Interspecific hybridisation and LTR-retrotransposon mobilisation-related structural variation in plants: A case study.
Identifieur interne : 000309 ( Main/Exploration ); précédent : 000308; suivant : 000310Interspecific hybridisation and LTR-retrotransposon mobilisation-related structural variation in plants: A case study.
Auteurs : Gabriele Usai [Italie] ; Flavia Mascagni [Italie] ; Alberto Vangelisti [Italie] ; Tommaso Giordani [Italie] ; Marilena Ceccarelli [Italie] ; Andrea Cavallini [Italie] ; Lucia Natali [Italie]Source :
- Genomics [ 1089-8646 ] ; 2020.
Abstract
The dynamics of long-terminal-repeat retrotransposons in two poplar species (Populus deltoides and P. nigra) and in an interspecific hybrid, recently synthesized, were investigated by analyzing the genomic abundance and transcription levels of a collection of 828 full-length retroelements identified in the genome sequence of P. trichocarpa, all occurring also in the genomes of P. deltoides and P. nigra. Overall, genomic abundance and transcription levels of many retrotransposons in the hybrid resulted higher or lower than expected by calculating the mean of the parental values. A bioinformatics procedure was established to ascertain the occurrence of the same retrotransposon loci in the three genotypes. The results indicated that retrotransposon abundance variations between the hybrid and the mean value of the parents were due to i) co-segregation of retrotransposon high- or low-abundant haplotypes; ii) new retroelement insertions; iii) retrotransposon loss. Concerning retrotransposon expression, this was generally low, with only 14/828 elements over- or under-expressed in the hybrid than expected by calculating the mean of the parents. It is concluded that interspecific hybridisation between the two poplar species determine quantitative variation and differential expression of some retrotransposons, with possible consequences for the genetic differentiation of the hybrid.
DOI: 10.1016/j.ygeno.2019.09.010
PubMed: 31605729
Affiliations:
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Electronic address: andrea.cavallini@unipi.it.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa</wicri:regionArea><orgName type="university">Université de Pise</orgName><placeName><settlement type="city">Pise</settlement><region type="region" nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Natali, Lucia" sort="Natali, Lucia" uniqKey="Natali L" first="Lucia" last="Natali">Lucia Natali</name><affiliation wicri:level="4"><nlm:affiliation>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy. Electronic address: lucia.natali@unipi.it.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa</wicri:regionArea><orgName type="university">Université de Pise</orgName><placeName><settlement type="city">Pise</settlement><region type="region" nuts="2">Toscane</region></placeName></affiliation></author></analytic><series><title level="j">Genomics</title><idno type="eISSN">1089-8646</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">The dynamics of long-terminal-repeat retrotransposons in two poplar species (Populus deltoides and P. nigra) and in an interspecific hybrid, recently synthesized, were investigated by analyzing the genomic abundance and transcription levels of a collection of 828 full-length retroelements identified in the genome sequence of P. trichocarpa, all occurring also in the genomes of P. deltoides and P. nigra. Overall, genomic abundance and transcription levels of many retrotransposons in the hybrid resulted higher or lower than expected by calculating the mean of the parental values. A bioinformatics procedure was established to ascertain the occurrence of the same retrotransposon loci in the three genotypes. The results indicated that retrotransposon abundance variations between the hybrid and the mean value of the parents were due to i) co-segregation of retrotransposon high- or low-abundant haplotypes; ii) new retroelement insertions; iii) retrotransposon loss. Concerning retrotransposon expression, this was generally low, with only 14/828 elements over- or under-expressed in the hybrid than expected by calculating the mean of the parents. It is concluded that interspecific hybridisation between the two poplar species determine quantitative variation and differential expression of some retrotransposons, with possible consequences for the genetic differentiation of the hybrid.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">31605729</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8646</ISSN><JournalIssue CitedMedium="Internet"><Volume>112</Volume><Issue>2</Issue><PubDate><Year>2020</Year><Month>03</Month></PubDate></JournalIssue><Title>Genomics</Title><ISOAbbreviation>Genomics</ISOAbbreviation></Journal><ArticleTitle>Interspecific hybridisation and LTR-retrotransposon mobilisation-related structural variation in plants: A case study.</ArticleTitle><Pagination><MedlinePgn>1611-1621</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0888-7543(19)30187-9</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ygeno.2019.09.010</ELocationID><Abstract><AbstractText>The dynamics of long-terminal-repeat retrotransposons in two poplar species (Populus deltoides and P. nigra) and in an interspecific hybrid, recently synthesized, were investigated by analyzing the genomic abundance and transcription levels of a collection of 828 full-length retroelements identified in the genome sequence of P. trichocarpa, all occurring also in the genomes of P. deltoides and P. nigra. Overall, genomic abundance and transcription levels of many retrotransposons in the hybrid resulted higher or lower than expected by calculating the mean of the parental values. A bioinformatics procedure was established to ascertain the occurrence of the same retrotransposon loci in the three genotypes. The results indicated that retrotransposon abundance variations between the hybrid and the mean value of the parents were due to i) co-segregation of retrotransposon high- or low-abundant haplotypes; ii) new retroelement insertions; iii) retrotransposon loss. Concerning retrotransposon expression, this was generally low, with only 14/828 elements over- or under-expressed in the hybrid than expected by calculating the mean of the parents. It is concluded that interspecific hybridisation between the two poplar species determine quantitative variation and differential expression of some retrotransposons, with possible consequences for the genetic differentiation of the hybrid.</AbstractText><CopyrightInformation>Copyright © 2019 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Usai</LastName><ForeName>Gabriele</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mascagni</LastName><ForeName>Flavia</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vangelisti</LastName><ForeName>Alberto</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giordani</LastName><ForeName>Tommaso</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ceccarelli</LastName><ForeName>Marilena</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di sotto 8, 06123 Perugia, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cavallini</LastName><ForeName>Andrea</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy. Electronic address: andrea.cavallini@unipi.it.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Natali</LastName><ForeName>Lucia</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy. Electronic address: lucia.natali@unipi.it.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>10</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genomics</MedlineTA><NlmUniqueID>8800135</NlmUniqueID><ISSNLinking>0888-7543</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Interspecific hybrid</Keyword><Keyword MajorTopicYN="Y">Long-terminal-repeats retrotransposons</Keyword><Keyword MajorTopicYN="Y">Poplar</Keyword><Keyword MajorTopicYN="Y">Retrotransposon insertions</Keyword><Keyword MajorTopicYN="Y">Retrotransposon transcription</Keyword><Keyword MajorTopicYN="Y">Retrotransposon-related structural variation</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest The authors declare that they have no conflicts of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>04</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>07</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>09</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>10</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>10</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>10</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31605729</ArticleId><ArticleId IdType="pii">S0888-7543(19)30187-9</ArticleId><ArticleId IdType="doi">10.1016/j.ygeno.2019.09.010</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Italie</li></country><region><li>Toscane</li></region><settlement><li>Pise</li></settlement><orgName><li>Université de Pise</li></orgName></list><tree><country name="Italie"><region name="Toscane"><name sortKey="Usai, Gabriele" sort="Usai, Gabriele" uniqKey="Usai G" first="Gabriele" last="Usai">Gabriele Usai</name></region><name sortKey="Cavallini, Andrea" sort="Cavallini, Andrea" uniqKey="Cavallini A" first="Andrea" last="Cavallini">Andrea Cavallini</name><name sortKey="Ceccarelli, Marilena" sort="Ceccarelli, Marilena" uniqKey="Ceccarelli M" first="Marilena" last="Ceccarelli">Marilena Ceccarelli</name><name sortKey="Giordani, Tommaso" sort="Giordani, Tommaso" uniqKey="Giordani T" first="Tommaso" last="Giordani">Tommaso Giordani</name><name sortKey="Mascagni, Flavia" sort="Mascagni, Flavia" uniqKey="Mascagni F" first="Flavia" last="Mascagni">Flavia Mascagni</name><name sortKey="Natali, Lucia" sort="Natali, Lucia" uniqKey="Natali L" first="Lucia" last="Natali">Lucia Natali</name><name sortKey="Vangelisti, Alberto" sort="Vangelisti, Alberto" uniqKey="Vangelisti A" first="Alberto" last="Vangelisti">Alberto Vangelisti</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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