The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.
Identifieur interne : 000362 ( Main/Exploration ); précédent : 000361; suivant : 000363The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.
Auteurs : Martha Rend N-Anaya [Mexique, Suède] ; Enrique Ibarra-Laclette [Mexique] ; Alfonso Méndez-Bravo [Mexique] ; Tianying Lan [États-Unis] ; Chunfang Zheng [Canada] ; Lorenzo Carretero-Paulet [Belgique] ; Claudia Anahí Perez-Torres [Mexique] ; Alejandra Chac N-L Pez [Mexique] ; Gustavo Hernandez-Guzmán [Mexique] ; Tien-Hao Chang [États-Unis] ; Kimberly M. Farr [États-Unis] ; W Brad Barbazuk [États-Unis] ; Srikar Chamala [États-Unis] ; Marek Mutwil ; Devendra Shivhare ; David Alvarez-Ponce [États-Unis] ; Neena Mitter [Australie] ; Alice Hayward [Australie] ; Stephen Fletcher [Australie] ; Julio Rozas [Espagne] ; Alejandro Sánchez Gracia [Espagne] ; David Kuhn [États-Unis] ; Alejandro F. Barrientos-Priego [Mexique] ; Jarkko Saloj Rvi ; Pablo Librado [Danemark, France] ; David Sankoff [Canada] ; Alfredo Herrera-Estrella [Mexique] ; Victor A. Albert [États-Unis] ; Luis Herrera-Estrella [États-Unis]Source :
- Proceedings of the National Academy of Sciences of the United States of America [ 1091-6490 ] ; 2019.
Descripteurs français
- KwdFr :
- ADN intergénique (MeSH), Colletotrichum (physiologie), Duplication de gène (MeSH), Génome végétal (MeSH), Interactions hôte-pathogène (génétique), Magnoliopsida (génétique), Magnoliopsida (microbiologie), Maladies des plantes (génétique), Maladies des plantes (microbiologie), Persea (génétique), Persea (microbiologie), Phylogenèse (MeSH).
- MESH :
- génétique : Interactions hôte-pathogène, Magnoliopsida, Maladies des plantes, Persea.
- microbiologie : Magnoliopsida, Maladies des plantes, Persea.
- physiologie : Colletotrichum.
- ADN intergénique, Duplication de gène, Génome végétal, Phylogenèse.
English descriptors
- KwdEn :
- Colletotrichum (physiology), DNA, Intergenic (MeSH), Gene Duplication (MeSH), Genetic Introgression (MeSH), Genome, Plant (MeSH), Host-Pathogen Interactions (genetics), Magnoliopsida (genetics), Magnoliopsida (microbiology), Persea (genetics), Persea (microbiology), Phylogeny (MeSH), Plant Diseases (genetics), Plant Diseases (microbiology).
- MESH :
- chemical : DNA, Intergenic.
- genetics : Host-Pathogen Interactions, Magnoliopsida, Persea, Plant Diseases.
- microbiology : Magnoliopsida, Persea, Plant Diseases.
- physiology : Colletotrichum.
- Gene Duplication, Genetic Introgression, Genome, Plant, Phylogeny.
Abstract
The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent "tuning knobs" in the genome adaptive landscapes of given species.
DOI: 10.1073/pnas.1822129116
PubMed: 31387975
PubMed Central: PMC6708331
Affiliations:
- Australie, Belgique, Canada, Danemark, Espagne, France, Mexique, Suède, États-Unis
- Catalogne, Floride, Hovedstaden, Midi-Pyrénées, Nevada, Occitanie (région administrative), Texas, État de New York
- Barcelone, Buffalo (New York), Copenhague, Toulouse
- Université d'État de New York à Buffalo, Université de Barcelone
Links toward previous steps (curation, corpus...)
Le document en format XML
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Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, 58190 Morelia, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Escuela Nacional de Estudios Superiores, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, 58190 Morelia</wicri:regionArea><wicri:noRegion>58190 Morelia</wicri:noRegion></affiliation></author><author><name sortKey="Lan, Tianying" sort="Lan, Tianying" uniqKey="Lan T" first="Tianying" last="Lan">Tianying Lan</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:cityArea></affiliation></author><author><name sortKey="Zheng, Chunfang" sort="Zheng, Chunfang" uniqKey="Zheng C" first="Chunfang" last="Zheng">Chunfang Zheng</name><affiliation wicri:level="1"><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada K1N 6N5.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Carretero Paulet, Lorenzo" sort="Carretero Paulet, Lorenzo" uniqKey="Carretero Paulet L" first="Lorenzo" last="Carretero-Paulet">Lorenzo Carretero-Paulet</name><affiliation wicri:level="1"><nlm:affiliation>Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), University of Ghent, 9052 Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), University of Ghent, 9052 Ghent</wicri:regionArea><wicri:noRegion>9052 Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Perez Torres, Claudia Anahi" sort="Perez Torres, Claudia Anahi" uniqKey="Perez Torres C" first="Claudia Anahí" last="Perez-Torres">Claudia Anahí Perez-Torres</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa</wicri:regionArea><wicri:noRegion>91070 Xalapa</wicri:noRegion></affiliation></author><author><name sortKey="Chac N L Pez, Alejandra" sort="Chac N L Pez, Alejandra" uniqKey="Chac N L Pez A" first="Alejandra" last="Chac N-L Pez">Alejandra Chac N-L Pez</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation></author><author><name sortKey="Hernandez Guzman, Gustavo" sort="Hernandez Guzman, Gustavo" uniqKey="Hernandez Guzman G" first="Gustavo" last="Hernandez-Guzmán">Gustavo Hernandez-Guzmán</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Departamento de Alimentos, Universidad de Guanajuato, 36500 Irapuato, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Departamento de Alimentos, Universidad de Guanajuato, 36500 Irapuato</wicri:regionArea><wicri:noRegion>36500 Irapuato</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>División de Ciencias de la Vida, Universidad de Guanajuato, 36500 Irapuato, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>División de Ciencias de la Vida, Universidad de Guanajuato, 36500 Irapuato</wicri:regionArea><wicri:noRegion>36500 Irapuato</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Tien Hao" sort="Chang, Tien Hao" uniqKey="Chang T" first="Tien-Hao" last="Chang">Tien-Hao Chang</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:cityArea></affiliation></author><author><name sortKey="Farr, Kimberly M" sort="Farr, Kimberly M" uniqKey="Farr K" first="Kimberly M" last="Farr">Kimberly M. Farr</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:cityArea></affiliation></author><author><name sortKey="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W Brad" last="Barbazuk">W Brad Barbazuk</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, FL 32611.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Department of Biology, University of Florida, Gainesville</wicri:cityArea></affiliation></author><author><name sortKey="Chamala, Srikar" sort="Chamala, Srikar" uniqKey="Chamala S" first="Srikar" last="Chamala">Srikar Chamala</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville</wicri:cityArea></affiliation></author><author><name sortKey="Mutwil, Marek" sort="Mutwil, Marek" uniqKey="Mutwil M" first="Marek" last="Mutwil">Marek Mutwil</name><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Shivhare, Devendra" sort="Shivhare, Devendra" uniqKey="Shivhare D" first="Devendra" last="Shivhare">Devendra Shivhare</name><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Alvarez Ponce, David" sort="Alvarez Ponce, David" uniqKey="Alvarez Ponce D" first="David" last="Alvarez-Ponce">David Alvarez-Ponce</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Nevada, Reno, NV 89557.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Nevada</region></placeName><wicri:cityArea>Department of Biology, University of Nevada, Reno</wicri:cityArea></affiliation></author><author><name sortKey="Mitter, Neena" sort="Mitter, Neena" uniqKey="Mitter N" first="Neena" last="Mitter">Neena Mitter</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Hayward, Alice" sort="Hayward, Alice" uniqKey="Hayward A" first="Alice" last="Hayward">Alice Hayward</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Fletcher, Stephen" sort="Fletcher, Stephen" uniqKey="Fletcher S" first="Stephen" last="Fletcher">Stephen Fletcher</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Rozas, Julio" sort="Rozas, Julio" uniqKey="Rozas J" first="Julio" last="Rozas">Julio Rozas</name><affiliation wicri:level="4"><nlm:affiliation>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation></author><author><name sortKey="Sanchez Gracia, Alejandro" sort="Sanchez Gracia, Alejandro" uniqKey="Sanchez Gracia A" first="Alejandro" last="Sánchez Gracia">Alejandro Sánchez Gracia</name><affiliation wicri:level="4"><nlm:affiliation>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation></author><author><name sortKey="Kuhn, David" sort="Kuhn, David" uniqKey="Kuhn D" first="David" last="Kuhn">David Kuhn</name><affiliation wicri:level="2"><nlm:affiliation>Subtropical Horticulture Research Station, Agricultural Research Service, US Department of Agriculture, Miami, FL 33158.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Subtropical Horticulture Research Station, Agricultural Research Service, US Department of Agriculture, Miami</wicri:cityArea></affiliation></author><author><name sortKey="Barrientos Priego, Alejandro F" sort="Barrientos Priego, Alejandro F" uniqKey="Barrientos Priego A" first="Alejandro F" last="Barrientos-Priego">Alejandro F. Barrientos-Priego</name><affiliation wicri:level="1"><nlm:affiliation>Posgrado en Horticultura, Departamento de Fitotecnia, Universidad Autónoma Chapingo, 56230 Texcoco, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Posgrado en Horticultura, Departamento de Fitotecnia, Universidad Autónoma Chapingo, 56230 Texcoco</wicri:regionArea><wicri:noRegion>56230 Texcoco</wicri:noRegion></affiliation></author><author><name sortKey="Saloj Rvi, Jarkko" sort="Saloj Rvi, Jarkko" uniqKey="Saloj Rvi J" first="Jarkko" last="Saloj Rvi">Jarkko Saloj Rvi</name><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Librado, Pablo" sort="Librado, Pablo" uniqKey="Librado P" first="Pablo" last="Librado">Pablo Librado</name><affiliation wicri:level="1"><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, 1017 Copenhagen, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, 1017 Copenhagen</wicri:regionArea><placeName><settlement type="city">Copenhague</settlement><region type="région" nuts="2">Hovedstaden</region></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS Unité Mixte de Recherche 5288, Université de Toulouse, Université Paul Sabatier, 31330 Toulouse, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS Unité Mixte de Recherche 5288, Université de Toulouse, Université Paul Sabatier, 31330 Toulouse</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Toulouse</settlement></placeName></affiliation></author><author><name sortKey="Sankoff, David" sort="Sankoff, David" uniqKey="Sankoff D" first="David" last="Sankoff">David Sankoff</name><affiliation wicri:level="1"><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada K1N 6N5.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Herrera Estrella, Alfredo" sort="Herrera Estrella, Alfredo" uniqKey="Herrera Estrella A" first="Alfredo" last="Herrera-Estrella">Alfredo Herrera-Estrella</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation></author><author><name sortKey="Albert, Victor A" sort="Albert, Victor A" uniqKey="Albert V" first="Victor A" last="Albert">Victor A. Albert</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260; vaalbert@buffalo.edu lherrerae@cinvestav.mx.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:regionArea><orgName type="university">Université d'État de New York à Buffalo</orgName><placeName><settlement type="city">Buffalo (New York)</settlement><region type="state">État de New York</region></placeName></affiliation><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Herrera Estrella, Luis" sort="Herrera Estrella, Luis" uniqKey="Herrera Estrella L" first="Luis" last="Herrera-Estrella">Luis Herrera-Estrella</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México; vaalbert@buffalo.edu lherrerae@cinvestav.mx.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Plant and Soil Science, Texas Tech University, Lubbock</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:31387975</idno><idno type="pmid">31387975</idno><idno type="doi">10.1073/pnas.1822129116</idno><idno type="pmc">PMC6708331</idno><idno type="wicri:Area/Main/Corpus">000413</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000413</idno><idno type="wicri:Area/Main/Curation">000413</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000413</idno><idno type="wicri:Area/Main/Exploration">000413</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.</title><author><name sortKey="Rend N Anaya, Martha" sort="Rend N Anaya, Martha" uniqKey="Rend N Anaya M" first="Martha" last="Rend N-Anaya">Martha Rend N-Anaya</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-750 07 Uppsala</wicri:regionArea><wicri:noRegion>SE-750 07 Uppsala</wicri:noRegion></affiliation></author><author><name sortKey="Ibarra Laclette, Enrique" sort="Ibarra Laclette, Enrique" uniqKey="Ibarra Laclette E" first="Enrique" last="Ibarra-Laclette">Enrique Ibarra-Laclette</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa</wicri:regionArea><wicri:noRegion>91070 Xalapa</wicri:noRegion></affiliation></author><author><name sortKey="Mendez Bravo, Alfonso" sort="Mendez Bravo, Alfonso" uniqKey="Mendez Bravo A" first="Alfonso" last="Méndez-Bravo">Alfonso Méndez-Bravo</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Escuela Nacional de Estudios Superiores, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, 58190 Morelia, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Escuela Nacional de Estudios Superiores, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, 58190 Morelia</wicri:regionArea><wicri:noRegion>58190 Morelia</wicri:noRegion></affiliation></author><author><name sortKey="Lan, Tianying" sort="Lan, Tianying" uniqKey="Lan T" first="Tianying" last="Lan">Tianying Lan</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:cityArea></affiliation></author><author><name sortKey="Zheng, Chunfang" sort="Zheng, Chunfang" uniqKey="Zheng C" first="Chunfang" last="Zheng">Chunfang Zheng</name><affiliation wicri:level="1"><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada K1N 6N5.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Carretero Paulet, Lorenzo" sort="Carretero Paulet, Lorenzo" uniqKey="Carretero Paulet L" first="Lorenzo" last="Carretero-Paulet">Lorenzo Carretero-Paulet</name><affiliation wicri:level="1"><nlm:affiliation>Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), University of Ghent, 9052 Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), University of Ghent, 9052 Ghent</wicri:regionArea><wicri:noRegion>9052 Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Perez Torres, Claudia Anahi" sort="Perez Torres, Claudia Anahi" uniqKey="Perez Torres C" first="Claudia Anahí" last="Perez-Torres">Claudia Anahí Perez-Torres</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa</wicri:regionArea><wicri:noRegion>91070 Xalapa</wicri:noRegion></affiliation></author><author><name sortKey="Chac N L Pez, Alejandra" sort="Chac N L Pez, Alejandra" uniqKey="Chac N L Pez A" first="Alejandra" last="Chac N-L Pez">Alejandra Chac N-L Pez</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation></author><author><name sortKey="Hernandez Guzman, Gustavo" sort="Hernandez Guzman, Gustavo" uniqKey="Hernandez Guzman G" first="Gustavo" last="Hernandez-Guzmán">Gustavo Hernandez-Guzmán</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Departamento de Alimentos, Universidad de Guanajuato, 36500 Irapuato, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Departamento de Alimentos, Universidad de Guanajuato, 36500 Irapuato</wicri:regionArea><wicri:noRegion>36500 Irapuato</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>División de Ciencias de la Vida, Universidad de Guanajuato, 36500 Irapuato, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>División de Ciencias de la Vida, Universidad de Guanajuato, 36500 Irapuato</wicri:regionArea><wicri:noRegion>36500 Irapuato</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Tien Hao" sort="Chang, Tien Hao" uniqKey="Chang T" first="Tien-Hao" last="Chang">Tien-Hao Chang</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:cityArea></affiliation></author><author><name sortKey="Farr, Kimberly M" sort="Farr, Kimberly M" uniqKey="Farr K" first="Kimberly M" last="Farr">Kimberly M. Farr</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:cityArea></affiliation></author><author><name sortKey="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W Brad" last="Barbazuk">W Brad Barbazuk</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, FL 32611.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Department of Biology, University of Florida, Gainesville</wicri:cityArea></affiliation></author><author><name sortKey="Chamala, Srikar" sort="Chamala, Srikar" uniqKey="Chamala S" first="Srikar" last="Chamala">Srikar Chamala</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville</wicri:cityArea></affiliation></author><author><name sortKey="Mutwil, Marek" sort="Mutwil, Marek" uniqKey="Mutwil M" first="Marek" last="Mutwil">Marek Mutwil</name><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Shivhare, Devendra" sort="Shivhare, Devendra" uniqKey="Shivhare D" first="Devendra" last="Shivhare">Devendra Shivhare</name><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Alvarez Ponce, David" sort="Alvarez Ponce, David" uniqKey="Alvarez Ponce D" first="David" last="Alvarez-Ponce">David Alvarez-Ponce</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Nevada, Reno, NV 89557.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Nevada</region></placeName><wicri:cityArea>Department of Biology, University of Nevada, Reno</wicri:cityArea></affiliation></author><author><name sortKey="Mitter, Neena" sort="Mitter, Neena" uniqKey="Mitter N" first="Neena" last="Mitter">Neena Mitter</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Hayward, Alice" sort="Hayward, Alice" uniqKey="Hayward A" first="Alice" last="Hayward">Alice Hayward</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Fletcher, Stephen" sort="Fletcher, Stephen" uniqKey="Fletcher S" first="Stephen" last="Fletcher">Stephen Fletcher</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Rozas, Julio" sort="Rozas, Julio" uniqKey="Rozas J" first="Julio" last="Rozas">Julio Rozas</name><affiliation wicri:level="4"><nlm:affiliation>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation></author><author><name sortKey="Sanchez Gracia, Alejandro" sort="Sanchez Gracia, Alejandro" uniqKey="Sanchez Gracia A" first="Alejandro" last="Sánchez Gracia">Alejandro Sánchez Gracia</name><affiliation wicri:level="4"><nlm:affiliation>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université de Barcelone</orgName></affiliation></author><author><name sortKey="Kuhn, David" sort="Kuhn, David" uniqKey="Kuhn D" first="David" last="Kuhn">David Kuhn</name><affiliation wicri:level="2"><nlm:affiliation>Subtropical Horticulture Research Station, Agricultural Research Service, US Department of Agriculture, Miami, FL 33158.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Subtropical Horticulture Research Station, Agricultural Research Service, US Department of Agriculture, Miami</wicri:cityArea></affiliation></author><author><name sortKey="Barrientos Priego, Alejandro F" sort="Barrientos Priego, Alejandro F" uniqKey="Barrientos Priego A" first="Alejandro F" last="Barrientos-Priego">Alejandro F. Barrientos-Priego</name><affiliation wicri:level="1"><nlm:affiliation>Posgrado en Horticultura, Departamento de Fitotecnia, Universidad Autónoma Chapingo, 56230 Texcoco, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Posgrado en Horticultura, Departamento de Fitotecnia, Universidad Autónoma Chapingo, 56230 Texcoco</wicri:regionArea><wicri:noRegion>56230 Texcoco</wicri:noRegion></affiliation></author><author><name sortKey="Saloj Rvi, Jarkko" sort="Saloj Rvi, Jarkko" uniqKey="Saloj Rvi J" first="Jarkko" last="Saloj Rvi">Jarkko Saloj Rvi</name><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Librado, Pablo" sort="Librado, Pablo" uniqKey="Librado P" first="Pablo" last="Librado">Pablo Librado</name><affiliation wicri:level="1"><nlm:affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, 1017 Copenhagen, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Centre for GeoGenetics, Natural History Museum of Denmark, 1017 Copenhagen</wicri:regionArea><placeName><settlement type="city">Copenhague</settlement><region type="région" nuts="2">Hovedstaden</region></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS Unité Mixte de Recherche 5288, Université de Toulouse, Université Paul Sabatier, 31330 Toulouse, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS Unité Mixte de Recherche 5288, Université de Toulouse, Université Paul Sabatier, 31330 Toulouse</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Midi-Pyrénées</region><settlement type="city">Toulouse</settlement></placeName></affiliation></author><author><name sortKey="Sankoff, David" sort="Sankoff, David" uniqKey="Sankoff D" first="David" last="Sankoff">David Sankoff</name><affiliation wicri:level="1"><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada K1N 6N5.</nlm:affiliation><country>Canada</country><wicri:regionArea>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author><author><name sortKey="Herrera Estrella, Alfredo" sort="Herrera Estrella, Alfredo" uniqKey="Herrera Estrella A" first="Alfredo" last="Herrera-Estrella">Alfredo Herrera-Estrella</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation></author><author><name sortKey="Albert, Victor A" sort="Albert, Victor A" uniqKey="Albert V" first="Victor A" last="Albert">Victor A. Albert</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260; vaalbert@buffalo.edu lherrerae@cinvestav.mx.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Biological Sciences, University at Buffalo, Buffalo</wicri:regionArea><orgName type="university">Université d'État de New York à Buffalo</orgName><placeName><settlement type="city">Buffalo (New York)</settlement><region type="state">État de New York</region></placeName></affiliation><affiliation><nlm:affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</nlm:affiliation><wicri:noCountry code="subField">Singapore 637551</wicri:noCountry></affiliation></author><author><name sortKey="Herrera Estrella, Luis" sort="Herrera Estrella, Luis" uniqKey="Herrera Estrella L" first="Luis" last="Herrera-Estrella">Luis Herrera-Estrella</name><affiliation wicri:level="1"><nlm:affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México; vaalbert@buffalo.edu lherrerae@cinvestav.mx.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821</wicri:regionArea><wicri:noRegion>Irapuato 36821</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Plant and Soil Science, Texas Tech University, Lubbock</wicri:cityArea></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="eISSN">1091-6490</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Colletotrichum (physiology)</term><term>DNA, Intergenic (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Genetic Introgression (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Host-Pathogen Interactions (genetics)</term><term>Magnoliopsida (genetics)</term><term>Magnoliopsida (microbiology)</term><term>Persea (genetics)</term><term>Persea (microbiology)</term><term>Phylogeny (MeSH)</term><term>Plant Diseases (genetics)</term><term>Plant Diseases (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN intergénique (MeSH)</term><term>Colletotrichum (physiologie)</term><term>Duplication de gène (MeSH)</term><term>Génome végétal (MeSH)</term><term>Interactions hôte-pathogène (génétique)</term><term>Magnoliopsida (génétique)</term><term>Magnoliopsida (microbiologie)</term><term>Maladies des plantes (génétique)</term><term>Maladies des plantes (microbiologie)</term><term>Persea (génétique)</term><term>Persea (microbiologie)</term><term>Phylogenèse (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA, Intergenic</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Host-Pathogen Interactions</term><term>Magnoliopsida</term><term>Persea</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Interactions hôte-pathogène</term><term>Magnoliopsida</term><term>Maladies des plantes</term><term>Persea</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Magnoliopsida</term><term>Maladies des plantes</term><term>Persea</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Magnoliopsida</term><term>Persea</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Colletotrichum</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Colletotrichum</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Duplication</term><term>Genetic Introgression</term><term>Genome, Plant</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN intergénique</term><term>Duplication de gène</term><term>Génome végétal</term><term>Phylogenèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The avocado, <i>Persea americana</i>, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, <i>P. americana</i> var. <i>drymifolia</i>, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by <i>Colletotrichum</i> (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent "tuning knobs" in the genome adaptive landscapes of given species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31387975</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>23</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1091-6490</ISSN><JournalIssue CitedMedium="Internet"><Volume>116</Volume><Issue>34</Issue><PubDate><Year>2019</Year><Month>08</Month><Day>20</Day></PubDate></JournalIssue><Title>Proceedings of the National Academy of Sciences of the United States of America</Title><ISOAbbreviation>Proc Natl Acad Sci U S A</ISOAbbreviation></Journal><ArticleTitle>The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.</ArticleTitle><Pagination><MedlinePgn>17081-17089</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1073/pnas.1822129116</ELocationID><Abstract><AbstractText>The avocado, <i>Persea americana</i>, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, <i>P. americana</i> var. <i>drymifolia</i>, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by <i>Colletotrichum</i> (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent "tuning knobs" in the genome adaptive landscapes of given species.</AbstractText><CopyrightInformation>Copyright © 2019 the Author(s). Published by PNAS.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rendón-Anaya</LastName><ForeName>Martha</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ibarra-Laclette</LastName><ForeName>Enrique</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa, México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Méndez-Bravo</LastName><ForeName>Alfonso</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0002-0991-5464</Identifier><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Escuela Nacional de Estudios Superiores, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, 58190 Morelia, México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lan</LastName><ForeName>Tianying</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Chunfang</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada K1N 6N5.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carretero-Paulet</LastName><ForeName>Lorenzo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), University of Ghent, 9052 Ghent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Perez-Torres</LastName><ForeName>Claudia Anahí</ForeName><Initials>CA</Initials><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070 Xalapa, México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chacón-López</LastName><ForeName>Alejandra</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hernandez-Guzmán</LastName><ForeName>Gustavo</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Departamento de Alimentos, Universidad de Guanajuato, 36500 Irapuato, México.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>División de Ciencias de la Vida, Universidad de Guanajuato, 36500 Irapuato, México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Tien-Hao</ForeName><Initials>TH</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Farr</LastName><ForeName>Kimberly M</ForeName><Initials>KM</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barbazuk</LastName><ForeName>W Brad</ForeName><Initials>WB</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Florida, Gainesville, FL 32611.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chamala</LastName><ForeName>Srikar</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mutwil</LastName><ForeName>Marek</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shivhare</LastName><ForeName>Devendra</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alvarez-Ponce</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Nevada, Reno, NV 89557.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mitter</LastName><ForeName>Neena</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hayward</LastName><ForeName>Alice</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fletcher</LastName><ForeName>Stephen</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rozas</LastName><ForeName>Julio</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona, Spain.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sánchez Gracia</LastName><ForeName>Alejandro</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0003-4543-4577</Identifier><AffiliationInfo><Affiliation>Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08007 Barcelona, Spain.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Recerca de la Biodiversitat, Universitat de Barcelona, 08007 Barcelona, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kuhn</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Subtropical Horticulture Research Station, Agricultural Research Service, US Department of Agriculture, Miami, FL 33158.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barrientos-Priego</LastName><ForeName>Alejandro F</ForeName><Initials>AF</Initials><AffiliationInfo><Affiliation>Posgrado en Horticultura, Departamento de Fitotecnia, Universidad Autónoma Chapingo, 56230 Texcoco, México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salojärvi</LastName><ForeName>Jarkko</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Librado</LastName><ForeName>Pablo</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Centre for GeoGenetics, Natural History Museum of Denmark, 1017 Copenhagen, Denmark.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS Unité Mixte de Recherche 5288, Université de Toulouse, Université Paul Sabatier, 31330 Toulouse, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sankoff</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada K1N 6N5.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Herrera-Estrella</LastName><ForeName>Alfredo</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Albert</LastName><ForeName>Victor A</ForeName><Initials>VA</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260; vaalbert@buffalo.edu lherrerae@cinvestav.mx.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Biological Sciences, Nanyang Technological University, Singapore 637551.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Herrera-Estrella</LastName><ForeName>Luis</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Unidad de Genomica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados, Irapuato 36821, México; vaalbert@buffalo.edu lherrerae@cinvestav.mx.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>SDXN00000000</AccessionNumber><AccessionNumber>SDSS00000000</AccessionNumber><AccessionNumber>SDXN01000000</AccessionNumber><AccessionNumber>SDSS01000000</AccessionNumber></AccessionNumberList></DataBank></DataBankList><GrantList CompleteYN="Y"><Grant><GrantID>55005946</GrantID><Acronym>HHMI</Acronym><Agency>Howard Hughes Medical Institute</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>08</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Proc Natl Acad Sci U S A</MedlineTA><NlmUniqueID>7505876</NlmUniqueID><ISSNLinking>0027-8424</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021901">DNA, Intergenic</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020231" MajorTopicYN="N">Colletotrichum</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021901" MajorTopicYN="Y">DNA, Intergenic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000079425" MajorTopicYN="Y">Genetic Introgression</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054884" MajorTopicYN="N">Host-Pathogen Interactions</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019684" MajorTopicYN="Y">Magnoliopsida</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D027421" MajorTopicYN="Y">Persea</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="Y">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Phytophthora</Keyword><Keyword MajorTopicYN="Y">angiosperm phylogeny</Keyword><Keyword MajorTopicYN="Y">avocado genome</Keyword><Keyword MajorTopicYN="Y">genome duplications</Keyword><Keyword MajorTopicYN="Y">genome evolution</Keyword></KeywordList><CoiStatement>The authors declare no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>8</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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