Variation in genomic methylation in natural populations of chinese white poplar.
Identifieur interne : 002425 ( Main/Exploration ); précédent : 002424; suivant : 002426Variation in genomic methylation in natural populations of chinese white poplar.
Auteurs : Kaifeng Ma [République populaire de Chine] ; Yuepeng Song ; Xiaohui Yang ; Zhiyi Zhang ; Deqiang ZhangSource :
- PloS one [ 1932-6203 ] ; 2013.
Descripteurs français
- KwdFr :
- Analyse en composantes principales (MeSH), Chine (MeSH), Génome végétal (génétique), Méthylation de l'ADN (génétique), Polymorphisme génétique (MeSH), Populus (génétique), Réaction de polymérisation en chaîne (MeSH), Séquence nucléotidique (MeSH), Variation génétique (MeSH), Épigenèse génétique (MeSH).
- MESH :
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- MESH :
- geographic : China.
- genetics : DNA Methylation, Genome, Plant, Populus.
- Base Sequence, Epigenesis, Genetic, Genetic Variation, Polymerase Chain Reaction, Polymorphism, Genetic, Principal Component Analysis.
Abstract
BACKGROUND
It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar.
PRINCIPAL FINDINGS
On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon's diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree.
CONCLUSIONS
Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5'-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.
DOI: 10.1371/journal.pone.0063977
PubMed: 23704963
PubMed Central: PMC3660595
Affiliations:
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uniqKey="Yang X" first="Xiaohui" last="Yang">Xiaohui Yang</name></author><author><name sortKey="Zhang, Zhiyi" sort="Zhang, Zhiyi" uniqKey="Zhang Z" first="Zhiyi" last="Zhang">Zhiyi Zhang</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23704963</idno><idno type="pmid">23704963</idno><idno type="doi">10.1371/journal.pone.0063977</idno><idno type="pmc">PMC3660595</idno><idno type="wicri:Area/Main/Corpus">002588</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002588</idno><idno type="wicri:Area/Main/Curation">002588</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002588</idno><idno type="wicri:Area/Main/Exploration">002588</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Variation in genomic methylation in natural populations of chinese white poplar.</title><author><name sortKey="Ma, Kaifeng" sort="Ma, Kaifeng" uniqKey="Ma K" first="Kaifeng" last="Ma">Kaifeng Ma</name><affiliation wicri:level="3"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Song, Yuepeng" sort="Song, Yuepeng" uniqKey="Song Y" first="Yuepeng" last="Song">Yuepeng Song</name></author><author><name sortKey="Yang, Xiaohui" sort="Yang, Xiaohui" uniqKey="Yang X" first="Xiaohui" last="Yang">Xiaohui Yang</name></author><author><name sortKey="Zhang, Zhiyi" sort="Zhang, Zhiyi" uniqKey="Zhang Z" first="Zhiyi" last="Zhang">Zhiyi Zhang</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>China (MeSH)</term><term>DNA Methylation (genetics)</term><term>Epigenesis, Genetic (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Plant (genetics)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Polymorphism, Genetic (MeSH)</term><term>Populus (genetics)</term><term>Principal Component Analysis (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse en composantes principales (MeSH)</term><term>Chine (MeSH)</term><term>Génome végétal (génétique)</term><term>Méthylation de l'ADN (génétique)</term><term>Polymorphisme génétique (MeSH)</term><term>Populus (génétique)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Variation génétique (MeSH)</term><term>Épigenèse génétique (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>DNA Methylation</term><term>Genome, Plant</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Génome végétal</term><term>Méthylation de l'ADN</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Epigenesis, Genetic</term><term>Genetic Variation</term><term>Polymerase Chain Reaction</term><term>Polymorphism, Genetic</term><term>Principal Component Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse en composantes principales</term><term>Chine</term><term>Polymorphisme génétique</term><term>Réaction de polymérisation en chaîne</term><term>Séquence nucléotidique</term><term>Variation génétique</term><term>Épigenèse génétique</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar.</p></div><div type="abstract" xml:lang="en"><p><b>PRINCIPAL FINDINGS</b></p><p>On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon's diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5'-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23704963</PMID><DateCompleted><Year>2013</Year><Month>12</Month><Day>30</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-Print"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>5</Issue><PubDate><Year>2013</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Variation in genomic methylation in natural populations of chinese white poplar.</ArticleTitle><Pagination><MedlinePgn>e63977</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0063977</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar.</AbstractText><AbstractText Label="PRINCIPAL FINDINGS" NlmCategory="RESULTS">On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon's diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5'-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. 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