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.