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Mouillaud T, Berger A, Buysse M, Rahola N, Daron J, Agbor J, Sango SN, Neafsey DE, Duron O, Ayala D. Limited association between Wolbachia and Plasmodium falciparum infections in natural populations of the major malaria mosquito Anopheles moucheti. Evol Appl 2023; 16:1999-2006. [PMID: 38143905 PMCID: PMC10739076 DOI: 10.1111/eva.13619] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 12/26/2023] Open
Abstract
Since the discovery of natural malaria vector populations infected by the endosymbiont bacterium Wolbachia, a renewed interest has arisen for using this bacterium as an alternative for malaria control. Among naturally infected mosquitoes, Anopheles moucheti, a major malaria mosquito in Central Africa, exhibits one of the highest prevalences of Wolbachia infection. To better understand whether this maternally inherited bacterium could be used for malaria control, we investigated Wolbachia influence in An. moucheti populations naturally infected by the malaria parasite Plasmodium falciparum. To this end, we collected mosquitoes in a village from Cameroon, Central Africa, where this mosquito is the main malaria vector. We found that the prevalence of Wolbachia bacterium was almost fixed in the studied mosquito population, and was higher than previously recorded. We also quantified Wolbachia in whole mosquitoes and dissected abdomens, confirming that the bacterium is also elsewhere than in the abdomen, but at lower density. Finally, we analyzed the association of Wolbachia presence and density on P. falciparum infection. Wolbachia density was slightly higher in mosquitoes infected with the malaria parasite than in uninfected mosquitoes. However, we observed no correlation between the P. falciparum and Wolbachia densities. In conclusion, our study indicates that naturally occurring Wolbachia infection is not associated to P. falciparum development within An. moucheti mosquitoes.
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Affiliation(s)
| | - Audric Berger
- MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellierFrance
| | - Marie Buysse
- MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellierFrance
- Montpellier Ecology and Evolution of Disease Network (MEEDiN)MontpellierFrance
| | - Nil Rahola
- MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellierFrance
| | - Josquin Daron
- MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellierFrance
| | - Jean‐Pierre Agbor
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de DoualaDoualaCameroon
| | - Sandrine N. Sango
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de DoualaDoualaCameroon
| | - Daniel E. Neafsey
- Department of Immunology and Infectious DiseasesHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
- Infectious Disease and Microbiome ProgramBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Olivier Duron
- MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellierFrance
- Montpellier Ecology and Evolution of Disease Network (MEEDiN)MontpellierFrance
| | - Diego Ayala
- MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellierFrance
- Medical Entomology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
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Lefebvre MJM, Daron J, Legrand E, Fontaine MC, Rougeron V, Prugnolle F. Population genomic evidence of adaptive response during the invasion history of Plasmodium falciparum in the Americas. Mol Biol Evol 2023; 40:7111314. [PMID: 37030000 PMCID: PMC10162688 DOI: 10.1093/molbev/msad082] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/08/2023] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
Plasmodium falciparum, the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations and mosquito species). Here, we analyzed the genome-wide polymorphisms of 2,635 isolates across the current P. falciparum distribution range in Africa, Asia, Oceania, and the Americas to investigate its genetic structure, invasion history, and selective pressures associated with its adaptation to the American environment. We confirmed that American populations originated from Africa with at least two independent introductions that led to two genetically distinct clusters, one in the North (Haiti and Colombia) and one in the South (French Guiana and Brazil), and the admixed Peruvian group. Genome scans revealed recent and more ancient signals of positive selection in the American populations. Particularly, we detected positive selection signals in genes involved in interactions with hosts (human and mosquito) cells and in genes involved in resistance to malaria drugs in both clusters. We found that some genes were under selection in both clusters. Analyses suggested that for five genes, adaptive introgression between clusters or selection on standing variation was at the origin of this repeated evolution. This study provides new genetic evidence on P. falciparum colonization history and on its local adaptation in the Americas.
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Affiliation(s)
| | - Josquin Daron
- MiVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
| | - Eric Legrand
- Malaria Biology and Vaccine Unit, Institut Pasteur, Paris, France
| | - Michael C Fontaine
- MiVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Virginie Rougeron
- REHABS, International Research Laboratory, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa
| | - Franck Prugnolle
- REHABS, International Research Laboratory, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa
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Picard MAL, Leblay F, Cassan C, Willemsen A, Daron J, Bauffe F, Decourcelle M, Demange A, Bravo IG. Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression. Protein Sci 2023; 32:e4576. [PMID: 36692287 PMCID: PMC9926478 DOI: 10.1002/pro.4576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/25/2023]
Abstract
Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analyzed by means of quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and protein levels, leading to differences of over 15 times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.
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Affiliation(s)
- Marion A. L. Picard
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Fiona Leblay
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Cécile Cassan
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Anouk Willemsen
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Josquin Daron
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Frédérique Bauffe
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Mathilde Decourcelle
- BioCampus Montpellier (University of Montpellier, CNRS, INSERM)MontpellierFrance
| | - Antonin Demange
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Ignacio G. Bravo
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
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Rougeron V, Daron J, Fontaine MC, Prugnolle F. Evolutionary history of Plasmodium vivax and Plasmodium simium in the Americas. Malar J 2022; 21:141. [PMID: 35505431 PMCID: PMC9066938 DOI: 10.1186/s12936-022-04132-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/18/2022] [Indexed: 11/12/2022] Open
Abstract
Malaria is a vector-borne disease caused by protozoan parasites of the genus Plasmodium. Plasmodium vivax is the most prevalent human-infecting species in the Americas. However, the origins of this parasite in this continent are still debated. Similarly, it is now accepted that the existence of Plasmodium simium is explained by a P. vivax transfer from humans to monkey in America. However, many uncertainties still exist concerning the origin of the transfer and whether several transfers occurred. In this review, the most recent studies that addressed these questions using genetic and genomic approaches are presented.
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Affiliation(s)
- Virginie Rougeron
- International Research Laboratory, REHABS, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa.
| | - Josquin Daron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900, rue Jean-François Breton, 34900, Montpellier, France
| | - Michael C Fontaine
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900, rue Jean-François Breton, 34900, Montpellier, France.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Franck Prugnolle
- International Research Laboratory, REHABS, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa
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Daron J, Bravo IG. Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide. Viruses 2021; 13:v13091800. [PMID: 34578381 PMCID: PMC8473333 DOI: 10.3390/v13091800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential of coronaviruses, it is critical to unravel their evolutionary history of host species breadth, host-switch potential, adaptation and emergence, to identify viruses posing a pandemic risk in humans. We present here a comprehensive analysis of the composition and codon usage bias of the 82 Orthocoronavirinae members, infecting 47 different avian and mammalian hosts. Our results clearly establish that synonymous codon usage varies widely among viruses, is only weakly dependent on their primary host, and is dominated by mutational bias towards AU-enrichment and by CpG avoidance. Indeed, variation in GC3 explains around 34%, while variation in CpG frequency explains around 14% of total variation in codon usage bias. Further insight on the mutational equilibrium within Orthocoronavirinae revealed that most coronavirus genomes are close to their neutral equilibrium, the exception being the three recently infecting human coronaviruses, which lie further away from the mutational equilibrium than their endemic human coronavirus counterparts. Finally, our results suggest that, while replicating in humans, SARS-CoV-2 is slowly becoming AU-richer, likely until attaining a new mutational equilibrium.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (CNRS, IRD, Université de Montpellier), 34394 Montpellier, France;
- Correspondence:
| | - Ignacio G. Bravo
- Laboratoire MIVEGEC (CNRS, IRD, Université de Montpellier), 34394 Montpellier, France;
- Center for Research on the Ecology and Evolution of Diseases (CREES), 34394 Montpellier, France
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6
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Daron J, Boissière A, Boundenga L, Ngoubangoye B, Houze S, Arnathau C, Sidobre C, Trape JF, Durand P, Renaud F, Fontaine MC, Prugnolle F, Rougeron V. Population genomic evidence of Plasmodium vivax Southeast Asian origin. Sci Adv 2021; 7:7/18/eabc3713. [PMID: 33910900 PMCID: PMC8081369 DOI: 10.1126/sciadv.abc3713] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 03/10/2021] [Indexed: 05/15/2023]
Abstract
Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives (P. vivax-like) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of this hypothesis. Here, we extensively characterized the genomic variations of 447 human P. vivax strains and 19 ape P. vivax-like strains collected worldwide. Phylogenetic relationships between human and ape Plasmodium strains revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like By investigating various aspects of P. vivax genetic variation, we identified several notable geographical patterns in summary statistics in function of the increasing geographic distance from Southeast Asia, suggesting that P. vivax may have derived from a single area in Asia through serial founder effects.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
| | - Anne Boissière
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Larson Boundenga
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, 46 rue H. Huchard, 75877 Paris Cedex 18, France
| | - Celine Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Christine Sidobre
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
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7
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Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, Weigel D, Benhamed M, Gutierrez-Marcos J. A new role for histone demethylases in the maintenance of plant genome integrity. eLife 2020. [PMID: 33107825 DOI: 10.7554/elife.58533.sa2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the transgenerational inheritance of histone marks, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases play a dual role in plants by helping to maintain transcriptional states through development and safeguard genome integrity during sexual reproduction.
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Affiliation(s)
| | - Matthew Naish
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | | | - Sho Ohno
- School of Life Science, University of Warwick, Coventry, United Kingdom
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Alexander Dawson
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | | | - Deborah Manza-Mianza
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Federico Ariel
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Cecile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Anjar Wibowo
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, United States
| | - Minako Ueda
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, United States
- Division of Biological Sciences, University of Missouri, Columbia, United States
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006, Paris, France
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8
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Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, Weigel D, Benhamed M, Gutierrez-Marcos J. A new role for histone demethylases in the maintenance of plant genome integrity. eLife 2020; 9:e58533. [PMID: 33107825 PMCID: PMC7671693 DOI: 10.7554/elife.58533] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022] Open
Abstract
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the transgenerational inheritance of histone marks, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases play a dual role in plants by helping to maintain transcriptional states through development and safeguard genome integrity during sexual reproduction.
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Affiliation(s)
| | - Matthew Naish
- School of Life Science, University of WarwickCoventryUnited Kingdom
| | | | - Sho Ohno
- School of Life Science, University of WarwickCoventryUnited Kingdom
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-kuKyotoJapan
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Alexander Dawson
- School of Life Science, University of WarwickCoventryUnited Kingdom
| | | | - Deborah Manza-Mianza
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Federico Ariel
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Cecile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Anjar Wibowo
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State UniversityColumbusUnited States
| | - Minako Ueda
- Institute of Transformative Bio-Molecules, Nagoya UniversityNagoyaJapan
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - R Keith Slotkin
- Donald Danforth Plant Science CenterSt. LouisUnited States
- Division of Biological Sciences, University of MissouriColumbiaUnited States
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006ParisFrance
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9
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Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, Tsuchiya T, Holub E, McDowell JM, Slotkin RK, Le Roch KG, Eulgem T. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genet 2020; 16:e1008993. [PMID: 32925902 PMCID: PMC7529245 DOI: 10.1371/journal.pgen.1008993] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/01/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dose-dependency of their defense-inducing activity. A genetic “arms race” with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7-associated H3K9me2 is required for optimal expression of RPP7. By profiling of genome-wide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the “raw material” for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase. We previously found the Arabidopsis thaliana PHD-finger protein EDM2 to serve as a chromatin-associated factor controlling expression of the NLR-type immune receptor gene RPP7. EDM2 binds to the transposon-silencing signal H3K9me2 and affects levels of this epigenetic mark at various loci. By genome-wide profiling of transcript- and H3K9me2-levels we now found EDM2 to have a broader role in controlling NLR gene expression. In order to mitigate fitness costs caused by its promoting effects on RPP7 expression and that of several other NLR genes, EDM2 seems to suppress expression of many additional members of this gene family. This observation is in line with multiple reports demonstrating the need for balanced expression of NLRs, which can substantially reduce overall plant fitness, but need to be present at certain minimal levels to confer sufficient immune protection. Our previous results demonstrated that the influence of EDM2 on RPP7 expression was co-opted to this immune receptor gene by the insertion of an EDM2-controlled transposon. Here, we are providing additional examples for transposon-associated effects on NLR gene expression, suggesting that these mobile elements play an important role for NLR genes by equipping members of this rapidly evolving gene family with regulatory mechanisms needed for balanced expression.
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Affiliation(s)
- Yan Lai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Xueqing Maggie Lu
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Songqin Pan
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Jianqiang Wang
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Wei Wang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne campus, United Kingdom
| | - John M. McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Karine G. Le Roch
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
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10
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Yates-Stewart AD, Daron J, Wijeratne S, Shahid S, Edgington HA, Slotkin RK, Michel A. Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements. Insect Biochem Mol Biol 2020; 121:103363. [PMID: 32201218 DOI: 10.1016/j.ibmb.2020.103363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
In agricultural systems, crops equipped with host-plant resistance (HPR) have enhanced protection against pests, and are used as a safe and sustainable tool in pest management. In soybean, HPR can control the soybean aphid (Aphis glycines), but certain aphid populations have overcome this resistance (i.e., virulence). The molecular mechanisms underlying aphid virulence to HPR are unknown, but likely involve effector proteins that are secreted by aphids to modulate plant defenses. Another mechanism to facilitate adaptation is through the activity of transposable elements, which can become activated by stress. In this study, we performed RNA sequencing of virulent and avirulent soybean aphids fed susceptible or resistant (Rag1 + Rag2) soybean. Our goal was to better understand the molecular mechanisms underlying soybean aphid virulence. Our data showed that virulent aphids mostly down regulate putative effector genes relative to avirulent aphids, especially when aphids were fed susceptible soybean. Decreased expression of effectors may help evade HPR plant defenses. Virulent aphids also transcriptionally up regulate a diverse set of transposable elements and nearby genes, which is consistent with stress adaptation. Our work demonstrates two mechanisms of pest adaptation to resistance, and identifies effector gene targets for future functional testing.
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Affiliation(s)
| | - Josquin Daron
- CNRS, Centre National de la Recherche Scientifique, Montpellier, France
| | - Saranga Wijeratne
- The Ohio State University, Molecular and Cellular Imaging Center, OARDC, Wooster, OH, USA
| | - Saima Shahid
- Donald Danforth Plant Science Center, St, Louis, MO, USA
| | - Hilary A Edgington
- The Ohio State University, Department of Entomology, CFAES Wooster Campus, Wooster, OH, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St, Louis, MO, USA; Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Andy Michel
- The Ohio State University, Center for Applied Plant Sciences, Wooster, OH, USA; The Ohio State University, Department of Entomology, CFAES Wooster Campus, Wooster, OH, USA.
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11
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Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Do Kim K, Daron J, Slotkin RK, Jackson SA, Parrott WA, Meyers BC, Schmitz RJ. Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean. Plant Cell 2019; 31:2315-2331. [PMID: 31439802 PMCID: PMC6790092 DOI: 10.1105/tpc.19.00255] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.
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Affiliation(s)
- Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | | | - Sarah Johnson
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Josquin Daron
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Wayne A Parrott
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 63132
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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12
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Daron J, Slotkin RK. EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels. Genome Biol 2017; 18:91. [PMID: 28499400 PMCID: PMC5429532 DOI: 10.1186/s13059-017-1232-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/05/2017] [Indexed: 11/15/2022] Open
Abstract
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads. EpiTEome characterizes the previously discarded fraction of DNA methylation at sites of new insertions, enabling future investigation into the epigenetic regulation of non-reference and transposed elements.
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Affiliation(s)
- Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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13
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Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biol 2016; 17:170. [PMID: 27506905 PMCID: PMC4977677 DOI: 10.1186/s13059-016-1032-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/26/2016] [Indexed: 01/06/2023] Open
Abstract
Background Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM). In plants, canonical RdDM functions through RNA polymerase IV to reinforce pre-existing transposable element silencing. Recent investigations have identified a “non-canonical” form of RdDM dependent on RNA polymerase II expression to initiate and re-establish silencing of active transposable elements. This expression-dependent RdDM mechanism functions through RNAi degradation of transposable element mRNAs into small RNAs guided by the RNA-dependent RNA polymerase 6 (RDR6) protein and is therefore referred to as RDR6-RdDM. Results We performed whole-genome MethylC-seq in 20 mutants that distinguish RdDM mechanisms when transposable elements are either transcriptionally silent or active. We identified a new mechanism of expression-dependent RdDM, which functions through DICER-LIKE3 (DCL3) but bypasses the requirement of both RNA polymerase IV and RDR6 (termed DCL3-RdDM). We found that RNA polymerase II expression-dependent forms of RdDM function on over 20 % of transcribed transposable elements, including the majority of full-length elements with all of the domains required for autonomous transposition. Lastly, we find that RDR6-RdDM preferentially targets long transposable elements due to the specificity of primary small RNAs to cleave full-length mRNAs. Conclusions Expression-dependent forms of RdDM function to critically target DNA methylation to full-length and transcriptionally active transposable elements, suggesting that these pathways are key to suppressing mobilization. This targeting specificity is initiated on the mRNA cleavage-level, yet manifested as chromatin-level silencing that in plants is epigenetically inherited from generation to generation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1032-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaushik Panda
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | | | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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14
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Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science 2014; 345:1249721. [PMID: 25035497 DOI: 10.1126/science.1249721] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
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Affiliation(s)
- Frédéric Choulet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France.
| | - Adriana Alberti
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Sébastien Theil
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Natasha Glover
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Josquin Daron
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Lise Pingault
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Etienne Paux
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Philippe Leroy
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Nicolas Guilhot
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jacques Le Gouis
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Francois Balfourier
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Michael Alaux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Véronique Jamilloux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Céline Durand
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Christine Gaspin
- Biométrie et Intelligence Artificielle, INRA, Chemin de Borde Rouge, BP 27, 31326 Castanet-Tolosan, France
| | - Jan Safar
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jane Rogers
- The Genome Analysis Centre, Norwich, Norwich Research Park, Norwich NR4 7UH, UK
| | - Klaas Vandepoele
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052 Gent, Belgium
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Klaus Mayer
- Munich Information Center for Protein Sequences, Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - Hélène Berges
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Hadi Quesneville
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France. CNRS UMR 8030, 2 Rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, CP5706 Evry, France
| | - Catherine Feuillet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
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15
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Daron J, Glover N, Pingault L, Theil S, Jamilloux V, Paux E, Barbe V, Mangenot S, Alberti A, Wincker P, Quesneville H, Feuillet C, Choulet F. Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome Biol 2014; 15:546. [PMID: 25476263 PMCID: PMC4290129 DOI: 10.1186/s13059-014-0546-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [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: 07/25/2014] [Accepted: 11/17/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far. RESULTS We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation. CONCLUSION Accurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.
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Affiliation(s)
- Josquin Daron
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Natasha Glover
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Lise Pingault
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Sébastien Theil
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Véronique Jamilloux
- />INRA-URGI, Centre de Versailles, Route de Saint Cyr, 78026 Versailles, France
| | - Etienne Paux
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
| | - Sophie Mangenot
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
| | - Adriana Alberti
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
| | - Patrick Wincker
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
- />CNRS UMR 8030, 2 rue Gaston Crémieux, 91000 Evry, France
- />Université d’Evry, P5706 Evry, France
| | - Hadi Quesneville
- />INRA-URGI, Centre de Versailles, Route de Saint Cyr, 78026 Versailles, France
| | - Catherine Feuillet
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
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16
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Adio AM, Casteel CL, De Vos M, Kim JH, Joshi V, Li B, Juéry C, Daron J, Kliebenstein DJ, Jander G. Biosynthesis and defensive function of Nδ-acetylornithine, a jasmonate-induced Arabidopsis metabolite. Plant Cell 2011; 23:3303-18. [PMID: 21917546 PMCID: PMC3203426 DOI: 10.1105/tpc.111.088989] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 08/19/2011] [Accepted: 08/26/2011] [Indexed: 05/20/2023]
Abstract
Since research on plant interactions with herbivores and pathogens is often constrained by the analysis of already known compounds, there is a need to identify new defense-related plant metabolites. The uncommon nonprotein amino acid N(δ)-acetylornithine was discovered in a targeted search for Arabidopsis thaliana metabolites that are strongly induced by the phytohormone methyl jasmonate (MeJA). Stable isotope labeling experiments show that, after MeJA elicitation, Arg, Pro, and Glu are converted to Orn, which is acetylated by NATA1 to produce N(δ)-acetylornithine. MeJA-induced N(δ)-acetylornithine accumulation occurs in all tested Arabidopsis accessions, other Arabidopsis species, Capsella rubella, and Boechera stricta, but not in less closely related Brassicaceae. Both insect feeding and Pseudomonas syringae infection increase NATA1 expression and N(δ)-acetylornithine accumulation. NATA1 transient expression in Nicotiana tabacum and the addition of N(δ)-acetylornithine to an artificial diet both decrease Myzus persicae (green peach aphid) reproduction, suggesting a direct toxic or deterrent effect. However, since broad metabolic changes that are induced by MeJA in wild-type Arabidopsis are attenuated in a nata1 mutant strain, there may also be indirect effects on herbivores and pathogens. In the case of P. syringae, growth on a nata1 mutant is reduced compared with wild-type Arabidopsis, but growth in vitro is unaffected by N(δ)-acetylornithine addition.
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Affiliation(s)
- Adewale M. Adio
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Clare L. Casteel
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Martin De Vos
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Jae Hak Kim
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Vijay Joshi
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Caroline Juéry
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Josquin Daron
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | | | - Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
- Address correspondence to
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