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Huang K, Jahani M, Gouzy J, Legendre A, Carrere S, Lázaro-Guevara JM, González Segovia EG, Todesco M, Mayjonade B, Rodde N, Cauet S, Dufau I, Staton SE, Pouilly N, Boniface MC, Tapy C, Mangin B, Duhnen A, Gautier V, Poncet C, Donnadieu C, Mandel T, Hübner S, Burke JM, Vautrin S, Bellec A, Owens GL, Langlade N, Muños S, Rieseberg LH. The genomics of linkage drag in inbred lines of sunflower. Proc Natl Acad Sci U S A 2023; 120:e2205783119. [PMID: 36972449 PMCID: PMC10083583 DOI: 10.1073/pnas.2205783119] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.
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Affiliation(s)
- Kaichi Huang
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Alexandra Legendre
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - José Miguel Lázaro-Guevara
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Eric Gerardo González Segovia
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Marco Todesco
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Nathalie Rodde
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France
| | - Isabelle Dufau
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France
| | - S Evan Staton
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Research and Development Department, NRGene Canada Inc., Saskatoon, SK S7N 3R3, Canada
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Camille Tapy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Brigitte Mangin
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Alexandra Duhnen
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Véronique Gautier
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000 France
| | - Charles Poncet
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000 France
| | - Cécile Donnadieu
- Plateforme Génome et Transcriptome (GeT-PlaGe), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France
| | - Tali Mandel
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016 Israel
| | - Sariel Hübner
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016 Israel
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA 30602
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France
| | - Arnaud Bellec
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Nicolas Langlade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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McCouch S, Navabi ZK, Abberton M, Anglin NL, Barbieri RL, Baum M, Bett K, Booker H, Brown GL, Bryan GJ, Cattivelli L, Charest D, Eversole K, Freitas M, Ghamkhar K, Grattapaglia D, Henry R, Valadares Inglis MC, Islam T, Kehel Z, Kersey PJ, King GJ, Kresovich S, Marden E, Mayes S, Ndjiondjop MN, Nguyen HT, Paiva SR, Papa R, Phillips PWB, Rasheed A, Richards C, Rouard M, Amstalden Sampaio MJ, Scholz U, Shaw PD, Sherman B, Staton SE, Stein N, Svensson J, Tester M, Montenegro Valls JF, Varshney R, Visscher S, von Wettberg E, Waugh R, Wenzl P, Rieseberg LH. Mobilizing Crop Biodiversity. Mol Plant 2020; 13:1341-1344. [PMID: 32835887 DOI: 10.1016/j.molp.2020.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
- Susan McCouch
- Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Zahra Katy Navabi
- DivSeek, Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, Nigeria
| | - Noelle L Anglin
- International Potato Center (CIP) 1895 Avenida La Molina, Lima Peru 12, Lima 15023, Peru
| | - Rosa Lia Barbieri
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK S7N 5A8, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Rm 316, Crop Science Bldg, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - Gerald L Brown
- Genome Prairie, 111 Research Drive, Suite 101, Saskatoon, SK, S7N 3R2, Canada
| | - Glenn J Bryan
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Luigi Cattivelli
- CREA, Research Centre for Genomics and Bioinformatics, via San Protaso 302, Fiorenzuola d'Arda, 29017, Italy
| | - David Charest
- Genome British Columbia, 400-575 West 8th Avenue, Vancouver, BC, V5Z 0C4, Canada
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee's Summit, MO, 64086, USA
| | - Marcelo Freitas
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Kioumars Ghamkhar
- Forage Science, Grasslands Research Centre, AgResearch, Palmerston North, 4410, New Zealand
| | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maria Cleria Valadares Inglis
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Graham J King
- Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Stephen Kresovich
- Feed the Future Innovation Lab for Crop Improvement, 431 Weill Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Marden
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Sean Mayes
- Crops For the Future (UK) CIC 76-80 Baddow Road, Chelmsford, Essex, CM2 7PJ, UK
| | - Marie Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Mbe Research Station, Bouaké, 01 BP 2511 Bouaké, Côte d'Ivoire
| | - Henry T Nguyen
- University of Missouri, Division of Plant Sciences, 25 Agriculture Lab Bldg, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Samuel Rezende Paiva
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Roberto Papa
- Università Politecnica delle Marche, D3A-Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Via Brecce Bianche, 60131, Ancona, Italy
| | - Peter W B Phillips
- Johnson Shoyama Graduate School of Public Policy, University of Saskatchewan, 101 Diefenbaker Place, Saskatoon, S7N 5B8, Canada
| | - Awais Rasheed
- CIMMYT-China office, Beijing 100081, Beijing, P.R. China
| | - Christopher Richards
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason St, Fort Collins, CO, 80521, USA
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Maria Jose Amstalden Sampaio
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany
| | - Paul D Shaw
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Brad Sherman
- Law School, University of Queensland, St Lucia, QLD, 4072, Australia
| | - S Evan Staton
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; CiBreed - Center for Integrated Breeding Research, Department of Crop Sciences, Georg-August University Göttingen, Von Siebold Straße 8, D-37075 Göttingen, Germany
| | | | - Mark Tester
- King Abdullah University of Science & Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jose Francisco Montenegro Valls
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Rajeev Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru - 502 324, Telangana State, India
| | - Stephen Visscher
- Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Eric von Wettberg
- University of Vermont, 63 Carrigan Drive, Jeffords Hall, Burlington, VT, 05405, USA
| | - Robbie Waugh
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Peter Wenzl
- Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, 763537 Cali, Colombia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada.
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Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Muños S, Bendahmane A, Bergès H, Niebel A, Buitink J, Frugier F, Benhamed M, Crespi M, Gouzy J, Gamas P. Whole-genome landscape of Medicago truncatula symbiotic genes. Nat Plants 2018; 4:1017-1025. [PMID: 30397259 DOI: 10.1038/s41477-018-0286-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 09/21/2018] [Indexed: 05/07/2023]
Abstract
Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.
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Affiliation(s)
- Yann Pecrix
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Erika Sallet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Christine Lelandais-Brière
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Sandra Moreau
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Thomas Blein
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | | | - David Latrasse
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Mohamed Zouine
- GBF, Université de Toulouse, INPT, ENSAT, Castanet-Tolosan, France
| | - Margot Zahm
- GBF, Université de Toulouse, INPT, ENSAT, Castanet-Tolosan, France
| | | | | | - Carine Satgé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- CNRGV, INRA, Castanet-Tolosan, France
| | - Magali Perez
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | | | | | | | | | | | - Aurélie Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - Frédéric Debellé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Abdelhafid Bendahmane
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | | | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Julia Buitink
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, Beaucouzé, France
| | - Florian Frugier
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Moussa Benhamed
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Martin Crespi
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
| | - Pascal Gamas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
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Staton SE, Burke JM. Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance. BMC Genomics 2015; 16:623. [PMID: 26290182 PMCID: PMC4546089 DOI: 10.1186/s12864-015-1830-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The transposable element (TE) content of the genomes of plant species varies from near zero in the genome of Utricularia gibba to more than 80% in many species. It is not well understood whether this variation in genome composition results from common mechanisms or stochastic variation. The major obstacles to investigating mechanisms of TE evolution have been a lack of comparative genomic data sets and efficient computational methods for measuring differences in TE composition between species. In this study, we describe patterns of TE evolution in 14 species in the flowering plant family Asteraceae and 1 outgroup species in the Calyceraceae to investigate phylogenetic patterns of TE dynamics in this important group of plants. RESULTS Our findings indicate that TE families in the Asteraceae exhibit distinct patterns of non-neutral evolution, and that there has been a directional increase in copy number of Gypsy retrotransposons since the origin of the Asteraceae. Specifically, there is marked increase in Gypsy abundance at the origin of the Asteraceae and at the base of the tribe Heliantheae. This latter shift in genome composition has had a significant impact on the diversity and abundance distribution of TEs in a lineage-specific manner. CONCLUSIONS We show that the TE-driven expansion of plant genomes can be facilitated by just a few TE families, and is likely accompanied by the modification and/or replacement of the TE community. Importantly, large shifts in TE composition may be correlated with major of phylogenetic transitions.
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Affiliation(s)
- S Evan Staton
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Current address: Beaty Biodiversity Research Centre and Department of Botany, 3529-6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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Staton SE, Burke JM. Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. ACTA ACUST UNITED AC 2015; 31:1827-9. [PMID: 25644271 DOI: 10.1093/bioinformatics/btv059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 06/26/2015] [Indexed: 11/12/2022]
Abstract
MOTIVATION Transposable elements (TEs) can be found in virtually all eukaryotic genomes and have the potential to produce evolutionary novelty. Despite the broad taxonomic distribution of TEs, the evolutionary history of these sequences is largely unknown for many taxa due to a lack of genomic resources and identification methods. Given that most TE annotation methods are designed to work on genome assemblies, we sought to develop a method to provide a fine-grained classification of TEs from DNA sequence reads. Here, we present a toolkit for the efficient annotation of TE families from low-coverage whole-genome shotgun (WGS) data, enabling the rapid identification of TEs in a large number of taxa. We compared our software, Transposome, with other approaches for annotating repeats from WGS data, and we show that it offers significant improvements in run time and produces more precise estimates of genomic repeat abundance. Transposome may also be used as a general toolkit for working with Next Generation Sequencing (NGS) data, and for constructing custom genome analysis pipelines. AVAILABILITY AND IMPLEMENTATION The source code for Transposome is freely available (http://sestaton.github.io/Transposome), implemented in Perl and is supported on Linux.
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Affiliation(s)
- S Evan Staton
- Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - John M Burke
- Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Mandel JR, Dikow RB, Funk VA, Masalia RR, Staton SE, Kozik A, Michelmore RW, Rieseberg LH, Burke JM. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae. Appl Plant Sci 2014; 2:apps.1300085. [PMID: 25202605 PMCID: PMC4103609 DOI: 10.3732/apps.1300085] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/13/2014] [Indexed: 05/18/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. • METHODS AND RESULTS We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. • CONCLUSIONS These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
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Affiliation(s)
- Jennifer R. Mandel
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152 USA
| | - Rebecca B. Dikow
- Center for Conservation and Evolutionary Genetics, National Zoological Park and Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Vicki A. Funk
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Rishi R. Masalia
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
| | - S. Evan Staton
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
| | - Alex Kozik
- The Genome Center, University of California, Davis, California 95616 USA
| | | | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - John M. Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
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Mandel JR, Dikow RB, Funk VA, Masalia RR, Staton SE, Kozik A, Michelmore RW, Rieseberg LH, Burke JM. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae. Appl Plant Sci 2014. [PMID: 25202605 DOI: 10.5061/dryad.gr93t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. • METHODS AND RESULTS We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. • CONCLUSIONS These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
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Affiliation(s)
- Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152 USA
| | - Rebecca B Dikow
- Center for Conservation and Evolutionary Genetics, National Zoological Park and Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Rishi R Masalia
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
| | - S Evan Staton
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
| | - Alex Kozik
- The Genome Center, University of California, Davis, California 95616 USA
| | | | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
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Staton SE, Bakken BH, Blackman BK, Chapman MA, Kane NC, Tang S, Ungerer MC, Knapp SJ, Rieseberg LH, Burke JM. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant J 2012; 72:142-53. [PMID: 22691070 DOI: 10.1111/j.1365-313x.2012.05072.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.
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Affiliation(s)
- S Evan Staton
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Staton SE, Ungerer MC, Moore RC. The genomic organization of Ty3/gypsy-like retrotransposons in Helianthus (Asteraceae) homoploid hybrid species. Am J Bot 2009; 96:1646-1655. [PMID: 21622351 DOI: 10.3732/ajb.0800337] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The origin of new diploid, or homoploid, hybrid species is associated with rapid genomic restructuring in the hybrid neospecies. This mode of speciation has been best characterized in wild sunflower species in the genus Helianthus, where three homoploid hybrid species (H. anomalus, H. deserticola, and H. paradoxus) have independently arisen via ancient hybridization events between the same two parental species (H. annuus and H. petiolaris). Most previous work examining genomic restructuring in these sunflower hybrid species has focused on chromosomal rearrangements. However, the origin of all three homoploid hybrid sunflower species also is associated with massive proliferation events of Ty3/gypsy-like retrotransposons in the hybrid species' genomes. We compared the genomic organization of these elements in the parent species and two of the homoploid hybrid species using fluorescence in situ hybridization (FISH). We found a significant expansion of Ty3/gypsy-like retrotransposons confined to the pericentromeric regions of two hybrid sunflower species, H. deserticola and H. paradoxus. In contrast, we detected no significant increase in the frequency or extent of dispersed retrotransposon populations in the hybrid species within the resolution limits of our assay. We discuss the potential role that transposable element proliferation and localization plays in the evolution of homoploid hybrid species.
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Affiliation(s)
- S Evan Staton
- Miami University, Department of Botany, 316 Pearson Hall, Oxford, Ohio 45056 USA
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