1
10
100
1000
10000
100000
100-500 501-1000 1001-2000 2000-5000 >5000
The length of non-redundant consensus sequences (bp)
Num
ber
of n
on-r
edun
dant
con
sens
us
Fig. S1 Distribution of the non-redundant consensus sequences.
A:Amino acid transport and metabolismB:Carbohydrate transport and metabolismC:Cell cycle control, cell division, chromosome partitioningD:Cell wall/membrane/envelope biogenesisE:Cell motilityF:Chromatin structure and dynamicsG:Coenzyme transport and metabolismH:CytoskeletonI:Defense mechanismsJ:Energy production and conversionK:Extracellular structuresL:Function unknownM:General function prediction onlyN:Intracellular trafficking, secretion, and vesicular transportO:Inorganic ion transport and metabolismP:Lipid transport and metabolismQ:Nucleotide transport and metabolismR:Nuclear structureS:Posttranslational modification, protein turnover, chaperonesT:Replication, recombination and repairU:RNA processing and modificationV:Secondary metabolites biosynthesis, transport and catabolismW:Signal transduction mechanismsX:TranscriptionY:Translation, ribosomal structure and biogenesis
0
1000
2000
3000
4000
AB C D E F G H I J K LMNO P Q R S T UVWXY
Function Class
Fre
quen
cy
Fig. S2 Histogram presentation of the clusters of eukaryotic orthologous groups (KOGs). Of the 93,488 identified unigenes, 29,828 sequences have a KOG classification within the 25 categories.
0
50
100
150
200
250
300
350
AP2
AR
FA
RR
-B B3
BB
R/B
PC
BE
S1bH
LH
bZIP
C2H
2C
3HC
AM
TA
CO
-lik
eC
PPD
BB
Dof
E2F
DP
EIL
ER
FG
2-lik
eG
AT
AG
eBP
GR
AS
GR
FH
B-o
ther
HB
-PH
DH
D-Z
IPH
RT
-lik
eH
SFL
BD
LFY
MIK
CM
-typ
eM
YB
MY
B_r
elat
edN
AC
NF-
X1
NF-
YA
NF-
YB
NF-
YC
Nin
-lik
eR
AV
S1Fa
-lik
eSB
PSR
SST
AT
TA
LE
TC
PT
rihe
lixV
OZ
WO
XW
RK
YZ
F-H
D
Fig. S3 The number of unigenes corresponding to transcription factors in each transcription factor family. A total of 2,023 putative Arabidopsis thaliana transcription factors were searched against the Antarctic moss transcriptome, and the target unigenes (1,309) were classified into their corresponding transcription factor families. The black bars are the number of reads per family.
Num
ber
of
gene
s
0
50
100
150
200
250
-5 0 5Log2Ratio(Treat/Control)
-Lg(
p-va
lue)
More reliable points Less reliable points
300
Fig. S4 A volcano plot of the differentially expressed genes. For each gene, the ratio of the expression levels in the treated sample versus that of the control sample was plotted against the -log error rate. The horizontal green line indicates the significance threshold (0.001), and the two vertical green lines indicate the fold-change threshold (log2(Treat/Control)≥1 or log2(Treat/Control)≤ -1).
MFC60113
MFC48132
MFC00614
MFC03221
MFC08686
MFC48409
MFC04509
MFC90936
0hr 1hr 3hr 6hr 12hr 24hr
Cold treatment
tubulin
MFC25111
Fig. S5 RT-PCR analysis of CRLK1, MEKK1, MKK2, MPK4 and CBF orthologs in Antarctic moss P. nutans after cold stress. MFC60113 is CRLK1 ortholog; MFC00614, MFC48132, MFC03221, MFC48409 and MFC08686 are MEKK1 orthologs; MFC04509 is MKK2 ortholog; MFC90936 is MPK4 ortholog; MFC25111 is CBF ortholog. β-tubulin was used to normalize the template.