DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems.
Identifieur interne : 000493 ( Main/Exploration ); précédent : 000492; suivant : 000494DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems.
Auteurs : Yang Zhang [République populaire de Chine] ; Cong Liu [République populaire de Chine] ; He Cheng [République populaire de Chine] ; Shuanghui Tian [République populaire de Chine] ; Yingying Liu [République populaire de Chine] ; Shuang Wang [République populaire de Chine] ; Huaxin Zhang [République populaire de Chine] ; Muhammad Saqib [Pakistan] ; Hairong Wei [États-Unis] ; Zhigang Wei [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2020.
Abstract
BACKGROUND
As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.
RESULTS
The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation.
CONCLUSIONS
DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.
DOI: 10.1186/s12864-020-06902-6
PubMed: 32689934
PubMed Central: PMC7372836
Affiliations:
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Shuanghui" uniqKey="Tian S" first="Shuanghui" last="Tian">Shuanghui Tian</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Yingying" sort="Liu, Yingying" uniqKey="Liu Y" first="Yingying" last="Liu">Yingying Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Shuang" sort="Wang, Shuang" uniqKey="Wang S" first="Shuang" last="Wang">Shuang Wang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Huaxin" sort="Zhang, Huaxin" uniqKey="Zhang H" first="Huaxin" last="Zhang">Huaxin Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></affiliation></author><author><name sortKey="Saqib, Muhammad" sort="Saqib, Muhammad" uniqKey="Saqib M" first="Muhammad" last="Saqib">Muhammad Saqib</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000</wicri:regionArea><wicri:noRegion>38000</wicri:noRegion></affiliation></author><author><name sortKey="Wei, Hairong" sort="Wei, Hairong" uniqKey="Wei H" first="Hairong" last="Wei">Hairong Wei</name><affiliation wicri:level="1"><nlm:affiliation>College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931</wicri:regionArea><wicri:noRegion>49931</wicri:noRegion></affiliation></author><author><name sortKey="Wei, Zhigang" sort="Wei, Zhigang" uniqKey="Wei Z" first="Zhigang" last="Wei">Zhigang Wei</name><affiliation wicri:level="1"><nlm:affiliation>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China. zhigangwei1973@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Research Center of Saline and Alkali Land of State Forestry and Grassland 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first="Yang" last="Zhang">Yang Zhang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Cong" sort="Liu, Cong" uniqKey="Liu C" first="Cong" last="Liu">Cong Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Cheng, He" sort="Cheng, He" uniqKey="Cheng H" first="He" last="Cheng">He Cheng</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Tian, Shuanghui" sort="Tian, Shuanghui" uniqKey="Tian S" first="Shuanghui" last="Tian">Shuanghui Tian</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Yingying" sort="Liu, Yingying" uniqKey="Liu Y" first="Yingying" last="Liu">Yingying Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Shuang" sort="Wang, Shuang" uniqKey="Wang S" first="Shuang" last="Wang">Shuang Wang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Huaxin" sort="Zhang, Huaxin" uniqKey="Zhang H" first="Huaxin" last="Zhang">Huaxin Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></affiliation></author><author><name sortKey="Saqib, Muhammad" sort="Saqib, Muhammad" uniqKey="Saqib M" first="Muhammad" last="Saqib">Muhammad Saqib</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000, Pakistan.</nlm:affiliation><country xml:lang="fr">Pakistan</country><wicri:regionArea>Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000</wicri:regionArea><wicri:noRegion>38000</wicri:noRegion></affiliation></author><author><name sortKey="Wei, Hairong" sort="Wei, Hairong" uniqKey="Wei H" first="Hairong" last="Wei">Hairong Wei</name><affiliation wicri:level="1"><nlm:affiliation>College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931</wicri:regionArea><wicri:noRegion>49931</wicri:noRegion></affiliation></author><author><name sortKey="Wei, Zhigang" sort="Wei, Zhigang" uniqKey="Wei Z" first="Zhigang" last="Wei">Zhigang Wei</name><affiliation wicri:level="1"><nlm:affiliation>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China. zhigangwei1973@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.</p></div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32689934</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>24</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>Jul</Month><Day>20</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems.</ArticleTitle><Pagination><MedlinePgn>498</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-020-06902-6</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Cong</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>He</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Shuanghui</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Yingying</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Shuang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Huaxin</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saqib</LastName><ForeName>Muhammad</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38000, Pakistan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Hairong</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Zhigang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China. zhigangwei1973@163.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>CAFYBB2018ZY001-5</GrantID><Agency>Fundamental Research Funds of Chinese Academy of Forestry</Agency><Country></Country></Grant><Grant><GrantID>CAFYBB2018GB001</GrantID><Agency>Fundamental Research Funds for the Central Non-profit Research Institution of CAF</Agency><Country></Country></Grant><Grant><GrantID>31770640</GrantID><Agency>National Natural Science Foundation of China</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">DNA methylation</Keyword><Keyword MajorTopicYN="N">Gene expression</Keyword><Keyword MajorTopicYN="N">Populus trichocarpa</Keyword><Keyword MajorTopicYN="N">Primary stems</Keyword><Keyword MajorTopicYN="N">Secondary stems</Keyword><Keyword MajorTopicYN="N">Transition stems</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>03</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32689934</ArticleId><ArticleId IdType="doi">10.1186/s12864-020-06902-6</ArticleId><ArticleId IdType="pii">10.1186/s12864-020-06902-6</ArticleId><ArticleId IdType="pmc">PMC7372836</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Nat Rev Genet. 2010 Mar;11(3):204-20</Citation><ArticleIdList><ArticleId IdType="pubmed">20142834</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2002 Jul 12;110(1):33-42</Citation><ArticleIdList><ArticleId 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