene body
Wallstawe
protein
NB-ARC domain
promoter
Wallstawe
(1584 bp)
dirigent-like protein, regulates gene body + Wallstawe
coupling of monolignol plant
promoter;
phenols to generate the cell wall promoter
polymers lignins and lignans
that are involved in structural
fortification and defense against
pathogens
m
potassium transporter 13
potassium transporter
ethylene-responsive
transcription factor 2
F-box-like, phloem protein 2
annotation
CHH; CHG
Anderlingen
CHH
promtor
(1905 bp)
Anderlingen
CHH
promoter
(1693bp)
gene body
gene body +
promoter
gene body +
promoter
Anderlingen
CpG
Anderlingen
Wallstawe
CHG
CHG
Anderlingen
CHG
chloroplast outer membrane
translocon subunit family
protein
Rix1 complex component
involved in 60S ribosome
maturation
serine carboxypeptidase S28
promoter
(362bp)
Anderlingen
CpG
promoter
(333 bp)
Wallstawe
CHG
gene body
Wallstawe
CpG
hydroxymethylglutaryl-CoA
lyase
gene body
Wallstawe
CHH
zinc knuckle – zinc ion
binding, nucleic acid binding
POPTR_0001s28070g
CHH
CHH
POPTR_0001s19460g
POPTR_0001s220902g
CHH
Anderlingen
agenet-tudor-like domain
present in plant sequences,
chromatin assembly factor
complex 1 subunit p60
pepsin-like aspartic proteases
from plants
PAUSED family protein
DNA polymerase III
POPTR_0001s21620g
CHH + CHG
CpG
CpG
CHH
POPTR_0001s15740g
POPTR_0001s21240g
C context
Wallstawe
Wallstawe
Wallstawe
crotonase/enoyl-coenzyme A
(CoA) hydratase superfamily
POPTR_0001s16820g
POPTR_0001s17820g
C loci
gene body
gene body
promoter
(1039 bp)
promoter
(1033 bp)
promoter
(803 bp)
POPTR_0001s15680g
POPTR_0001s15870g
m
POPTR_0001s28350g
DNA binding domains involved gene body
in the transcriptional regulation
of key eukaryotic
developmental processes
Anderlingen
CpG
POPTR_0001s29620g
target of rapamycin family
gene body
protein
glycosyltransferase family 28 C- promoter
terminal domain
(862bp)
lysophospholipid
gene body
acyltransferases (LPLATs) of
glycerophospholipid
biosynthesis: MGAT-like
reverse transcriptases (RTs)
gene body
from retrotransposons and
retroviruses
Wallstawe
CHG
Wallstawe
CpG
Wallstawe
CHH
Wallstawe
CHG
POPTR_0001s31940g
POPTR_0001s33130g
POPTR_0001s37410g
POPTR_0001s37490g
POPTR_0001s42010g
ZIP zinc transporter
catalytic domain of protein
kinases
POPTR_0001s44180g
formin homology 2 domaincontaining family protein
alpha-ketoglutarate
decarboxylase
POPTR_0001s46630g
gene body
Anderlingen
gene body + Wallstawe
promoter;
gene body
gene body
Wallstawe
CHH
CHH; CpG
gene body
Anderlingen
CHG + CpG
gene body + Anderlingen
promoter
CHH + CHG
POPTR_0002s03260g
horseradish peroxidase and
related secretory plant
peroxidases
POPTR_0002s07850g
gene body + Wallstawe
component of the thylakoid- promoter
CHG
CHG
localized Sec system
involved in the translocation
of cytoplasmic proteins into
plastid
POPTR_0002s13530g
POPTR_0002s13560g
POPTR_0002s15770g
POPTR_0002s15950g
POPTR_0002s18400g
PPPDE putative peptidase
gene body
domain
cytochrome P450 family protein gene body
Wallstawe
CpG
Anderlingen
CHH + CHG
porcine testicular carbonyl
gene body
reductase (PTCR)-like
C2 domain third repeat found in gene body
multiple C2 domain and
transmembrane region proteins
Wallstawe
CHH + CHG
Wallstawe
CpG
saccharomyces cerevisiae
promoter
DCR2 phosphatase and related (1645 bp)
proteins, metallophosphatase
domain
Anderlingen
CHH
POPTR_0002s20620g
NADH-ubiquinone
oxidoreductase-related family
protein
gene body
Wallstawe
CHH
POPTR_0002s23200g
gene body + Wallstawe
aconitate hydratase, encodes promoter
CHG
a aconitase that can catalyze
the conversion of citrate to
isocitrate through a cisaconitate intermediate,
indicating a role in the
response to oxidative stress
POPTR_0002s24770g
wound-response family protein promoter
(1674 bp)
protein kinase superfamily
promoter
protein
(793bp)
NLI interacting factor-like
promoter
phosphatase
(113 bp)
alpha-crystallin domain (ACD) promoter
found in alpha-crystallin-type (1938bp)
small heat shock proteins, and a
similar domain found in p23 (a
cochaperone for Hsp90) and in
other p23-like proteins
Anderlingen
CpG
Wallstawe
CpG
Anderlingen
CHG
Anderlingen
CpG
POPTR_0003s06000g
BCCP, acetyl-CoA carboxylase, gene body
biotin carboxyl carrier protein
Anderlingen
CHH
POPTR_0003s06000g
biotinyl-domain or biotin
gene body
carboxyl carrier protein (BCCP)
domain
TITAN3 family protein,
gene body
condensin complex components
Anderlingen
CHG
Wallstawe
CpG
C2 domain-containing family
protein
glycosyl hydrolase family 32,
beta-fructosidases
Wallstawe
CpG
POPTR_0002s26350g
POPTR_0003s00520g
POPTR_0003s02310g
POPTR_0003s10790g
POPTR_0003s12600g
POPTR_0003s12640g
POPTR_0003s12640g
POPTR_0003s12980g
POPTR_0003s16640g
POPTR_0004s00680g
POPTR_0004s02520g
gene body
gene body + Wallstawe
promoter;
promoter
GH32 B fructosidase, glycosyl promoter
Wallstawe
hydrolase family 32, beta(787bp)
fructosidases
ubiquitin-conjugating enzyme promoter
Anderlingen
E2-21 kDa 3 family protein
(1852 bp)
CHH; CHG
putative zinc finger motif,
C2HC5-type
peptidases S8, S53 families
cysteine-rich receptor-like
protein kinase
CpG
CHG + CpG
gene body
Wallstawe
CHG
gene body
gene body
Anderlingen
Wallstawe
CHH
CHH
POPTR_0004s05180g
glutamate-gated kainate-type
ion channel receptor
POPTR_0004s08710g
POPTR_0004s19540g
tir-nbs-lrr resistance protein
peptidase/protease-associated
domain
leucine-rich repeat receptor-like
protein kinase
leucine-rich repeat (LRR)
protein
PPR repeat family, DYW
family of nucleic acid
deaminases
lipoxygenase
mitogen-activated protein
kinase
leucine-rich repeat (LRR)
receptor-like protein kinase
NAC domain protein
POPTR_0004s24010g
POPTR_0005s01150g
POPTR_0005s01450g
POPTR_0005s03560g
POPTR_0005s06330g
POPTR_0005s08180g
POPTR_0005s08440g
POPTR_0005s10180g
POPTR_0005s10180g
tonoplast monosaccharide
transporter2
major facilitator superfamily
(MFS): secondary transporters
that includes uniporters,
symporters and antiporters
promoter
(1209 bp);
gene body
gene body
gene body
Wallstawe
CHG; CpG
Wallstawe
Wallstawe
CHG
CHH + CHG
gene body
Wallstawe
CHH + CHG
gene body
Anderlingen
CHH
gene body + Wallstawe
promoter
CHH
gene body
gene body
Wallstawe
Wallstawe
CHH
CpG
gene body
Anderlingen
CHH
gene body + Wallstawe
promoter
gene body
Anderlingen
CHG
gene body
CHG + CpG
POPTR_0005s11730g
cytochrome BC1 synthesis
POPTR_0005s15370g
tyrosine kinase, catalytic
domain
protein kinase superfamily
promoter
protein
(1194bp)
oligopeptide transporter protein promoter
(707 bp)
OPT oligopeptide transporter
promoter
protein
(813bp)
glutathione S-transferases
gene body +
promoter
probable cinnamyl alcohol
gene body
dehydrogenase
MBD; MeCP2, MBD1, MBD2, promoter
MBD3, MBD4, CLLD8-like
(1515bp)
and BAZ2A-like proteins
constitute a family of proteins
that share the methyl-CpGbinding domain (MBD)
POPTR_0005s18260g
POPTR_0006s00560g
POPTR_0006s00560g
POPTR_0006s02510g
POPTR_0006s02520g
POPTR_0006s066902g
POPTR_0006s08960g
catalytic domain of protein
kinases
Anderlingen
gene body + Anderlingen
promoter
gene body
Wallstawe
promoter
(1597 bp)
CHH
CHH
CpG
Wallstawe
CpG
Wallstawe
CHH
Wallstawe
CpG
Anderlingen
CHH
Anderlingen
CHH + CpG
Anderlingen
CpG
Wallstawe
CHG + CpG
POPTR_0006s09150g
gene body + Anderlingen
promoter
CHH + CHG
glutamate-1-semialdehyde 2,1aminomutase
member of cyclic nucleotide
gated channel family
promoter
Wallstawe
(1230bp)
gene body + Anderlingen
promoter
CpG
gene body + Wallstawe
promoter
gene body
Wallstawe
CHG
POPTR_0006s22010g
elongation factor Tu family
protein
Vps51/Vps67 family
(components of vesicular
transport) protein
diadenosine 5' family protein
Wallstawe
CpG
POPTR_0006s22450g
POPTR_0006s22680g
Rossmann-like domain
NAD(P)-binding domain
Anderlingen
Anderlingen
CpG
CHG
POPTR_0006s25450g
POPTR_0006s28950g
promoter
(62bp)
gene body
gene body +
promoter
gene body
gene body
Nup85 nucleoporin
plant calmodulin-binding
domain
wall-associated receptor kinase gene body
galacturonan-binding
catalytic domain of protein
gene body
kinases
secretory peroxidase and related gene body
secretory plant peroxidases
Wallstawe
Anderlingen
CpG
CHH
Wallstawe
CHG
Wallstawe
CHG
Anderlingen
CHH
exostosin
putative glucosyltransferase
family protein
chromosome segregation
protein SMC
aspartyl protease family protein
gene body
gene body
Anderlingen
Wallstawe
CHH
CHG
promoter
(1356bp)
promoter
(1763bp)
promoter
(879 bp)
Wallstawe
CpG
Wallstawe
CpG
Anderlingen
CHH
gene body
Anderlingen
CHH + CHG
Wallstawe
CHH + CHG
Wallstawe
CpG
aldo-keto reductases, a
superfamily of soluble
NAD(P)(H) oxidoreductases
whose chief purpose is to
reduce aldehydes and ketones
to primary and secondary
alcohols
POPTR_0006s16120g
POPTR_0006s18990g
POPTR_0006s20500g
POPTR_0006s21230g
POPTR_0007s02230g
POPTR_0007s02310g
POPTR_0007s02590g
POPTR_0007s02970g
POPTR_0007s03070g
POPTR_0007s03470g
POPTR_0007s04120g
POPTR_0007s07470g
prefoldin alpha subunit,
prefoldin is a hexameric
molecular chaperone complex
POPTR_0007s07590g
inorganic H+ pyrophosphatase
POPTR_0007s07830g
histone-like transcription factor gene body
(CBF/NF-Y)
red chlorophyll catabolite
gene body
reductase
POPTR_0007s11070g
CHH
CHH
POPTR_0008s01270g
POPTR_0008s03700g
allantoate amidohydrolase
gene body
serine/threonine protein kinases gene body
Anderlingen
Anderlingen
CpG
CHH
POPTR_0008s08960g
POPTR_0008s09320g
ribosomal protein L32
gene body
MPP superfamily,
promoter
metallophosphatase superfamily (155 bp)
Anderlingen
Anderlingen
CHH
CHH
POPTR_0008s13460g
flavin-binding kelch domain F- gene body
box family protein
leucine-rich repeats (LRRs),
gene body
ribonuclease inhibitor (RI)-like
subfamily
cryptochrome, plant family;
gene body
DNA photolyase, FAD binding
domain of DNA polymerase
Wallstawe
CpG
Wallstawe
CHG
Anderlingen
CpG
NBD sugar-kinase HSP70 actin
superfamily
chromosome segregation
protein SMC
putative histidine-containing
phosphotransfer protein 2
zinc knuckle
histidine phosphatase domain
found in phosphoglycerate
mutases and related proteins
promoter
(1875 bp)
gene body +
promoter
promoter
(1732bp)
gene body
gene body
Anderlingen
CHH
Wallstawe
CHG
Anderlingen
CpG
Wallstawe
Wallstawe
CHG
CpG
POPTR_0009s09810g
UDP-glucosyl transferase
CHG
POPTR_0009s11510g
gene body
Anderlingen
CHH + CHG
POPTR_0009s17130g
Cf-4/9 disease resistance-like
family protein
retinal pigment epithelial
membrane protein
beta-glucosidase-related
glycosidases
lectin L-type, legume lectins
gene body + Anderlingen
promoter
promoter
Anderlingen
(1250 bp)
gene body
Anderlingen
Wallstawe
CHH + CpG
POPTR_0010s04460g
actin cross-linking protein
Anderlingen
CpG
POPTR_0010s05110g
gene body +
promoter
promoter
(1310bp)
gene body +
promoter
gene body
catalytic domain of protein
kinases
non-repetitive/WGA-negative
nucleoporin family protein
heavy-metal-associated domain gene body
(HMA)
kinase family protein
gene body
peptidases S8 3
gene body +
promoter
abhydrolase 6, alpha/beta
promoter
hydrolase family
(1555 bp)
Anderlingen
CHG
Anderlingen
CHH
Anderlingen
CHH
Wallstawe
Wallstawe
CHH
CHH
Wallstawe
CHH
POPTR_0008s13710g
POPTR_0008s16650g
POPTR_0008s18310g
POPTR_0008s18840g
POPTR_0008s20220g
POPTR_0008s21940g
POPTR_0009s08380g
POPTR_0009s15440g
POPTR_0009s15600g
POPTR_0010s11680g
POPTR_0010s19000g
POPTR_0010s19570g
POPTR_0010s20390g
POPTR_0010s24430g
CHH
CHH
POPTR_0011s10635g
Anderlingen
CHH
Wallstawe
CHG + CpG
POPTR_0011s14640g
UBN2, gag-polypeptide of LTR gene body
copia-type
PC-esterase; GDSL/SGNH-like gene body
acyl-esterase family
peptidase family S64
gene body
Wallstawe
CHH + CHG
POPTR_0011s15760g
S-locus glycoprotein family
gene body +
promoter
galactose mutarotas 2, galactose gene body +
mutarotase-like
promoter
chaperonin family protein
gene body
ubiquitin activating enzyme
gene body
(E1) subunit APPBP1; APPBP1
is part of the heterodimeric
activating enzyme (E1), specific
for the Rub family of ubiquitinlike proteins
Wallstawe
CHH
Wallstawe
CHH
Anderlingen
Anderlingen
CpG
CpG
POPTR_0012s06870g
DEAD-like helicases
superfamily; diverse family of
proteins involved in ATPdependent RNA or DNA
unwinding
promoter
(387 bp)
Anderlingen
CpG
POPTR_0012s07680g
phosphatidylinositol 3-kinase
family protein
C2 domain present in genes
regulated by Cold 2 (SRC2)like proteins
PPR repeat family
promoter
(1666 bp)
gene body
Wallstawe
CHG + CpG
Anderlingen
CpG
promoter
(1932bp)
gene body
gene body
promoter
(1675bp)
gene body
promoter
(906 bp)
Wallstawe
CpG
Anderlingen
Anderlingen
Wallstawe
CpG
CHH
CpG
Wallstawe
Anderlingen
CHG
CHH
6a-hydroxymaackiain
gene body
methyltransferase family
protein
exocyst subunit EXO70 family gene body
protein
NBS resistance protein
gene body
Wallstawe
CHH
Anderlingen
CpG
Wallstawe
CHG
POPTR_0011s10730g
POPTR_0011s15770g
POPTR_0012s04860g
POPTR_0012s06310g
POPTR_0012s12880g
POPTR_0012s13170g
POPTR_0013s02480g
POPTR_0013s07610g
POPTR_0013s10090g
POPTR_0013s10355g
POPTR_0013s10710g
POPTR_0013s12510g
POPTR_0013s14910g
POPTR_0014s00960g
PRK06128; oxidoreductase
PLATZ transcription factor
rossmann-fold NAD(P)(+)binding proteins
zinc knuckle
AAA+ (ATPases Associated
with a wide variety of cellular
activities) superfamily
represents an ancient group of
ATPases belonging to the
ASCE (for additional strand,
catalytic E) division of the Ploop NTPase fold
POPTR_0014s01810g
peroxisomal membrane 22 kDa gene body + Anderlingen
(Mpv17/PMP22) family protein promoter
CHH + CHG
POPTR_0014s01860g
FAD dependent oxidoreductase promoter
(842bp)
cytochrome P450 family protein gene body
Anderlingen
CpG
Anderlingen
CHH + CpG
UDP-glucosyl transferase
pre-50S ribosomal subunits,
which implies a function in
ribosome assembly
cellulose synthase-like protein
gene body
gene body
Wallstawe
Wallstawe
CpG
CpG
gene body
Wallstawe
CHH
nucleoporin N; Nup133 N
terminal like
GT1-Gtf-like; family includes
the Gtfs, a group of
homologous
glycosyltransferases
glycosyltransferase family A
(GT-A) includes diverse
families of glycosyl transferases
with a common GT-A type
structural fold
gene body
Anderlingen
CHG
promoter
(506bp)
Anderlingen
CpG
gene body
Wallstawe
CHG
glycosyltransferase like family gene body + Wallstawe
promoter
F-box family protein
gene body
Wallstawe
RING-finger domain, a
promoter
Wallstawe
specialized type of Zn-finger of (954bp)
40 to 60 residues that binds two
atoms of zinc)
CpG
POPTR_0015s09330g
galactinol-sucrose
galactosyltransferase
CHH; CHG
+ CpG
POPTR_0015s10290g
protein kinase superfamily
protein
40 S ribosomal protein S20
POPTR_0014s02060g
POPTR_0014s04140g
POPTR_0014s07040g
POPTR_0014s15350g
POPTR_0014s16310g
POPTR_0014s17340g
POPTR_0014s18950g
POPTR_0014s18950g
POPTR_0015s00420g
POPTR_0015s07790g
POPTR_0015s14510g
POPTR_0015s15150g
POPTR_0016s00660g
POPTR_0016s021501g
gene body + Anderlingen
promoter;
gene body
promoter
Anderlingen
(675 bp)
promoter
Anderlingen
(713bp)
leucine-rich repeats (LRRs),
gene body
Wallstawe
ribonuclease inhibitor (RI)-like
subfamily
STKc-phototropin-like;
gene body
Anderlingen
catalytic domain of phototropinlike protein serine/threonine
kinases
glycosyltransferase family 28 C- gene body + Wallstawe
terminal domain
promoter
CpG
CpG
CHH
CpG
CHG
CpG
CHG
POPTR_0016s04630g
cysteine/histidine-rich C1
domain family protein
POPTR_0016s04750g
cysteine/histidine-rich C1
domain family protein
universal minicircle sequence
binding protein
chloroplast signal recognition
particle subunit
PRA1 family protein
POPTR_0016s06380g
gene body + Anderlingen; CHH; CHH
promoter;
Wallstawe
gene body
gene body
Wallstawe
CpG
gene body
Anderlingen
CHH
gene body
Wallstawe
CpG
promoter
(1694 bp)
gene body
Anderlingen
CHG
putative GTPase activating
protein for Arf
zinc knuckle
gene body
PQQ-dependent dehydrogenase, gene body;
methanol/ethanol family
promoter (13
bp)
NB-ARC domain-containing
gene body
disease resistance protein
Anderlingen
CHG + CpG
Wallstawe
Anderlingen
Wallstawe
CHG
CHH + CHG
+ CpG;
CHH
CHH
POPTR_0017s00770g
POPTR_0017s01260g
POPTR_0017s01300g
POPTR_0017s02120g
leucine-rich repeats (LRRs)
PTR2, POT family
POT family
zinc finger family protein
Anderlingen
Anderlingen
Anderlingen
Anderlingen
CpG
CHH
CHH
CHH
POPTR_0017s02540g
patatin-like phospholipase of
plants
transcription factor Tfb4
gene body
gene body
gene body
promtor
(1944 bp)
promoter
(709 bp)
gene body +
promoter
gene body +
promoter
Wallstawe
CHG + CpG
Anderlingen
CHG
Wallstawe
CHH + CHG
+ CpG
POPTR_0016s07950g
POPTR_0016s10360g
POPTR_0016s11100g
POPTR_0016s11490g
POPTR_0016s14620g
POPTR_0017s00570g
POPTR_0017s03570g
POPTR_0017s04440g
leucine-rich repeat (LRR)
receptor-like protein kinase
POPTR_0017s04700g
CC-NBS-LRR resistance
protein
peptidase C48; Ulp1 protease
family, C-terminal catalytic
domain
AAA+ (ATPases associated
with a wide variety of cellular
activities) superfamily
represents an ancient group of
ATPases belonging to the
ASCE (for additional strand,
catalytic E) division of the Ploop NTPase fold
gene body
Wallstawe
CHG + CpG
gene body
Anderlingen
CHG
gene body + Wallstawe
promoter
CHH
PPR repeat family
PHA03247; large tegument
protein UL36
nodulin-like
gene body
gene body
Wallstawe
Anderlingen
CHH
CHG
gene body
Wallstawe
CHH
POPTR_0017s05000g
POPTR_0017s06300g
POPTR_0017s06960g
POPTR_0017s09440g
POPTR_0017s09660g
POPTR_0017s09830g
GYF domain: contains
promoter
conserved Gly-Tyr-Phe residues (472 bp)
Wallstawe
CHG
POPTR_0017s10460g
SGNH hydrolase or GDSL
hydrolase (diverse family of
lipases and esterases)
nodule-enhanced malate
dehydrogenase family protein
promoter
(1168 bp)
Anderlingen
CHG
gene body
Anderlingen
CpG
gene body
Anderlingen
CHH + CHG
POPTR_0017s14590g
DNA-dependent RNA
polymerase
T3/T7-like RNA polymerase
gene body
Anderlingen
CHH + CHG
POPTR_0018s04140g
trypsin-like peptidase domain
gene body
Anderlingen
CHH
POPTR_0018s11150g
POPTR_0018s11370g
tetratricopeptide repeat
gene body
hydroxycinnamoyl-coenzyme A promoter
shikimate/quinate
(540 bp)
hydroxycinnamoyltransferase
(HCT)
Wallstawe
Anderlingen
CpG
CHH
POPTR_0018s11710g
omega-6 fatty acid desaturase
gene body
Wallstawe
CHH + CHG
POPTR_0018s14780g
vacuolar protein sortingassociated protein 26
leucine-rich repeat (LRR)
receptor
HXXXD-type acyl-transferase
family protein
Sec23/Sec24 protein transport
family protein
leucine rich repeats (LRRs)
tandem copies of the domain
bind telomeric DNA tandem
repeats as part of the capping
complex
leucine-rich repeat receptor-like
protein kinase
peptidase C1A subfamily
promoter
(1001 bp)
gene body +
promoter
promoter
(478 bp)
promoter
(1833 bp)
gene body
promoter
(1336 bp)
Anderlingen
CHH
Anderlingen
CHH
Anderlingen
CHH + CpG
Anderlingen
CHH
Anderlingen
Wallstawe
CpG
CHG + CpG
promoter
(848bp)
gene body
Anderlingen
CpG
Wallstawe
CHH + CHG
Wallstawe
CpG
POPTR_0017s13630g
POPTR_0017s137702g
POPTR_0019s00260g
POPTR_0019s01690g
POPTR_0019s01710g
POPTR_0019s02030g
POPTR_0019s06290g
POPTR_0019s08830g
POPTR_0019s11980g
POPTR_0019s14500g
exocyst subunit EXO70 family gene body
protein