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Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy.

Wang H, Qi X, Chen S, Fang W, Guan Z, Teng N, Liao Y, Jiang J, Chen F - Front Plant Sci (2015)

Bottom Line: The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96).The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content.Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University Nanjing, China ; Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment Nanjing, China.

ABSTRACT
Polyploidy has been recognized as a widespread and common phenomenon among flowering plants. DNA-5'-CCGG site cytosine methylation (C-methylation) is one of the major and immediate epigenetic responses of the plant genome. Elucidating the ways in which altered C-methylation patterns, either at the whole genomic level or at specific sites can affect genome stability in polyploidy will require substantial additional investigation. Methylation sensitive amplification polymorphism profiling was used to evaluate variation in C-methylation among a set of 20 Chrysanthemum species and their close relatives of varying ploidy levels from diploid to decaploid. The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96). The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content. Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation.

No MeSH data available.


Phylogeny of MET and DDM1 proteins.Arabidopsis thaliana AtMET1 (NP_199727.1), Prunus persica PpMET (AAM96952.1), Medicago truncatula MtMET (XP_003619753.1), Pisum sativum PsMET (AAC49931.1), Populus trichocarpa PtMET (XP_002305346.1), Ricinus communis RcMET (XP_002518029.1), Daucus carota DcMET1 (AAC39355.1), Solanum lycopersicum SlMET (NP_001234748.1), Nicotiana sylvestris NsMET (CAQ18900.1), N. tabacum NtMET1 (BAF36443.1), Oryza sativa OsMET (BAG15930.1), Zea mays ZmMET1 (NP_001105186.1), Elaeis guineensis EgMET1 (ABW96888.1), Hieracium pilosella HpMET (ACX83570.1), H. piloselloides HpMET (ACX83569.1), Vitis vinifera VvDDM1 (XP_002267239.2), Glycine max GmDDM1(XP_003516571.1), S. lycopersicum SlDDM1 (XP_004232396.1), Crocus sativus CsDDM1 (XP_004149166.1), B. rapa BrDDM1 (BAG30707.1), Cicer arietinum CaDDM1 (XP_004512037.1), Fragaria vesca FvDDM1 (XP_004289144.1), O. sativa OsDDM1 (BAF34942.1), Setaria italica SiDDM1 (XP_004981943.1), Triticum urartu TuDDM1 (EMS59856.1), Brachypodium distachyon BdDDM1 (XP_003560489.1), Arabidopsis arenosa AaDDM1 (AAP92713.1), A. thaliana AtDDM1 (NP_201476.1).
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Figure 2: Phylogeny of MET and DDM1 proteins.Arabidopsis thaliana AtMET1 (NP_199727.1), Prunus persica PpMET (AAM96952.1), Medicago truncatula MtMET (XP_003619753.1), Pisum sativum PsMET (AAC49931.1), Populus trichocarpa PtMET (XP_002305346.1), Ricinus communis RcMET (XP_002518029.1), Daucus carota DcMET1 (AAC39355.1), Solanum lycopersicum SlMET (NP_001234748.1), Nicotiana sylvestris NsMET (CAQ18900.1), N. tabacum NtMET1 (BAF36443.1), Oryza sativa OsMET (BAG15930.1), Zea mays ZmMET1 (NP_001105186.1), Elaeis guineensis EgMET1 (ABW96888.1), Hieracium pilosella HpMET (ACX83570.1), H. piloselloides HpMET (ACX83569.1), Vitis vinifera VvDDM1 (XP_002267239.2), Glycine max GmDDM1(XP_003516571.1), S. lycopersicum SlDDM1 (XP_004232396.1), Crocus sativus CsDDM1 (XP_004149166.1), B. rapa BrDDM1 (BAG30707.1), Cicer arietinum CaDDM1 (XP_004512037.1), Fragaria vesca FvDDM1 (XP_004289144.1), O. sativa OsDDM1 (BAF34942.1), Setaria italica SiDDM1 (XP_004981943.1), Triticum urartu TuDDM1 (EMS59856.1), Brachypodium distachyon BdDDM1 (XP_003560489.1), Arabidopsis arenosa AaDDM1 (AAP92713.1), A. thaliana AtDDM1 (NP_201476.1).

Mentions: The full length CnMET1 (Genbank accession KF305682) cDNA was a 5,124 nt sequence, comprising a 4,803 nt ORF, a 92 nt 5′-UTR and a 229 nt 3′-UTR. The sequence showed significant homology to other plant MET genes. At the peptide level, the mean level of identity was 71.8%, reaching >80% in the most conserved regions (data not shown). A phylogenetic analysis showed that the most closely related sequences to CnMET1 were the homologs from H. pilosella and H. piloselloides (both Asteraceae species); in the conserved regions of the gene, the level of sequence identity was >90% (Figure 2). The CnDDM1 (Genbank KJ560359) sequence encodes a 752 residue product, sharing substantial homology with other plant DDM genes (data not shown). Its most closely related sequences were its homologs from Brassica rapa and A. thaliana (Figure 2) and the CnMET1/AtMET1 and CnDDM1/AtMET1 motifs lie parallel to one another and in the most conserved regions. The MET1 cytosine-C5 specific DNA methylase domain and the DDM1 N-terminal domain had an almost identical three-dimensional structure (Data not shown).


Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy.

Wang H, Qi X, Chen S, Fang W, Guan Z, Teng N, Liao Y, Jiang J, Chen F - Front Plant Sci (2015)

Phylogeny of MET and DDM1 proteins.Arabidopsis thaliana AtMET1 (NP_199727.1), Prunus persica PpMET (AAM96952.1), Medicago truncatula MtMET (XP_003619753.1), Pisum sativum PsMET (AAC49931.1), Populus trichocarpa PtMET (XP_002305346.1), Ricinus communis RcMET (XP_002518029.1), Daucus carota DcMET1 (AAC39355.1), Solanum lycopersicum SlMET (NP_001234748.1), Nicotiana sylvestris NsMET (CAQ18900.1), N. tabacum NtMET1 (BAF36443.1), Oryza sativa OsMET (BAG15930.1), Zea mays ZmMET1 (NP_001105186.1), Elaeis guineensis EgMET1 (ABW96888.1), Hieracium pilosella HpMET (ACX83570.1), H. piloselloides HpMET (ACX83569.1), Vitis vinifera VvDDM1 (XP_002267239.2), Glycine max GmDDM1(XP_003516571.1), S. lycopersicum SlDDM1 (XP_004232396.1), Crocus sativus CsDDM1 (XP_004149166.1), B. rapa BrDDM1 (BAG30707.1), Cicer arietinum CaDDM1 (XP_004512037.1), Fragaria vesca FvDDM1 (XP_004289144.1), O. sativa OsDDM1 (BAF34942.1), Setaria italica SiDDM1 (XP_004981943.1), Triticum urartu TuDDM1 (EMS59856.1), Brachypodium distachyon BdDDM1 (XP_003560489.1), Arabidopsis arenosa AaDDM1 (AAP92713.1), A. thaliana AtDDM1 (NP_201476.1).
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Figure 2: Phylogeny of MET and DDM1 proteins.Arabidopsis thaliana AtMET1 (NP_199727.1), Prunus persica PpMET (AAM96952.1), Medicago truncatula MtMET (XP_003619753.1), Pisum sativum PsMET (AAC49931.1), Populus trichocarpa PtMET (XP_002305346.1), Ricinus communis RcMET (XP_002518029.1), Daucus carota DcMET1 (AAC39355.1), Solanum lycopersicum SlMET (NP_001234748.1), Nicotiana sylvestris NsMET (CAQ18900.1), N. tabacum NtMET1 (BAF36443.1), Oryza sativa OsMET (BAG15930.1), Zea mays ZmMET1 (NP_001105186.1), Elaeis guineensis EgMET1 (ABW96888.1), Hieracium pilosella HpMET (ACX83570.1), H. piloselloides HpMET (ACX83569.1), Vitis vinifera VvDDM1 (XP_002267239.2), Glycine max GmDDM1(XP_003516571.1), S. lycopersicum SlDDM1 (XP_004232396.1), Crocus sativus CsDDM1 (XP_004149166.1), B. rapa BrDDM1 (BAG30707.1), Cicer arietinum CaDDM1 (XP_004512037.1), Fragaria vesca FvDDM1 (XP_004289144.1), O. sativa OsDDM1 (BAF34942.1), Setaria italica SiDDM1 (XP_004981943.1), Triticum urartu TuDDM1 (EMS59856.1), Brachypodium distachyon BdDDM1 (XP_003560489.1), Arabidopsis arenosa AaDDM1 (AAP92713.1), A. thaliana AtDDM1 (NP_201476.1).
Mentions: The full length CnMET1 (Genbank accession KF305682) cDNA was a 5,124 nt sequence, comprising a 4,803 nt ORF, a 92 nt 5′-UTR and a 229 nt 3′-UTR. The sequence showed significant homology to other plant MET genes. At the peptide level, the mean level of identity was 71.8%, reaching >80% in the most conserved regions (data not shown). A phylogenetic analysis showed that the most closely related sequences to CnMET1 were the homologs from H. pilosella and H. piloselloides (both Asteraceae species); in the conserved regions of the gene, the level of sequence identity was >90% (Figure 2). The CnDDM1 (Genbank KJ560359) sequence encodes a 752 residue product, sharing substantial homology with other plant DDM genes (data not shown). Its most closely related sequences were its homologs from Brassica rapa and A. thaliana (Figure 2) and the CnMET1/AtMET1 and CnDDM1/AtMET1 motifs lie parallel to one another and in the most conserved regions. The MET1 cytosine-C5 specific DNA methylase domain and the DDM1 N-terminal domain had an almost identical three-dimensional structure (Data not shown).

Bottom Line: The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96).The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content.Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University Nanjing, China ; Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment Nanjing, China.

ABSTRACT
Polyploidy has been recognized as a widespread and common phenomenon among flowering plants. DNA-5'-CCGG site cytosine methylation (C-methylation) is one of the major and immediate epigenetic responses of the plant genome. Elucidating the ways in which altered C-methylation patterns, either at the whole genomic level or at specific sites can affect genome stability in polyploidy will require substantial additional investigation. Methylation sensitive amplification polymorphism profiling was used to evaluate variation in C-methylation among a set of 20 Chrysanthemum species and their close relatives of varying ploidy levels from diploid to decaploid. The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96). The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content. Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation.

No MeSH data available.