Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.
Identifieur interne : 001859 ( Main/Exploration ); précédent : 001858; suivant : 001860Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.
Auteurs : Birgit Kersten [Allemagne] ; Patricia Faivre Rampant [France] ; Malte Mader [Allemagne] ; Marie-Christine Le Paslier [France] ; Rémi Bounon [France] ; Aurélie Berard [France] ; Cristina Vettori [Italie] ; Hilke Schroeder [Allemagne] ; Jean-Charles Leplé [France] ; Matthias Fladung [Allemagne]Source :
- PloS one [ 1932-6203 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Chloroplastes, Mitochondries, Populus.
- classification : Amélioration des plantes, Génome végétal, Phylogenèse, Populus.
English descriptors
- KwdEn :
- MESH :
- classification : Populus.
- genetics : Chloroplasts, Mitochondria, Populus.
- Genome, Plant, Phylogeny, Plant Breeding.
Abstract
Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.
DOI: 10.1371/journal.pone.0147209
PubMed: 26800039
PubMed Central: PMC4723046
Affiliations:
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Rampant">Patricia Faivre Rampant</name><affiliation wicri:level="3"><nlm:affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>URGV-Plant Genomics Research, INRA, Evry</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Mader, Malte" sort="Mader, Malte" uniqKey="Mader M" first="Malte" last="Mader">Malte Mader</name><affiliation wicri:level="1"><nlm:affiliation>Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf</wicri:regionArea><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion></affiliation></author><author><name sortKey="Le Paslier, Marie Christine" sort="Le Paslier, Marie Christine" uniqKey="Le Paslier M" first="Marie-Christine" last="Le Paslier">Marie-Christine Le Paslier</name><affiliation wicri:level="3"><nlm:affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>URGV-Plant Genomics Research, INRA, Evry</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Bounon, Remi" sort="Bounon, Remi" uniqKey="Bounon R" first="Rémi" last="Bounon">Rémi Bounon</name><affiliation wicri:level="3"><nlm:affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>URGV-Plant Genomics Research, INRA, Evry</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Berard, Aurelie" sort="Berard, Aurelie" uniqKey="Berard A" first="Aurélie" last="Berard">Aurélie Berard</name><affiliation wicri:level="3"><nlm:affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>URGV-Plant Genomics Research, INRA, Evry</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Vettori, Cristina" sort="Vettori, Cristina" uniqKey="Vettori C" first="Cristina" last="Vettori">Cristina Vettori</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Bioscience and Bioresources (IBBR), National Research Council, Sesto Fiorentino, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Bioscience and Bioresources (IBBR), National Research Council, Sesto Fiorentino</wicri:regionArea><wicri:noRegion>Sesto Fiorentino</wicri:noRegion></affiliation></author><author><name sortKey="Schroeder, Hilke" sort="Schroeder, Hilke" uniqKey="Schroeder H" first="Hilke" last="Schroeder">Hilke Schroeder</name><affiliation wicri:level="1"><nlm:affiliation>Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf</wicri:regionArea><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf</wicri:regionArea><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion></affiliation></author><author><name sortKey="Leple, Jean Charles" sort="Leple, Jean Charles" uniqKey="Leple J" first="Jean-Charles" last="Leplé">Jean-Charles Leplé</name><affiliation wicri:level="3"><nlm:affiliation>Research Unit AGPF, INRA, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Research Unit AGPF, INRA, Orléans</wicri:regionArea><placeName><region type="region">Centre-Val de Loire</region><region type="old region">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Fladung, Matthias" sort="Fladung, Matthias" uniqKey="Fladung M" first="Matthias" last="Fladung">Matthias Fladung</name><affiliation wicri:level="1"><nlm:affiliation>Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf</wicri:regionArea><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion><wicri:noRegion>Grosshansdorf</wicri:noRegion></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chloroplasts (genetics)</term><term>Genome, Plant (MeSH)</term><term>Mitochondria (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Breeding (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amélioration des plantes (MeSH)</term><term>Chloroplastes (génétique)</term><term>Génome végétal (MeSH)</term><term>Mitochondries (génétique)</term><term>Phylogenèse (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chloroplasts</term><term>Mitochondria</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chloroplastes</term><term>Mitochondries</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term><term>Phylogeny</term><term>Plant Breeding</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Amélioration des plantes</term><term>Génome végétal</term><term>Phylogenèse</term><term>Populus</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26800039</PMID><DateCompleted><Year>2016</Year><Month>07</Month><Day>08</Day></DateCompleted><DateRevised><Year>2019</Year><Month>02</Month><Day>22</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>1</Issue><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.</ArticleTitle><Pagination><MedlinePgn>e0147209</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0147209</ELocationID><Abstract><AbstractText>Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kersten</LastName><ForeName>Birgit</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Faivre Rampant</LastName><ForeName>Patricia</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mader</LastName><ForeName>Malte</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Le Paslier</LastName><ForeName>Marie-Christine</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bounon</LastName><ForeName>Rémi</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berard</LastName><ForeName>Aurélie</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>URGV-Plant Genomics Research, INRA, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vettori</LastName><ForeName>Cristina</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute of Bioscience and Bioresources (IBBR), National Research Council, Sesto Fiorentino, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schroeder</LastName><ForeName>Hilke</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Leplé</LastName><ForeName>Jean-Charles</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Research Unit AGPF, INRA, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fladung</LastName><ForeName>Matthias</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.</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>2016</Year><Month>01</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002736" MajorTopicYN="N">Chloroplasts</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008928" MajorTopicYN="N">Mitochondria</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName 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first="Rémi" last="Bounon">Rémi Bounon</name><name sortKey="Le Paslier, Marie Christine" sort="Le Paslier, Marie Christine" uniqKey="Le Paslier M" first="Marie-Christine" last="Le Paslier">Marie-Christine Le Paslier</name><name sortKey="Leple, Jean Charles" sort="Leple, Jean Charles" uniqKey="Leple J" first="Jean-Charles" last="Leplé">Jean-Charles Leplé</name></country><country name="Italie"><noRegion><name sortKey="Vettori, Cristina" sort="Vettori, Cristina" uniqKey="Vettori C" first="Cristina" last="Vettori">Cristina Vettori</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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