Towards improved reconstruction of ancestral gene order in angiosperm phylogeny.
Identifieur interne : 003451 ( Main/Exploration ); précédent : 003450; suivant : 003452Towards improved reconstruction of ancestral gene order in angiosperm phylogeny.
Auteurs : David Sankoff [Canada] ; Chunfang Zheng ; P Kerr Wall ; Claude Depamphilis ; Jim Leebens-Mack ; Victor A. AlbertSource :
- Journal of computational biology : a journal of computational molecular cell biology [ 1557-8666 ] ; 2009.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Carica (classification), Carica (génétique), Génome végétal (MeSH), Magnoliopsida (classification), Magnoliopsida (génétique), Modèles génétiques (MeSH), Ordre des gènes (MeSH), Phylogenèse (MeSH), Populus (classification), Populus (génétique), Vitis (classification), Vitis (génétique), Évolution biologique (MeSH).
- MESH :
- génétique : Carica, Magnoliopsida, Populus, Vitis.
- classification : Algorithmes, Carica, Génome végétal, Magnoliopsida, Modèles génétiques, Ordre des gènes, Phylogenèse, Populus, Vitis, Évolution biologique.
English descriptors
- KwdEn :
- Algorithms (MeSH), Biological Evolution (MeSH), Carica (classification), Carica (genetics), Gene Order (MeSH), Genome, Plant (MeSH), Magnoliopsida (classification), Magnoliopsida (genetics), Models, Genetic (MeSH), Phylogeny (MeSH), Populus (classification), Populus (genetics), Vitis (classification), Vitis (genetics).
- MESH :
- classification : Carica, Magnoliopsida, Populus, Vitis.
- genetics : Carica, Magnoliopsida, Populus, Vitis.
- Algorithms, Biological Evolution, Gene Order, Genome, Plant, Models, Genetic, Phylogeny.
Abstract
Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiosperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, including an unbiased version of the guided genome halving algorithm, reference to two related genomes instead of only one to guide the reconstruction, use of draft genome sequences in contig form only, incorporation of incomplete sets of homology correspondences among the genomes, and addition of large numbers of "singleton" correspondences. We make use of genomic distance, breakpoint reuse rate, dispersion of sets of alternate solutions, and other means to evaluate these techniques, and employ the papaya (Carica papaya) and grapevine (Vitis vinifera) genomes to reconstruct the pre-WGD ancestor of poplar (Populus trichocarpa), as well as an early rosid ancestor. A significant result is that the papaya genome has rearranged at a greater rate from the rosid ancestor than phylogenetic relationships would predict.
DOI: 10.1089/cmb.2009.0103
PubMed: 19803735
Affiliations:
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Le document en format XML
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Albert</name></author></analytic><series><title level="j">Journal of computational biology : a journal of computational molecular cell biology</title><idno type="eISSN">1557-8666</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Biological Evolution (MeSH)</term><term>Carica (classification)</term><term>Carica (genetics)</term><term>Gene Order (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (genetics)</term><term>Models, Genetic (MeSH)</term><term>Phylogeny (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>Vitis (classification)</term><term>Vitis (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes (MeSH)</term><term>Carica (classification)</term><term>Carica (génétique)</term><term>Génome végétal (MeSH)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (génétique)</term><term>Modèles génétiques (MeSH)</term><term>Ordre des gènes (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Vitis (classification)</term><term>Vitis (génétique)</term><term>Évolution biologique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Carica</term><term>Magnoliopsida</term><term>Populus</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Carica</term><term>Magnoliopsida</term><term>Populus</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Carica</term><term>Magnoliopsida</term><term>Populus</term><term>Vitis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Biological Evolution</term><term>Gene Order</term><term>Genome, Plant</term><term>Models, Genetic</term><term>Phylogeny</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Algorithmes</term><term>Carica</term><term>Génome végétal</term><term>Magnoliopsida</term><term>Modèles génétiques</term><term>Ordre des gènes</term><term>Phylogenèse</term><term>Populus</term><term>Vitis</term><term>Évolution biologique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiosperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, including an unbiased version of the guided genome halving algorithm, reference to two related genomes instead of only one to guide the reconstruction, use of draft genome sequences in contig form only, incorporation of incomplete sets of homology correspondences among the genomes, and addition of large numbers of "singleton" correspondences. We make use of genomic distance, breakpoint reuse rate, dispersion of sets of alternate solutions, and other means to evaluate these techniques, and employ the papaya (Carica papaya) and grapevine (Vitis vinifera) genomes to reconstruct the pre-WGD ancestor of poplar (Populus trichocarpa), as well as an early rosid ancestor. A significant result is that the papaya genome has rearranged at a greater rate from the rosid ancestor than phylogenetic relationships would predict.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19803735</PMID><DateCompleted><Year>2009</Year><Month>12</Month><Day>01</Day></DateCompleted><DateRevised><Year>2017</Year><Month>11</Month><Day>16</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1557-8666</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><Issue>10</Issue><PubDate><Year>2009</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Journal of computational biology : a journal of computational molecular cell biology</Title><ISOAbbreviation>J Comput Biol</ISOAbbreviation></Journal><ArticleTitle>Towards improved reconstruction of ancestral gene order in angiosperm phylogeny.</ArticleTitle><Pagination><MedlinePgn>1353-67</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1089/cmb.2009.0103</ELocationID><Abstract><AbstractText>Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiosperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, including an unbiased version of the guided genome halving algorithm, reference to two related genomes instead of only one to guide the reconstruction, use of draft genome sequences in contig form only, incorporation of incomplete sets of homology correspondences among the genomes, and addition of large numbers of "singleton" correspondences. We make use of genomic distance, breakpoint reuse rate, dispersion of sets of alternate solutions, and other means to evaluate these techniques, and employ the papaya (Carica papaya) and grapevine (Vitis vinifera) genomes to reconstruct the pre-WGD ancestor of poplar (Populus trichocarpa), as well as an early rosid ancestor. 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Albert</name><name sortKey="Depamphilis, Claude" sort="Depamphilis, Claude" uniqKey="Depamphilis C" first="Claude" last="Depamphilis">Claude Depamphilis</name><name sortKey="Leebens Mack, Jim" sort="Leebens Mack, Jim" uniqKey="Leebens Mack J" first="Jim" last="Leebens-Mack">Jim Leebens-Mack</name><name sortKey="Wall, P Kerr" sort="Wall, P Kerr" uniqKey="Wall P" first="P Kerr" last="Wall">P Kerr Wall</name><name sortKey="Zheng, Chunfang" sort="Zheng, Chunfang" uniqKey="Zheng C" first="Chunfang" last="Zheng">Chunfang Zheng</name></noCountry><country name="Canada"><noRegion><name sortKey="Sankoff, David" sort="Sankoff, David" uniqKey="Sankoff D" first="David" last="Sankoff">David Sankoff</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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