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RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

Lei X, Xiao Y, Xia W, Mason AS, Yang Y, Ma Z, Peng M - PLoS ONE (2014)

Bottom Line: Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide.Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed.These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

View Article: PubMed Central - PubMed

Affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, P. R. China.

ABSTRACT
Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated) samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors) of COG (Cluster of Orthologous Group) annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family) may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR). CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

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Chromosome positions of the expressed sequences involved in the CBF-mediated signal transduction pathway.The left number “KE……” represents the scaffold ID number in the Elaeis guineensis genome in the NCBI database. Chromosomes are comprised of Elaeis guineensis scaffolds and the spaces between the scaffolds represent gaps between the scaffolds. A length of 1 centimeter represents 10000 kb.
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pone-0114482-g003: Chromosome positions of the expressed sequences involved in the CBF-mediated signal transduction pathway.The left number “KE……” represents the scaffold ID number in the Elaeis guineensis genome in the NCBI database. Chromosomes are comprised of Elaeis guineensis scaffolds and the spaces between the scaffolds represent gaps between the scaffolds. A length of 1 centimeter represents 10000 kb.

Mentions: Based on transcriptome data in response to cold stress, three expressed gene sequences (Unigene615, Unigene5046 and Unigene21287) showed high similarity to known ICE1 gene sequences which may participate in activating CBF gene expression when oil palm is exposed to low temperatures. Using in-silico mapping, Unigene615 and Unigene21287 were located on to chromosome 9 and chromosome 3 of oil palm respectively (Figure 3). Moreover, Unigene2502, CL1094.Contig1, and CL1094.Contig3 also showed high similarity to known SIZ1 gene sequences: SIZ1 can facilitate conjugation of SUMO to ICE1 proteins to activate the CBF gene expression. These three expressed sequence were located on chromosome 5 (Unigene2502), chromosome 14 (CL1094.Contig1), and chromosome 5 (CL1094.Contig3). Meanwhile, the conjunction of SUMO and ICE1 protein can also repress the expression of the MYB15 gene (a repressor of CBF gene expression). The expressed sequence Unigene6283 showed high similarity to the known MYB15 gene sequence, and was mapped to chromosome 6. ICE1 proteins are ultimately degraded by HOS1-mediated ubiquitination. Based on the transcriptome data, one expressed sequence (Unigene8210) showed high similarity to known HOS1 gene sequences, but could not be mapped to a chromosomal location in oil palm.


RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

Lei X, Xiao Y, Xia W, Mason AS, Yang Y, Ma Z, Peng M - PLoS ONE (2014)

Chromosome positions of the expressed sequences involved in the CBF-mediated signal transduction pathway.The left number “KE……” represents the scaffold ID number in the Elaeis guineensis genome in the NCBI database. Chromosomes are comprised of Elaeis guineensis scaffolds and the spaces between the scaffolds represent gaps between the scaffolds. A length of 1 centimeter represents 10000 kb.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257668&req=5

pone-0114482-g003: Chromosome positions of the expressed sequences involved in the CBF-mediated signal transduction pathway.The left number “KE……” represents the scaffold ID number in the Elaeis guineensis genome in the NCBI database. Chromosomes are comprised of Elaeis guineensis scaffolds and the spaces between the scaffolds represent gaps between the scaffolds. A length of 1 centimeter represents 10000 kb.
Mentions: Based on transcriptome data in response to cold stress, three expressed gene sequences (Unigene615, Unigene5046 and Unigene21287) showed high similarity to known ICE1 gene sequences which may participate in activating CBF gene expression when oil palm is exposed to low temperatures. Using in-silico mapping, Unigene615 and Unigene21287 were located on to chromosome 9 and chromosome 3 of oil palm respectively (Figure 3). Moreover, Unigene2502, CL1094.Contig1, and CL1094.Contig3 also showed high similarity to known SIZ1 gene sequences: SIZ1 can facilitate conjugation of SUMO to ICE1 proteins to activate the CBF gene expression. These three expressed sequence were located on chromosome 5 (Unigene2502), chromosome 14 (CL1094.Contig1), and chromosome 5 (CL1094.Contig3). Meanwhile, the conjunction of SUMO and ICE1 protein can also repress the expression of the MYB15 gene (a repressor of CBF gene expression). The expressed sequence Unigene6283 showed high similarity to the known MYB15 gene sequence, and was mapped to chromosome 6. ICE1 proteins are ultimately degraded by HOS1-mediated ubiquitination. Based on the transcriptome data, one expressed sequence (Unigene8210) showed high similarity to known HOS1 gene sequences, but could not be mapped to a chromosomal location in oil palm.

Bottom Line: Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide.Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed.These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

View Article: PubMed Central - PubMed

Affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, P. R. China.

ABSTRACT
Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated) samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors) of COG (Cluster of Orthologous Group) annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family) may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR). CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

Show MeSH
Related in: MedlinePlus