1. 1 10 100 1000 10000 100000 100-500501-10001001-20002000-5000>5000 The length of non-redundant consensus sequences (bp) Number of non-redundant consensus Fig. S1 Distribution of the non-redundant consensus sequences.

2. A:Amino acid transport and metabolism B:Carbohydrate transport and metabolism C:Cell cycle control, cell division, chromosome partitioning D:Cell wall/membrane/envelope biogenesis E:Cell motility F:Chromatin structure and dynamics G:Coenzyme transport and metabolism H:Cytoskeleton I:Defense mechanisms J:Energy production and conversion K:Extracellular structures L:Function unknown M:General function prediction only N:Intracellular trafficking, secretion, and vesicular transport O:Inorganic ion transport and metabolism P:Lipid transport and metabolism Q:Nucleotide transport and metabolism R:Nuclear structure S:Posttranslational modification, protein turnover, chaperones T:Replication, recombination and repair U:RNA processing and modification V:Secondary metabolites biosynthesis, transport and catabolism W:Signal transduction mechanisms X:Transcription Y:Translation, ribosomal structure and biogenesis 0 1000 2000 3000 4000 ABCDEFGHIJKLMNOPQRSTUVWXY Function Class Frequency 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.

3. 0 50 100 150 200 250 300 350 AP2 ARF ARR-B B3 BBR/BPC BES1 bHLH bZIP C2H2 C3H CAMTA CO-like CPP DBB Dof E2FDP EIL ERF G2-like GATA GeBP GRAS GRF HB-other HB-PHD HD-ZIP HRT-like HSF LBD LFY MIKC M-type MYB MYB_related NAC NF-X1 NF-YA NF-YBNF-YC Nin-like RAV S1Fa-like SBPSRS STAT TALE TCP Trihelix VOZ WOX WRKY ZF-HD 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. Number of genes

4. 0 50 100 150 200 250 -505 Log 2 Ratio(Treat/Control) -Lg(p-value) 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 (log 2 (Treat/Control)≥1 or log 2 (Treat/Control)≤ -1).

5. 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.