A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Persistent Link:
http://hdl.handle.net/10150/610149
Title:
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
Author:
Zuccolo, Andrea; Bowers, John; Estill, James; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, Jose; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; Duarte, Jill; Tang, Haibao; Ayyampalayam, Saravanaraj; Rounsley, Steve; Kudrna, Dave; Paterson, Andrew; Pires, J.; Chanderbali, Andre; Soltis, Douglas; Chamala, Srikar; Barbazuk, Brad; Soltis, Pamela; Albert, Victor; Ma, Hong; Mandoli, Dina; Banks, Jody; Carlson, John; Tomkins, Jeffrey; dePamphilis, Claude; Wing, Rod; Leebens-Mack, Jim
Affiliation:
Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA; Department of Plant Biology, University of Georgia, 4504 Miller Plant Sciences, Athens, GA 30602, USA; Department of Biological Sciences, University of Missouri, 371B Life Sciences Center, Columbia, MO 65211, USA; College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Intercollege Graduate Degree Program in Plant Biology and Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, 405 Life Sciences Building, University Park, Pennsylvania 16802, USA; Department of Plant and Microbiology, College of Natural Resources, University of California, 311 Koshland Hall, Berkeley 94709, CA, USA; Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30605, USA; School of Plant Sciences and BIO5, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA; Dow Agrosciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA; Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA; Florida Museum of Natural History, Museum Road and Newell Drive, University of Florida, Gainesville, FL 32611, USA; Department of Biological Sciences, University at Buffalo (SUNY), 637 Hochstetter Hall, Buffalo, NY 14260, USA; State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Plant Biology, Center for Evolutionary Biology, and Institutes of Biomedical Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China; Northern Lights, 4500 NE 40th Street, Seattle WA 98105, USA; Department of Botany and Plant Pathology, Purdue University, B028 Whistler Hall, West Lafayette, IN 47906, USA; School of Forest Resources, The Pennsylvania State University, 323 Forest Resources Building, University Park, PA 16802, USA; Clemson University Genomics Institute, Clemson University, 51 Cherry St, Clemson, NC 29634, USA
Issue Date:
2011
Publisher:
BioMed Central
Citation:
Zuccolo et al. Genome Biology 2011, 12:R48 http://genomebiology.com/2011/12/5/R48
Journal:
Genome Biology
Rights:
© 2011 Zuccolo et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.RESULTS:Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.CONCLUSIONS:When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.
DOI:
10.1186/gb-2011-12-5-r48
Version:
Final published version
Additional Links:
http://genomebiology.com/2011/12/5/R48

Full metadata record

DC FieldValue Language
dc.contributor.authorZuccolo, Andreaen
dc.contributor.authorBowers, Johnen
dc.contributor.authorEstill, Jamesen
dc.contributor.authorXiong, Zhiyongen
dc.contributor.authorLuo, Meizhongen
dc.contributor.authorSebastian, Aswathyen
dc.contributor.authorGoicoechea, Joseen
dc.contributor.authorCollura, Kristien
dc.contributor.authorYu, Yeisooen
dc.contributor.authorJiao, Yuannianen
dc.contributor.authorDuarte, Jillen
dc.contributor.authorTang, Haibaoen
dc.contributor.authorAyyampalayam, Saravanarajen
dc.contributor.authorRounsley, Steveen
dc.contributor.authorKudrna, Daveen
dc.contributor.authorPaterson, Andrewen
dc.contributor.authorPires, J.en
dc.contributor.authorChanderbali, Andreen
dc.contributor.authorSoltis, Douglasen
dc.contributor.authorChamala, Srikaren
dc.contributor.authorBarbazuk, Braden
dc.contributor.authorSoltis, Pamelaen
dc.contributor.authorAlbert, Victoren
dc.contributor.authorMa, Hongen
dc.contributor.authorMandoli, Dinaen
dc.contributor.authorBanks, Jodyen
dc.contributor.authorCarlson, Johnen
dc.contributor.authorTomkins, Jeffreyen
dc.contributor.authordePamphilis, Claudeen
dc.contributor.authorWing, Roden
dc.contributor.authorLeebens-Mack, Jimen
dc.date.accessioned2016-05-20T08:59:39Z-
dc.date.available2016-05-20T08:59:39Z-
dc.date.issued2011en
dc.identifier.citationZuccolo et al. Genome Biology 2011, 12:R48 http://genomebiology.com/2011/12/5/R48en
dc.identifier.doi10.1186/gb-2011-12-5-r48en
dc.identifier.urihttp://hdl.handle.net/10150/610149-
dc.description.abstractBACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.RESULTS:Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.CONCLUSIONS:When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://genomebiology.com/2011/12/5/R48en
dc.rights© 2011 Zuccolo et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleA physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structureen
dc.typeArticleen
dc.contributor.departmentArizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USAen
dc.contributor.departmentDepartment of Plant Biology, University of Georgia, 4504 Miller Plant Sciences, Athens, GA 30602, USAen
dc.contributor.departmentDepartment of Biological Sciences, University of Missouri, 371B Life Sciences Center, Columbia, MO 65211, USAen
dc.contributor.departmentCollege of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, Chinaen
dc.contributor.departmentIntercollege Graduate Degree Program in Plant Biology and Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, 405 Life Sciences Building, University Park, Pennsylvania 16802, USAen
dc.contributor.departmentDepartment of Plant and Microbiology, College of Natural Resources, University of California, 311 Koshland Hall, Berkeley 94709, CA, USAen
dc.contributor.departmentPlant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30605, USAen
dc.contributor.departmentSchool of Plant Sciences and BIO5, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USAen
dc.contributor.departmentDow Agrosciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USAen
dc.contributor.departmentDepartment of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USAen
dc.contributor.departmentFlorida Museum of Natural History, Museum Road and Newell Drive, University of Florida, Gainesville, FL 32611, USAen
dc.contributor.departmentDepartment of Biological Sciences, University at Buffalo (SUNY), 637 Hochstetter Hall, Buffalo, NY 14260, USAen
dc.contributor.departmentState Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Plant Biology, Center for Evolutionary Biology, and Institutes of Biomedical Sciences, Fudan University, 220 Handan Road, Shanghai 200433, Chinaen
dc.contributor.departmentNorthern Lights, 4500 NE 40th Street, Seattle WA 98105, USAen
dc.contributor.departmentDepartment of Botany and Plant Pathology, Purdue University, B028 Whistler Hall, West Lafayette, IN 47906, USAen
dc.contributor.departmentSchool of Forest Resources, The Pennsylvania State University, 323 Forest Resources Building, University Park, PA 16802, USAen
dc.contributor.departmentClemson University Genomics Institute, Clemson University, 51 Cherry St, Clemson, NC 29634, USAen
dc.identifier.journalGenome Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
All Items in UA Campus Repository are protected by copyright, with all rights reserved, unless otherwise indicated.