Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant, Chorispora bungeana
- Zhiguang Zhao†1, 2,
- Lingling Tan†1,
- Chunyan Dang1,
- Hua Zhang1,
- Qingbai Wu2 and
- Lizhe An1Email author
© Zhao et al.; licensee BioMed Central Ltd. 2012
Received: 23 July 2012
Accepted: 19 November 2012
Published: 21 November 2012
The plant tolerance mechanisms to low temperature have been studied extensively in the model plant Arabidopsis at the transcriptional level. However, few studies were carried out in plants with strong inherited cold tolerance. Chorispora bungeana is a subnival alpine plant possessing strong cold tolerance mechanisms. To get a deeper insight into its cold tolerance mechanisms, the transcriptome profiles of chilling-treated C. bungeana seedlings were analyzed by Illumina deep-sequencing and compared with Arabidopsis.
Two cDNA libraries constructed from mRNAs of control and chilling-treated seedlings were sequenced by Illumina technology. A total of 54,870 unigenes were obtained by de novo assembly, and 3,484 chilling up-regulated and 4,571 down-regulated unigenes were identified. The expressions of 18 out of top 20 up-regulated unigenes were confirmed by qPCR analysis. Functional network analysis of the up-regulated genes revealed some common biological processes, including cold responses, and molecular functions in C. bungeana and Arabidopsis responding to chilling. Karrikins were found as new plant growth regulators involved in chilling responses of C. bungeana and Arabidopsis. However, genes involved in cold acclimation were enriched in chilling up-regulated genes in Arabidopsis but not in C. bungeana. In addition, although transcription activations were stimulated in both C. bungeana and Arabidopsis, no CBF putative ortholog was up-regulated in C. bungeana while CBF2 and CBF3 were chilling up-regulated in Arabidopsis. On the other hand, up-regulated genes related to protein phosphorylation and auto-ubiquitination processes were over-represented in C. bungeana but not in Arabidopsis.
We conducted the first deep-sequencing transcriptome profiling and chilling stress regulatory network analysis of C. bungeana, a subnival alpine plant with inherited cold tolerance. Comparative transcriptome analysis suggests that cold acclimation is not a major chilling tolerance mechanism of C. bungeana. Activation of protein phosphorylation and ubiquitination may confer chilling tolerance to C. bungeana in a more rapid and flexible way than cold acclimation. Such differences may have contributed to the differences in cold tolerance between C. bungeana and Arabidopsis. The results presented in this paper will be informative for gene discovery and the molecular mechanisms related to plant cold tolerance.
KeywordsAlpine plant Chorispora bungeana Chilling tolerance Cold acclimation Transcriptome
Chorispora bungeana Fisch. & C.A. Mey (C. bungeana) is a perennial subnival alpine plant that can survive freezing temperature . In the natural environments where C. bungeana is growing (origin of Urumqi River in Tianshan Mountains, Xinjiang Autonomous Region, China), snowing and hailing often occur during favorable growing seasons, and air temperature fluctuates frequently ranging from above 20°C to below −10°C. C. bungeana in local environment can survive, grow and flower even in snow. Our previous studies performed at physiological and molecular levels showed that this plant has strong cold (chilling and freezing) tolerance [1–6]. However, little is known about its tolerance mechanisms, if any, distinguishing C. bungeana from other tropical or temperate plants.
Not all plants are always ready to tolerate freezing temperatures. However, studies have shown many plants are tolerant of freezing temperature after exposure to non-freezing low temperature, a phenomenon called cold acclimation [7, 8]. In such a process, various physiological and biochemical changes occur in plant cells, which may confer subsequent acquired chilling and freezing tolerance to plants. For example, during cold acclimation, plants accumulate compatible solutes such as sucrose, raffinose and proline [9–12]; membrane compositions and behaviors are changed [13–16]; and the biosynthesis pathways of secondary metabolites such as flavonoids are activated [17, 18].
The physiological and biochemical changes during plant cold acclimation result mainly from expression changes of cold-responsive (COR) genes. A large number of studies demonstrate that gene expression changes occur in a wide range of plant species in cold responses, and it is believed that differences in COR gene expressions contribute to differences in plant cold tolerance. For example, considerable differences in the members of COR genes were found in Solanum commersonii and Solanum tuberosum, which are closely related species that differ in cold acclimation abilities .
The expressions of COR genes in plant cold responses are under the control of some key transcription factors (TFs). The best characterized TFs involved in plant cold responses are a class of AP2/EFR TFs known as DREB/CBF [20–23], which regulate COR gene expressions by binding to the DRE/CRT cis-elements in the promoter regions of COR genes. In Arabidopsis, there are three major CBFs - CBF1, CBF2 and CBF3 (also known as DREB1b, DREB1c, and DREB1a, respectively) . Constitutive expression of CBF1 and CBF3 can enhance freezing tolerance in non-acclimated Arabidopsis . Moreover, by studying the interactions with CBFs pathway, the roles of some cellular or environmental factors, such as calcium , light , and circadian rhythm , in plant cold tolerance are revealed. Nonetheless, CBFs may not represent all TFs that regulate the expressions of COR genes and confer cold tolerance to plants. Although CBF over-expression increases the freezing tolerance of Arabidopsis, potato  and poplar , it does not increase the freezing tolerance of tomato  and rice . Besides CBFs, some other TFs, such as ZAT12 and RAV1 [33, 34], are also discovered to regulate the expressions of COR genes.
Given the importance of COR genes in plant cold tolerance, studying the cold responses at transcription level may be a key step to identify specific tolerance mechanisms of plants. During the last two decades, numerous studies were carried out to reveal the transcriptional regulatory network of plants in response to cold stress. However, most of the studies were performed with Arabidopsis and others were conducted with crops such as Brassica napus, rice , barley  and potato . Some studies were performed with species adapted to arctic or alpine cold environments, such as Draba [38, 39] and Oxytropis , suggesting that plants may adapt to cold environments with different strategies and COR genes. However, due to lack of reference genome sequence, such studies are relatively few. Sequencing the genome of Coccomyxa subellipsoidea from the Antarctic suggested that gene losses and gains may contribute to low temperature adaptations , highlighting the importance of studying cold tolerance at whole genome or transcriptome level. Recently, the development of high-throughput deep-sequencing technologies makes it possible to study gene expressions at whole genome level without prior knowledge about reference genome sequence. In this study, we used Illumina deep-sequencing technology to study the transcriptome profiles of chilling-treated seedlings of C. bungeana.
C. bungeana is a Cruciferae species closely related to Arabidopsis. Our previous studies showed that the callus and suspension cells from C. bungeana were ready to endure freezing temperature (−4°C) without cold acclimation [3, 6]. The aim of this study is to examine what kinds of mechanisms contribute to the specific cold tolerance of C. bungeana. Our results showed a complicated regulatory network of C. bungeana responding to chilling stress. By comparative transcriptome analysis, a large number of common chilling responding processes, including a newly found karrikins responding process, were found in both C. bungeana and Arabidopsis. Furthermore, our results implied the differences between C. bungeana and Arabidopsis in cold acclimation and TF regulation networks. Importantly, our results suggested that protein phosphorylation and ubiquitination might serve as rapid and flexible mechanisms for cold tolerance regulations in C. bungeana.
Results and discussion
Sequencing and de novo assembly of C. bungeana transcriptome
Statistics of deep-sequencing
Total nucleotides (nt)
Statistics of the assembly (unigene number and percentage) with the Trinity method
> = 2000nt
Length of all Unigene (nt)
Statistics of the assembly (unigene number and percentage) with the SOAPdenovo software
> = 2000nt
Length of all Unigene (nt)
Functional annotation of all the unigenes of C. bungeana
Expression analysis, differential expression genes (DEGs) identification and qPCR verifications
The expressions of unigenes were analyzed with DEGseq R package. Firstly, we tried to identify DEGs by applying screening thresholds of 2 fold changes and Benjamini q value <0.001. We got 12,808 DEG candidates out of 52,753 expressed unigenes (Additional file 2). However, when we verified the expressions of the top 10 up-regulated and down-regulated unigenes by RT-PCR and qPCR, only 3 of them were amplified and none of them showed up or down-regulated trends in chilling-treated seedlings (data not shown). In addition, we found that 80% and 90% of the top 200 up and down-regulated unigenes presented only in one sample’s RNA-seq data, respectively. PCR amplification failures of the selected sequences suggested that such genes were most likely to be the artifacts of de novo assembly.
Top 50 up-regulated unigenes of C. bungeana by chilling stress. The homologs of Arabidopsis genes were presented for functional description of unigenes
log2 (Fold change)
cold-regulated 15a (COR15A)
ABA REPRESSOR1 (ABR1)
cytochrome P450, family 94, subfamily B, polypeptide 1 (CYP94B1)
Plant invertase/pectin methylesterase inhibitor superfamily protein
Integrase-type DNA-binding superfamily protein
mitogen-activated protein kinase kinase kinase 13 (MAPKKK13)
2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
Haloacid dehalogenase-like hydrolase (HAD) superfamily protein
chlorophyllase 1 (CLH1)
cytochrome P450, family 94, subfamily B, polypeptide 1 (CYP94B1)
heat shock transcription factor A1E (HSFA1E)
PYR1-like 11 (PYL11)
UDP-glucosyl transferase 73B3 (UGT73B3)
Stigma-specific Stig1 family protein
gibberellin 2-oxidase 6 (GA2OX6)
myb domain protein 108 (MYB108)
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
O-Glycosyl hydrolases family 17 protein
EARLY LIGHT-INDUCIBLE PROTEIN 2 (ELIP2)
anthranilate synthase beta subunit 1 (ASB1)
LOW-TEMPERATURE-INDUCED 65 (LTI65)
Integrase-type DNA-binding superfamily protein
purine permease 18 (PUP18)
cytochrome P450, family 709, subfamily B, polypeptide 2 (CYP709B2)
Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family
receptor like protein 39 (RLP39)
disease resistance family protein / LRR family protein
UDP-glucosyl transferase 75B2 (UGT75B2)
UDP-glycosyltransferase 74 F1 (UGT74F1)
Integrase-type DNA-binding superfamily protein
FAD-binding Berberine family protein
Top 50 down-regulated unigenes of C. bungeana by chilling stress. The homologs of Arabidopsis genes were presented for functional description of unigenes
Protein of unknown function (DUF1442)
GATA transcription factor 15 (GATA15)
BARELY ANY MERISTEM 3 (BAM3)
ENHANCER OF ATNSI ACTIVITY (ENA)
Heavy metal transport/detoxification superfamily protein
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein
Polynucleotidyl transferase, ribonuclease H-like superfamily protein
TORNADO 1 (TRN1)
histone H2A 11 (HTA11)
Protein of unknown function (DUF295)
lon protease 1 (LON1)
TOO MANY MOUTHS (TMM)
CBS domain-containing protein with a domain of unknown function (DUF21)
alpha/beta-Hydrolases superfamily protein
High throughput deep-sequencing is a powerful tool for DEGs screening, especially for species without available genomic information [45, 47, 48]. However, since Illumina sequencing is highly sensitive to templates presented in DNA samples, some traced transcripts or contaminants can be sequenced in one sample but not in other samples. This will have huge effects on the results of de novo assembly and increase false positive rate in DEGs identification. One strategy to reduce the false positive results is to set up biological repeats for sequencing and increase sequencing depth, but it will greatly increase the experimental costs. In this study, by simply applying an additional threshold (RPKM > =1) for DEGs screening without increasing costs, we got a high quality (confirmed by qPCR) list of chilling regulated DEGs.
GO network analysis of up-regulated DEGs of C. bungeana in response to chilling stress and comparison with Arabidopsis
Since both C. bungeana and Arabidopsis are Cruciferae species, it is more reliable to use the well-established GO and KEGG annotation systems of Arabidopsis to analyze the functions of C. bungeana DEGs. GO term and KEGG pathway enrichment analysis of DEGs were conducted with BiNGO , a Cytoscape plugin assessing overrepresentation of ontologies in biological networks, using the list of all unigenes with a minimal RPKM of 1 in both sequencing libraries as a reference set. To compare the chilling responding network of C. bungeana with Arabidopsis, the networks of chilling-regulated DEGs of Arabidopsis were constructed using previously published RNA-seq and microarray data (referred to ATH-SR and ATH-MA, respectively; see Methods for details).
Over-representative GO terms* in chilling-treated C. bungeana and Arabidopsis
GO functional description
response to karrikin
response to wounding
response to chitin
regulation of transcription, DNA-dependent
response to water deprivation
response to abscisic acid stimulus
response to cold
defense response to fungus
response to oxidative stress
response to salt stress
response to UV-B
flavonoid biosynthetic process
sequence-specific DNA binding transcription factor activity
Besides abscisic acid  and chitin responses , which were known to be involved in cold tolerance of plants, the biological process “response to karrikin” was found to be a common response to chilling stress in both C. bungeana and Arabidopsis. To our knowledge, no previous study reported the involvement of karrikins in cold tolerance of plants. Karrikins are a new group of plant growth regulators discovered in smoke that can stimulate seed germination . The biological and molecular functions of karrikins are largely unknown at present. Our results suggested that karrikins might play important roles in chilling tolerance of C. bungeana and Arabidopsis.
Nineteen biological processes were over-represented in chilling-treated C. bungeana but not in Arabidopsis. Nonetheless, it did not mean that such processes were specific to chilling responses of C. bungeana since most of them, such as salicylic acid [53, 54], jasmonic acid , and immune response , were reported to be involved in chilling response of Arabidopsis or other plants. However, two processes, “protein phosphorylation” and “protein autoubiquitination”, should be emphasized. Post-translational modifications of pre-existing proteins are believed to be a rapid pathway to get tolerance in plant responses to chilling stress and have important roles in plant cold acclimation . In alfafa, low temperature lead to rapid inhibition of PP2A activity, and in turn lead to phosphorylation of proteins involved in cold tolerance acquisitions [56, 57]. Transcriptional activation of genes of several kinase families were also found under low temperature stress, such as MAP kinase family genes MKK2, OsMEK1 and OsMAP1, CDPK family genes OsCDPK7[60, 61], OsCDPK13 and PaCDPK1, and CIPK family genes CIPK3 and CIPK7. Although many studies reported that certain protein kinases were activated and their transcriptional expression increased in response to cold stress, few studies reported that the expressions of protein kinases as a whole increased at transcriptome level. In our study, a large number of genes whose products were involved in protein phosphorylation were over-represented in chilling up-regulated DEGs in C. bungeana. Given the habitats of C. bungeana, in which the daytime temperatures fluctuate frequently and during almost the whole plant growing seasons, our results suggest that protein phosphorylation may be an important mechanism for rapid and flexible regulation of cold tolerance of C. bungeana.
Chilling up-regulated unigenes annotated with ubiquitination function
ubiquitin ligase, XB3 ortholog 2 in Arabidopsis thaliana (XBAT32)
ubiquitin ligase, XB3 ortholog 2 in Arabidopsis thaliana (XBAT32)
U-box domain E3 ubiquitin ligase protein, plant U-box 22 (PUB22)
U-box domain E3 ubiquitin ligase protein, plant U-box 23 (PUB23)
U-box domain E3 ubiquitin ligase protein, plant U-box 24 (PUB24)
A20/AN1-like zinc finger family protein
zinc finger (C3HC4-type RING finger) family protein
Chilling up-regulated TFs overlapped in C. bungeana and Arabidopsis
All gene symbols
Homologous to the flowering-time gene CONSTANS.
CZF1; SZF2; ZFAR1
Encodes a transcription factor that specifically binds to DRE/CRT cis elements (responsive to drought and low-temperature stress)
Member of Heat Stress Transcription Factor (Hsf) family
Related to AP2.7 (RAP2.7)
Encodes a zinc finger protein involved in high light and cold acclimation
Myb-like transcription factor that regulates hypocotyl growth by regulating free auxin levels in a time-of-day specific manner.
TEOSINTE BRANCHED 1; TCP2
TEOSINTE BRANCHED 1, cycloidea and PCF transcription factor 2 (TCP2)
Pseudo response regulator involved in the generation of circadian rhythms.
Encodes a member of WRKY Transcription Factor
Member of the plant WRKY transcription factor family
Pathogen-induced transcription factor
B-box type zinc finger family protein
Zinc finger (CCCH-type) family protein
Sequence-specific DNA binding transcription factors
B-box type zinc finger protein with CCT domain
Over-representative GO terms* in chilling stressed C. bungeana but not in Arabidopsis
Stimulus responses related:
response to salicylic acid stimulus
response to jasmonic acid stimulus
defense response by callose deposition in cell wall
defense response to bacterium
innate immune response
cellular response to abiotic stimulus
response to starvation
jasmonic acid biosynthetic process
indole glucosinolate metabolic process
aromatic amino acid family catabolic process
glutamine family amino acid catabolic process
camalexin biosynthetic process
L-phenylalanine metabolic process
recognition of pollen
organic substance transport
sequence-specific DNA binding
iron ion binding
electron carrier activity
structural constituent of cell wall
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
nutrient reservoir activity
protein serine/threonine kinase activity
carbon-nitrogen lyase activity
KEGG pathway analysis of up-regulated DEGs of C. bungeana in response to chilling stress and comparison with Arabidopsis
All over-represented pathways in C. bungeana, regardless of whether they were enriched in Arabidopsis, had proved to be important in plant cold tolerance. For instance, circadian rhythm regulates the expression of CBFs [28, 69], the core identified TFs that involved in plant cold tolerance. As another example, under chilling stress, plants preferentially accumulate polyunsaturated fatty acids such as linoleic and linolenic fatty acids [70–72], and genetically increasing of unsaturated fatty acids or lipids could enhance cold tolerance of transgenic plants, probably by maintaining membrane fluidity under cold stress [73, 74]. Our previous findings indicated that cold tolerance of C. bungeana was correlated with changes in membrane lipids and membrane-associated enzymes . Under chilling treatment, the proportion of unsaturated fatty acid in the plasma membrane increased significantly in callus of C. bungeana. Paralleling to these results, KEGG analysis in this study showed that unigenes involved in "alpha-Linolenic acid metabolism" were enriched significantly in chilling up-regulated DEGs, suggesting that lipid metabolism, especially linolenic acid metabolism, might play a role in chilling tolerance of C. bungeana.
GO network analysis of down-regulated DEGs of C. bungeana in response to chilling stress and comparison with Arabidopsis
C. bungeana is a perennial subnival alpine plant with high capacity of chilling and freezing resistance. In recent years, much effort has been taken in our research group to reveal the cold tolerance mechanisms of this plant at physiological and molecular levels. In this paper, we provide the first study on the transcriptome of chilling stressed seedlings of C. bungeana. We got 54,870 assembled unigenes using the Trinity de novo assembly method, and a number of chilling regulated genes were identified, providing useful resources for gene mining to improve cold tolerance of plants. Furthermore, the comparison of the functional networks of chilling regulated genes in C. bungeana and Arabidopsis provided informative results, which could help us tell the differences in cold tolerance mechanisms between C. bungeana and Arabidopsis. We found that karrikins might be new plant growth regulators involved in chilling tolerance of plants. Although gene expressions at the transcriptional level were stimulated by chilling in both C. bungeana and Arabidopsis, their activation networks were different as suggested by TFs analysis. Cold acclimation mechanism may be weak in or absent from C. bungeana because of lack of some CBFs orthologs. Alternatively, protein phosphorylation and ubiquitination may serve as more rapid and flexible cold tolerance mechanisms for C. bungeana to adapt to the harsh cold environments.
Plant material, growth conditions and treatments
Plant regeneration of C. bungeana via somatic embryogenesis was performed as described by Wang et al. . Callus was induced from matured seeds of C. bungeana on MS medium containing 4.0 mg l-1 GA3, 2.0 mg l-1 NAA, and 2.0 mg l-1 2,4-D. Seedlings were regenerated from callus on MS medium containing 3% sucrose in about 3 weeks. Regenerated plants were transferred to new MS medium containing 3% sucrose and grown at 22°C with a 14 h photoperiod under 80 μmol m-2 s-1 fluorescent light for further 7 days before treatments. For each treatment, ten plants (roots, shoots and leaves) were randomly pooled and treated in MS liquid medium containing 3% sucrose at 22°C or 2°C. Chilling stress was initiated 4 hours after dawn (zeitgeber time 4; ZT4). Upon the treatment time reaching 24 hours, both control and chilling stressed samples were collected at the same time point and frozen immediately with liquid nitrogen.
RNA extraction, cDNA library construction and RNA sequencing
For RNA sequencing, total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The quality of total RNA was checked using the NanoDrop Spectrometer (ND-1000 Spectrophotometer, Peqlab) and the Agilent 2100 Bioanalyzer (RNA Nano Chip, Agilent). High quality RNA samples (20 μg each) were sent to Beijing Genomics Institute (BGI, Shenzhen) for cDNA libraries construction and sequencing using Illumina HiSeq™ 2000. The cDNA library construction method and Illumina deep-sequencing processes were the same as described by Xu et al. .
De novo assembly and sequences clustering
The Trinity method  was used for de novo assembly of the clean reads to generate Trinity unigenes, with optimized k-mer length of 25. Then, the Trinity unigenes of both libraries were clustered with TGICL software  to get sequences (final unigenes) that cannot be extended on either end. De novo assembly was also conducted with SOAPdenovo software  with optimized k-mer length of 41.
Files containing the raw read sequences and their quality scores are available from the National Center for Biotechnology Information (NCBI) Short Read Archive with the accession number: SRA054354. The Trinity unigenes have been deposited in the Transcriptome Shotgun Assembly Sequence Database (TSA) at NCBI [GenBank: JW988067-JW999999, KA000001-KA089547].
Expression analysis and identification of differentially expressed genes (DEGs)
Clean reads were mapped back to assembled unigenes with SOAPaligner (version 2.21)  allowing maximum 2 mismatches. The reads with unique best hits were counted for each unigene. The expression level of C. bungeana unigene was normalized by the number of RPKM (reads per kilobase exon region per million mapped reads) . Since Illumina sequencing method is highly sensitive, we only used a subset of unigenes which presented in both sequencing libraries with a minimal RPKM of 1 for DEGs analysis. Unigene expressions were analyzed using DEGseq R package  with MARS method. Chilling-regulated DEGs were identified with Benjamini q < 0.001  and normalized fold change > =2.
For comparisons, two public available data sets of Arabidopsis were used in our study. One data set (referred to ATH-SR, means Arabidopsis short reads) was RNA sequencing data downloaded from NCBI Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov), including a chilling-treated sample (4°C; SRA accession: SRX006193) and a control (21°C; SRA accession: SRX006704) sample . After removing low quality reads (polyA/T/G/C sequences) and trimming off four NTs of both ends, all clean reads (28 NTs long) were mapped to Arabidopsis cDNAs (TAIR10) with SOAPaligner. DEGs identification was the same as described above. The DEGs and indentified gene with RPKM > =1 were listed in Additional file 6.
The other data set (referred to ATH-AR, means Arabidopsis array) was Affimetrix microarray data set (Expression Set: ME00325)  downloaded from TAIR (http://www.arabidopsis.org). Only cel files for 4 chilling-treated samples (2 for roots and 2 for shoots, 24-hour chilling-treated) and 4 control samples were used here. The cel files were imported into R and analyzed with Affy package . Root and shoot arrays were analyzed separately. Probes expressed in all root or shoot arrays were considered to be presented probes (by mas5 present calls). Differential expressed probes were identified using mas5 method of with FDR corrected p < 0.05 and fold change > =2 and mapped to Arabidopsis transcripts. The gene lists of roots and shoots were combined together to get chilling regulated DEGs and all expressed genes for further analysis (Additional file 7).
We used two methods for functional categorization of unigenes.
To get general gene ontology (GO) annotations for all unigenes, sequences longer than 200 bp were aligned to three public databases (NR, Swiss-Prot and KEGG) by BLASTX with E-value < =1e-5. The GO annotations for the top blast hits were retrieved with Blast2GO program  and used to annotate the C. bungeana transcripts. GO functional classification was performed by WEGO website tool .
For GO terms and KEGG pathways enrichment analysis, we used the Arabidopsis annotation systems. Briefly, the sequences of all unigenes were aligned against Arabidopsis peptide database (TAIR10) using BLASTX program with E-value < =1e-5. The top blast hits were considered to be putative orthologous genes (POGs). Then the C. bungeana unigenes were annotated with GO (downloaded from TAIR) and KEGG annotations (ath00001.keg, from http://www.kegg.jp/) for Arabidopsis POGs, respectively. The ontology (GO and KEGG) enrichment was analyzed with BiNGO plugins  for Cytoscape , using hypergeometric test for statistical analysis. For p value correction, we used rigorous Bonferroni correction method. The cutoff p value after correction was 0.05. For ATH-SR dataset, since the stressed sample was pooled from seedlings subjected to various periods of chilling-treated (1, 2, 5, 10, 24 hours of stressed) , the expressions of DEGs specific to a certain stage might have been “normalized”. Therefore, to get more information, we used FDR method instead of Bonferronic method for p value correction to find over-representative terms with BiNGO.
Quantitative real-time PCR (qPCR)
The gene-specific primers for real-time PCR analysis were designed using Primer Premier (version 5.0) software (PREMIER Biosoft). The specifities of primer pairs were confirmed by BLASTN with non-redundant unigene set of C. bungeana transcripts and the PCR products were checked by agrose electrophoresis to ensure single band amplifications. The primer sequences for all unigenes used in this study were listed in Additional file 8.
For qPCR analysis, total RNAs were extracted from control or chilling stressed C. bungeana seedlings (two biological repeats) with TRIZOL reagent and treated (20 μg RNA) with 1U DNase (TAKARA, Japan). cDNA was transcribed reversely from 1 μg of DNase-treated RNA with 200U M-MLV reverse transcriptase (Promega, USA) and analyzed with Platinum SYBR green qPCR supermix-UDG reagents (Invitrogen).
Before quantification of unigenes, the geNorm method was applied to select stable expressed unigenes in the four samples as reference genes . A total of 8 candidate reference unigenes were selected for reference genes screening, including an ACTIN2 ortholog, 3 unigenes showed stable expression levels in RNA-seq analysis and the other 4 unigenes were orthologs of recommended Arabidopsis reference genes . The information of reference gene candidates and the geNorm analysis results were shown Additional file 8. Three unigenes (CBT10872/AT3G60800, CBT28565/AT5G27630 and CBT12464/AT2G28390) expressed most stably in control and chilling-treated samples were selected and used for all qPCR analysis.
qPCR analysis was performed with three technical repeats for each sample. The relative expression levels of unigenes were normalized with the three selected reference genes with Pfaffl method [86, 88].
Availability of supporting data
The data sets supporting the results of this article are available in the NCBI GenBank repository, [http://www.ncbi.nlm.nih.gov/sites/nuccore?term=104929[BioProject], and in the NCBI SRA repository, [http://www.ncbi.nlm.nih.gov/sra?term=SRA054354].
CRT binding transcription factor
Differentially expressed gene
Kyoto Encyclopedia of Genes and Genomes
Putative orthologous gene
Quantitative real-time PCR
This work was funded by the Major Project of Cultivating New Varieties of Transgenic Organisms (2009ZX08009-029B), State Key Laboratory of Frozen Soil Engineering (SKLFSE201004) and the National Science Foundation of China (31070353).
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