DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.)
Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we per...
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| Veröffentlicht in: | Horticulture research 2021-07, Vol.8 (1), Article 142 |
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| creator | Yin, Liqin Zhu, Zhendong Huang, Liangjun Luo, Xuan Li, Yun Xiao, Chaowen Yang, Jin Wang, Jisheng Zou, Qiong Tao, Lanrong Kang, Zeming Tang, Rong Wang, Maolin Fu, Shaohong |
| description | Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (
Brassica napus
). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of
B. napus
. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in
B. napus
might be partially regulated by
MET1
. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed
Brassica
polyploids. |
| doi_str_mv | 10.1038/s41438-021-00576-1 |
| format | Article |
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Brassica napus
). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of
B. napus
. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in
B. napus
might be partially regulated by
MET1
. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed
Brassica
polyploids.</description><identifier>ISSN: 2662-6810</identifier><identifier>EISSN: 2052-7276</identifier><identifier>DOI: 10.1038/s41438-021-00576-1</identifier><identifier>PMID: 34193846</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/181 ; 631/208/177 ; 631/208/199 ; 631/208/211 ; 631/449/2669 ; Agriculture ; Biological evolution ; Biomedical and Life Sciences ; Brassica ; Brassica napus ; Cell cycle ; Damage ; Deoxyribonucleic acid ; DNA ; DNA damage ; DNA methylation ; DNA repair ; Ecology ; Epigenetics ; Genes ; Genomic instability ; Life Sciences ; Metabolism ; Molecular modelling ; Nucleotides ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Plant Sciences ; Polyploidy ; Rape plants ; Rapeseed ; Repair ; Stability</subject><ispartof>Horticulture research, 2021-07, Vol.8 (1), Article 142</ispartof><rights>The Author(s) 2021</rights><rights>The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c483t-ce808d915ebac47cdbac91a10b9585856fc122e7e283bee0d58c5342be0015a03</citedby><cites>FETCH-LOGICAL-c483t-ce808d915ebac47cdbac91a10b9585856fc122e7e283bee0d58c5342be0015a03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245426/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245426/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids></links><search><creatorcontrib>Yin, Liqin</creatorcontrib><creatorcontrib>Zhu, Zhendong</creatorcontrib><creatorcontrib>Huang, Liangjun</creatorcontrib><creatorcontrib>Luo, Xuan</creatorcontrib><creatorcontrib>Li, Yun</creatorcontrib><creatorcontrib>Xiao, Chaowen</creatorcontrib><creatorcontrib>Yang, Jin</creatorcontrib><creatorcontrib>Wang, Jisheng</creatorcontrib><creatorcontrib>Zou, Qiong</creatorcontrib><creatorcontrib>Tao, Lanrong</creatorcontrib><creatorcontrib>Kang, Zeming</creatorcontrib><creatorcontrib>Tang, Rong</creatorcontrib><creatorcontrib>Wang, Maolin</creatorcontrib><creatorcontrib>Fu, Shaohong</creatorcontrib><title>DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.)</title><title>Horticulture research</title><addtitle>Hortic Res</addtitle><description>Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (
Brassica napus
). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of
B. napus
. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in
B. napus
might be partially regulated by
MET1
. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed
Brassica
polyploids.</description><subject>631/181</subject><subject>631/208/177</subject><subject>631/208/199</subject><subject>631/208/211</subject><subject>631/449/2669</subject><subject>Agriculture</subject><subject>Biological evolution</subject><subject>Biomedical and Life Sciences</subject><subject>Brassica</subject><subject>Brassica napus</subject><subject>Cell cycle</subject><subject>Damage</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA damage</subject><subject>DNA methylation</subject><subject>DNA repair</subject><subject>Ecology</subject><subject>Epigenetics</subject><subject>Genes</subject><subject>Genomic instability</subject><subject>Life Sciences</subject><subject>Metabolism</subject><subject>Molecular modelling</subject><subject>Nucleotides</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Sciences</subject><subject>Polyploidy</subject><subject>Rape 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Press</general><scope>C6C</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>5PM</scope></search><sort><creationdate>20210701</creationdate><title>DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.)</title><author>Yin, Liqin ; Zhu, Zhendong ; Huang, Liangjun ; Luo, Xuan ; Li, Yun 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Sciences</topic><topic>Metabolism</topic><topic>Molecular modelling</topic><topic>Nucleotides</topic><topic>Plant Breeding/Biotechnology</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Sciences</topic><topic>Polyploidy</topic><topic>Rape plants</topic><topic>Rapeseed</topic><topic>Repair</topic><topic>Stability</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yin, Liqin</creatorcontrib><creatorcontrib>Zhu, Zhendong</creatorcontrib><creatorcontrib>Huang, Liangjun</creatorcontrib><creatorcontrib>Luo, Xuan</creatorcontrib><creatorcontrib>Li, Yun</creatorcontrib><creatorcontrib>Xiao, Chaowen</creatorcontrib><creatorcontrib>Yang, Jin</creatorcontrib><creatorcontrib>Wang, Jisheng</creatorcontrib><creatorcontrib>Zou, Qiong</creatorcontrib><creatorcontrib>Tao, Lanrong</creatorcontrib><creatorcontrib>Kang, Zeming</creatorcontrib><creatorcontrib>Tang, Rong</creatorcontrib><creatorcontrib>Wang, Maolin</creatorcontrib><creatorcontrib>Fu, 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titles)</collection><jtitle>Horticulture research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yin, Liqin</au><au>Zhu, Zhendong</au><au>Huang, Liangjun</au><au>Luo, Xuan</au><au>Li, Yun</au><au>Xiao, Chaowen</au><au>Yang, Jin</au><au>Wang, Jisheng</au><au>Zou, Qiong</au><au>Tao, Lanrong</au><au>Kang, Zeming</au><au>Tang, Rong</au><au>Wang, Maolin</au><au>Fu, Shaohong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.)</atitle><jtitle>Horticulture research</jtitle><stitle>Hortic Res</stitle><date>2021-07-01</date><risdate>2021</risdate><volume>8</volume><issue>1</issue><artnum>142</artnum><issn>2662-6810</issn><eissn>2052-7276</eissn><abstract>Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (
Brassica napus
). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of
B. napus
. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in
B. napus
might be partially regulated by
MET1
. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed
Brassica
polyploids.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>34193846</pmid><doi>10.1038/s41438-021-00576-1</doi><oa>free_for_read</oa></addata></record> |
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| subjects | 631/181 631/208/177 631/208/199 631/208/211 631/449/2669 Agriculture Biological evolution Biomedical and Life Sciences Brassica Brassica napus Cell cycle Damage Deoxyribonucleic acid DNA DNA damage DNA methylation DNA repair Ecology Epigenetics Genes Genomic instability Life Sciences Metabolism Molecular modelling Nucleotides Plant Breeding/Biotechnology Plant Genetics and Genomics Plant Sciences Polyploidy Rape plants Rapeseed Repair Stability |
| title | DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.) |
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