1
|
Tran Van Canh L, Aubourg S. Bioinformatics Methods for Prediction of Gene Families Encoding Extracellular Peptides. Methods Mol Biol 2024; 2731:3-21. [PMID: 38019422 DOI: 10.1007/978-1-0716-3511-7_1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Genes encoding small secreted peptides are widely distributed among plant genomes but their detection and annotation remains challenging. The bioinformatics protocol described here aims to identify as exhaustively as possible secreted peptide precursors belonging to a family of interest. First, homology searches are performed at the protein and genome levels. Next, multiple sequence alignments and predictions of a secretion signal are used to define a set of homologous proteins sharing features of secreted peptide precursors. These protein sequences are then used as input of motif detection and profile-based tools to build representative matrices and profiles that are used iteratively as guides to scan again the proteome and genome until family completion.
Collapse
Affiliation(s)
- Loup Tran Van Canh
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, Angers, France
| | - Sébastien Aubourg
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, Angers, France
| |
Collapse
|
2
|
Yang H, Kim X, Skłenar J, Aubourg S, Sancho-Andrés G, Stahl E, Guillou MC, Gigli-Bisceglia N, Tran Van Canh L, Bender KW, Stintzi A, Reymond P, Sánchez-Rodríguez C, Testerink C, Renou JP, Menke FLH, Schaller A, Rhodes J, Zipfel C. Subtilase-mediated biogenesis of the expanded family of SERINE RICH ENDOGENOUS PEPTIDES. Nat Plants 2023; 9:2085-2094. [PMID: 38049516 DOI: 10.1038/s41477-023-01583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 11/03/2023] [Indexed: 12/06/2023]
Abstract
Plant signalling peptides are typically released from larger precursors by proteolytic cleavage to regulate plant growth, development and stress responses. Recent studies reported the characterization of a divergent family of Brassicaceae-specific peptides, SERINE RICH ENDOGENOUS PEPTIDES (SCOOPs), and their perception by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2). Here, we reveal that the SCOOP family is highly expanded, containing at least 50 members in the Columbia-0 reference Arabidopsis thaliana genome. Notably, perception of these peptides is strictly MIK2-dependent. How bioactive SCOOP peptides are produced, and to what extent their perception is responsible for the multiple physiological roles associated with MIK2 are currently unclear. Using N-terminomics, we validate the N-terminal cleavage site of representative PROSCOOPs. The cleavage sites are determined by conserved motifs upstream of the minimal SCOOP bioactive epitope. We identified subtilases necessary and sufficient to process PROSCOOP peptides at conserved cleavage motifs. Mutation of these subtilases, or their recognition motifs, suppressed PROSCOOP cleavage and associated overexpression phenotypes. Furthermore, we show that higher-order mutants of these subtilases show phenotypes reminiscent of mik2 null mutant plants, consistent with impaired PROSCOOP biogenesis, and demonstrating biological relevance of SCOOP perception by MIK2. Together, this work provides insights into the molecular mechanisms underlying the functions of the recently identified SCOOP peptides and their receptor MIK2.
Collapse
Affiliation(s)
- Huanjie Yang
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xeniya Kim
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Jan Skłenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sébastien Aubourg
- Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Elia Stahl
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Nora Gigli-Bisceglia
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Loup Tran Van Canh
- Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Kyle W Bender
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Annick Stintzi
- Institute of Biology, Plant Physiology and Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Jean-Pierre Renou
- Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andreas Schaller
- Institute of Biology, Plant Physiology and Biochemistry, University of Hohenheim, Stuttgart, Germany
| | - Jack Rhodes
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| |
Collapse
|
3
|
Lallemand T, Leduc M, Desmazières A, Aubourg S, Rizzon C, Landès C, Celton JM. Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica. Genome Biol Evol 2023; 15:evad178. [PMID: 37847638 PMCID: PMC10601995 DOI: 10.1093/gbe/evad178] [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] [Received: 06/02/2023] [Revised: 08/25/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
A Whole Genome Duplication (WGD) event occurred several Ma in a Rosaceae ancestor, giving rise to the Maloideae subfamily which includes today many pome fruits such as pear (Pyrus communis) and apple (Malus domestica). This complete and well-conserved genome duplication makes the apple an organism of choice to study the early evolutionary events occurring to ohnologous chromosome fragments. In this study, we investigated gene sequence evolution and expression, transposable elements (TE) density, and DNA methylation level. Overall, we identified 16,779 ohnologous gene pairs in the apple genome, confirming the relatively recent WGD. We identified several imbalances in QTL localization among duplicated chromosomal fragments and characterized various biases in genome fractionation, gene transcription, TE densities, and DNA methylation. Our results suggest a particular chromosome dominance in this autopolyploid species, a phenomenon that displays similarities with subgenome dominance that has only been described so far in allopolyploids.
Collapse
Affiliation(s)
- Tanguy Lallemand
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Martin Leduc
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Adèle Desmazières
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Sébastien Aubourg
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d’Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d’Evry Val d’Essonne, Evry, France
| | - Claudine Landès
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Jean-Marc Celton
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| |
Collapse
|
4
|
Guillou MC, Balliau T, Vergne E, Canut H, Chourré J, Herrera-León C, Ramos-Martín F, Ahmadi-Afzadi M, D’Amelio N, Ruelland E, Zivy M, Renou JP, Jamet E, Aubourg S. The PROSCOOP10 Gene Encodes Two Extracellular Hydroxylated Peptides and Impacts Flowering Time in Arabidopsis. Plants (Basel) 2022; 11:3554. [PMID: 36559666 PMCID: PMC9784617 DOI: 10.3390/plants11243554] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The Arabidopsis PROSCOOP genes belong to a family predicted to encode secreted pro-peptides, which undergo maturation steps to produce peptides named SCOOP. Some of them are involved in defence signalling through their perception by a receptor complex including MIK2, BAK1 and BKK1. Here, we focused on the PROSCOOP10 gene, which is highly and constitutively expressed in aerial organs. The MS/MS analyses of leaf apoplastic fluids allowed the identification of two distinct peptides (named SCOOP10#1 and SCOOP10#2) covering two different regions of PROSCOOP10. They both possess the canonical S-X-S family motif and have hydroxylated prolines. This identification in apoplastic fluids confirms the biological reality of SCOOP peptides for the first time. NMR and molecular dynamics studies showed that the SCOOP10 peptides, although largely unstructured in solution, tend to assume a hairpin-like fold, exposing the two serine residues previously identified as essential for the peptide activity. Furthermore, PROSCOOP10 mutations led to an early-flowering phenotype and increased expression of the floral integrators SOC1 and LEAFY, consistent with the de-regulated transcription of PROSCOOP10 in several other mutants displaying early- or late-flowering phenotypes. These results suggest a role for PROSCOOP10 in flowering time, highlighting the functional diversity within the PROSCOOP family.
Collapse
Affiliation(s)
| | - Thierry Balliau
- AgroParisTech, GQE—Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, F-91190 Gif-sur-Yvette, France
| | - Emilie Vergne
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
| | - Hervé Canut
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, Toulouse INP, CNRS, F-31320 Auzeville-Tolosane, France
| | - Josiane Chourré
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, Toulouse INP, CNRS, F-31320 Auzeville-Tolosane, France
| | - Claudia Herrera-León
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, F-80039 Amiens, France
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, F-80039 Amiens, France
| | - Masoud Ahmadi-Afzadi
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 117-76315, Iran
| | - Nicola D’Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, F-80039 Amiens, France
| | - Eric Ruelland
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Technologie de Compiègne, F-60203 Compiègne, France
| | - Michel Zivy
- AgroParisTech, GQE—Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, F-91190 Gif-sur-Yvette, France
| | - Jean-Pierre Renou
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, Toulouse INP, CNRS, F-31320 Auzeville-Tolosane, France
| | - Sébastien Aubourg
- Institut Agro, SFR QUASAV, IRHS, Université Angers, INRAE, F-49000 Angers, France
| |
Collapse
|
5
|
Guillou MC, Vergne E, Aligon S, Pelletier S, Simonneau F, Rolland A, Chabout S, Mouille G, Gully K, Grappin P, Montrichard F, Aubourg S, Renou JP. The peptide SCOOP12 acts on reactive oxygen species homeostasis to modulate cell division and elongation in Arabidopsis primary root. J Exp Bot 2022; 73:6115-6132. [PMID: 35639812 DOI: 10.1093/jxb/erac240] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/22/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Small secreted peptides have been described as key contributors to complex signalling networks that control plant development and stress responses. The Brassicaceae-specific PROSCOOP family encodes precursors of Serine riCh endOgenOus Peptides (SCOOPs). In Arabidopsis SCOOP12 has been shown to promote the defence response against pathogens and to be involved in root development. Here, we explore its role as a moderator of Arabidopsis primary root development. We show that the PROSCOOP12 null mutation leads to longer primary roots through the development of longer differentiated cells while PROSCOOP12 overexpression induces dramatic plant growth impairments. In comparison, the exogenous application of synthetic SCOOP12 peptide shortens roots through meristem size and cell length reductions. Moreover, superoxide anion (O2·-) and hydrogen peroxide (H2O2) production in root tips vary according to SCOOP12 abundance. By using reactive oxygen species scavengers that suppress the proscoop12 phenotype, we showed that root growth regulation by SCOOP12 is associated with reactive oxygen species metabolism. Furthermore, our results suggest that peroxidases act as potential SCOOP12 downstream targets to regulate H2O2 production, which in turn triggers cell wall modifications in root. Finally, a massive transcriptional reprogramming, including the induction of genes from numerous other pathways, including ethylene, salicylic acid, and glucosinolates biosynthesis, was observed, emphasizing its dual role in defence and development.
Collapse
Affiliation(s)
| | - Emilie Vergne
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Sophie Aligon
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Sandra Pelletier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Aurélia Rolland
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Salem Chabout
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Gregory Mouille
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Kay Gully
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Philippe Grappin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | | | | |
Collapse
|
6
|
Gaucher M, Righetti L, Aubourg S, Dugé de Bernonville T, Brisset MN, Chevreau E, Vergne E. Correction to: An Erwinia amylovora inducible promoter for improvement of apple fire blight resistance. Plant Cell Rep 2022; 41:1789. [PMID: 35674790 PMCID: PMC9304045 DOI: 10.1007/s00299-022-02887-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Matthieu Gaucher
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Laura Righetti
- Research Centre for Cereal and Industrial Crops (CREA-CI), Council for Agricultural Research and Agricultural Economics Analysis, Via di Corticella 133, 40128, Bologna, Italy
| | - Sébastien Aubourg
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Thomas Dugé de Bernonville
- EA2106 Biomolécules et Biotechnologies Végétales, UFR Sciences Pharmaceutiques, Université François Rabelais, 31 avenue Monge, 37200, Tours, France
| | | | - Elisabeth Chevreau
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Emilie Vergne
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France.
| |
Collapse
|
7
|
Gaucher M, Righetti L, Aubourg S, Dugé de Bernonville T, Brisset MN, Chevreau E, Vergne E. An Erwinia amylovora inducible promoter for improvement of apple fire blight resistance. Plant Cell Rep 2022; 41:1499-1513. [PMID: 35385991 PMCID: PMC9270298 DOI: 10.1007/s00299-022-02869-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes. Intragenesis is an important alternative to transgenesis to produce modified plants containing native DNA only. A key point to develop such a strategy is the availability of regulatory sequences controlling the expression of the gene of interest. With the aim of finding apple gene promoters either inducible by the fire blight pathogen Erwinia amylovora (Ea) or moderately constitutive, we focused on polyphenoloxidase genes (PPO). These genes encode oxidative enzymes involved in many physiological processes and have been previously shown to be upregulated during the Ea infection process. We found ten PPO and two PPO-like sequences in the apple genome and characterized the promoters of MdPPO16 (pPPO16) and MdKFDV02 PPO-like (pKFDV02) for their potential as Ea-inducible and low-constitutive regulatory sequences, respectively. Expression levels of reporter genes fused to these promoters and transiently or stably expressed in apple were quantified after various treatments. Unlike pKFDV02 which displayed a variable activity, pPPO16 allowed a fast and strong expression of transgenes in apple following Ea infection in a Type 3 Secretion System dependent manner. Altogether our results does not confirmed pKFDV02 as a constitutive and weak promoter whereas pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes.
Collapse
Affiliation(s)
- Matthieu Gaucher
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Laura Righetti
- Research Centre for Cereal and Industrial Crops (CREA-CI), Council for Agricultural Research and Agricultural Economics Analysis, Via di Corticella 133, 40128, Bologna, Italy
| | - Sébastien Aubourg
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Thomas Dugé de Bernonville
- EA2106 Biomolécules et Biotechnologies Végétales, UFR Sciences Pharmaceutiques, Université François Rabelais, 31 avenue Monge, 37200, Tours, France
| | | | - Elisabeth Chevreau
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Emilie Vergne
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France.
| |
Collapse
|
8
|
Stahl E, Fernandez Martin A, Glauser G, Guillou MC, Aubourg S, Renou JP, Reymond P. The MIK2/SCOOP Signaling System Contributes to Arabidopsis Resistance Against Herbivory by Modulating Jasmonate and Indole Glucosinolate Biosynthesis. Front Plant Sci 2022; 13:852808. [PMID: 35401621 PMCID: PMC8984487 DOI: 10.3389/fpls.2022.852808] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/22/2022] [Indexed: 05/14/2023]
Abstract
Initiation of plant immune signaling requires recognition of conserved molecular patterns from microbes and herbivores by plasma membrane-localized pattern recognition receptors. Additionally, plants produce and secrete numerous small peptide hormones, termed phytocytokines, which act as secondary danger signals to modulate immunity. In Arabidopsis, the Brassicae-specific SERINE RICH ENDOGENOUS PEPTIDE (SCOOP) family consists of 14 members that are perceived by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR LIKE KINASE 2 (MIK2). Recognition of SCOOP peptides elicits generic early signaling responses but knowledge on how and if SCOOPs modulate specific downstream immune defenses is limited. We report here that depletion of MIK2 or the single PROSCOOP12 precursor results in decreased Arabidopsis resistance against the generalist herbivore Spodoptera littoralis but not the specialist Pieris brassicae. Increased performance of S. littoralis on mik2-1 and proscoop12 is accompanied by a diminished accumulation of jasmonic acid, jasmonate-isoleucine and indolic glucosinolates. Additionally, we show transcriptional activation of the PROSCOOP gene family in response to insect herbivory. Our data therefore indicate that perception of endogenous SCOOP peptides by MIK2 modulates the jasmonate pathway and thereby contributes to enhanced defense against a generalist herbivore.
Collapse
Affiliation(s)
- Elia Stahl
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
- *Correspondence: Elia Stahl,
| | | | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Neuchâtel, Switzerland
| | - Marie-Charlotte Guillou
- Institut de Recherche en Horticulture et Semences, UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, Beaucouzé, France
| | - Sébastien Aubourg
- Institut de Recherche en Horticulture et Semences, UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, Beaucouzé, France
| | - Jean-Pierre Renou
- Institut de Recherche en Horticulture et Semences, UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, Beaucouzé, France
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
9
|
Gully K, Pelletier S, Guillou MC, Ferrand M, Aligon S, Pokotylo I, Perrin A, Vergne E, Fagard M, Ruelland E, Grappin P, Bucher E, Renou JP, Aubourg S. The SCOOP12 peptide regulates defense response and root elongation in Arabidopsis thaliana. J Exp Bot 2019; 70:1349-1365. [PMID: 30715439 PMCID: PMC6382344 DOI: 10.1093/jxb/ery454] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 08/27/2018] [Accepted: 12/12/2018] [Indexed: 05/20/2023]
Abstract
Small secreted peptides are important players in plant development and stress response. Using a targeted in silico approach, we identified a family of 14 Arabidopsis genes encoding precursors of serine-rich endogenous peptides (PROSCOOP). Transcriptomic analyses revealed that one member of this family, PROSCOOP12, is involved in processes linked to biotic and oxidative stress as well as root growth. Plants defective in this gene were less susceptible to Erwinia amylovora infection and showed an enhanced root growth phenotype. In PROSCOOP12 we identified a conserved motif potentially coding for a small secreted peptide. Exogenous application of synthetic SCOOP12 peptide induces various defense responses in Arabidopsis. Our findings show that SCOOP12 has numerous properties of phytocytokines, activates the phospholipid signaling pathway, regulates reactive oxygen species response, and is perceived in a BAK1 co-receptor-dependent manner.
Collapse
Affiliation(s)
- Kay Gully
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Sandra Pelletier
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Marie-Charlotte Guillou
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Marina Ferrand
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Sophie Aligon
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Igor Pokotylo
- iEES-Paris (Interaction Plantes-Environnement Institut d’Ecologie et des Sciences de l’Environnement de Paris), UMR CNRS 7618, Université Paris Est Créteil, 61 avenue du général de Gaulle, Créteil, France
| | - Adrien Perrin
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Emilie Vergne
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Mathilde Fagard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Eric Ruelland
- iEES-Paris (Interaction Plantes-Environnement Institut d’Ecologie et des Sciences de l’Environnement de Paris), UMR CNRS 7618, Université Paris Est Créteil, 61 avenue du général de Gaulle, Créteil, France
| | - Philippe Grappin
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Etienne Bucher
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
| | - Jean-Pierre Renou
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
- Correspondence: or
| | - Sébastien Aubourg
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, QuaSaV, Beaucouzé, France
- Correspondence: or
| |
Collapse
|
10
|
Warneys R, Gaucher M, Robert P, Aligon S, Anton S, Aubourg S, Barthes N, Braud F, Cournol R, Gadenne C, Heintz C, Brisset MN, Degrave A. Acibenzolar- S-Methyl Reprograms Apple Transcriptome Toward Resistance to Rosy Apple Aphid. Front Plant Sci 2018; 9:1795. [PMID: 30619387 PMCID: PMC6299034 DOI: 10.3389/fpls.2018.01795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/19/2018] [Indexed: 05/09/2023]
Abstract
Acibenzolar-S-methyl (ASM) is a chemical compound, which is able to induce resistance in several model and non-model plants, but the end-players of this induced defense remain ill-defined. Here, we test the hypothesis that treatment with ASM can protect apple (Malus × domestica) against the rosy apple aphid (Dysaphis plantaginea) and investigate the defense molecules potentially involved in resistance. We measured aphid life traits and performed behavioral assays to study the effect of ASM on plant resistance against the aphid, and then combined transcriptomic, bioinformatics, metabolic and biochemical analyses to identify the plant compounds involved in resistance. Plants treated with ASM negatively affected several life traits of the aphid and modified its feeding and host seeking behaviors. ASM treatment elicited up-regulation of terpene synthase genes in apple and led to the emission of (E,E)-α-farnesene, a sesquiterpene that was repellent to the aphid. Several genes encoding amaranthin-like lectins were also strongly up-regulated upon treatment and the corresponding proteins accumulated in leaves, petioles and stems. Our results link the production of specific apple proteins and metabolites to the antibiosis and antixenosis effects observed against Dysaphis plantaginea, providing insight into the mechanisms underlying ASM-induced herbivore resistance.
Collapse
Affiliation(s)
- Romain Warneys
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Matthieu Gaucher
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Philippe Robert
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Sophie Aligon
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Sylvia Anton
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, Angers, France
| | - Sébastien Aubourg
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Nicolas Barthes
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS – Université de Montpellier – Université Paul Valery Montpellier 3 – EPHE – IRD, Montpellier, France
| | - Ferréol Braud
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Raphaël Cournol
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Christelle Heintz
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Marie-Noëlle Brisset
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Alexandre Degrave
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| |
Collapse
|
11
|
Abstract
Background Systems biology aims to analyse regulation mechanisms into the cell. By mapping interactions observed in different situations, differential network analysis has shown its power to reveal specific cellular responses or specific dysfunctional regulations. In this work, we propose to explore on a large scale the role of natural anti-sense transcription on gene regulation mechanisms, and we focus our study on apple (Malus domestica) in the context of fruit ripening in cold storage. Results We present a differential functional analysis of the sense and anti-sense transcriptomic data that reveals functional terms linked to the ripening process. To develop our differential network analysis, we introduce our inference method of an Extended Core Network; this method is inspired by C3NET, but extends the notion of significant interactions. By comparing two extended core networks, one inferred with sense data and the other one inferred with sense and anti-sense data, our differential analysis is first performed on a local view and reveals AS-impacted genes, genes that have important interactions impacted by anti-sense transcription. The motifs surrounding AS-impacted genes gather transcripts with functions mostly consistent with the biological context of the data used and the method allows us to identify new actors involved in ripening and cold acclimation pathways and to decipher their interactions. Then from a more global view, we compute minimal sub-networks that connect the AS-impacted genes using Steiner trees. Those Steiner trees allow us to study the rewiring of the AS-impacted genes in the network with anti-sense actors. Conclusion Anti-sense transcription is usually ignored in transcriptomic studies. The large-scale differential analysis of apple data that we propose reveals that anti-sense regulation may have an important impact in several cellular stress response mechanisms. Our data mining process enables to highlight specific interactions that deserve further experimental investigations. Electronic supplementary material The online version of this article (10.1186/s12918-018-0613-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marc Legeay
- LERIA, Université d'Angers, 2 bd Lavoisier, Angers, 49045, France.,IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Sébastien Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Jean-Pierre Renou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Béatrice Duval
- LERIA, Université d'Angers, 2 bd Lavoisier, Angers, 49045, France.
| |
Collapse
|
12
|
Rigaill G, Balzergue S, Brunaud V, Blondet E, Rau A, Rogier O, Caius J, Maugis-Rabusseau C, Soubigou-Taconnat L, Aubourg S, Lurin C, Martin-Magniette ML, Delannoy E. Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis. Brief Bioinform 2018; 19:65-76. [PMID: 27742662 DOI: 10.1093/bib/bbw092] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 12/16/2022] Open
Abstract
Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most of them are based on similar statistical frameworks after normalization, differing primarily in the choice of data distribution, mean and variance estimation strategy and data filtering. We propose an evaluation of the impact of these choices when few biological replicates are available through the use of synthetic data sets. This framework is based on real data sets and allows the exploration of various scenarios differing in the proportion of non-differentially expressed genes. Hence, it provides an evaluation of the key ingredients of the differential analysis, free of the biases associated with the simulation of data using parametric models. Our results show the relevance of a proper modeling of the mean by using linear or generalized linear modeling. Once the mean is properly modeled, the impact of the other parameters on the performance of the test is much less important. Finally, we propose to use the simple visualization of the raw P-value histogram as a practical evaluation criterion of the performance of differential analysis methods on real data sets.
Collapse
|
13
|
Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat Plants 2018; 4:473-484. [PMID: 29892093 DOI: 10.1101/254102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/27/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
Collapse
Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| |
Collapse
|
14
|
Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat Plants 2018; 4:473-484. [PMID: 29892093 PMCID: PMC6786968 DOI: 10.1038/s41477-018-0166-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [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: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/18/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
Collapse
Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| |
Collapse
|
15
|
Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. Front Plant Sci 2017; 8:1923. [PMID: 29176988 PMCID: PMC5686452 DOI: 10.3389/fpls.2017.01923] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 05/17/2023]
Abstract
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
Collapse
Affiliation(s)
- Jorge Urrestarazu
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
- Department of Agricultural Sciences, Public University of Navarre, Pamplona, Spain
- *Correspondence: Jorge Urrestarazu
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Diane Leforestier
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Elisa Ravon
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Arnaud Guyader
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Rémi Guisnel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Laurence Feugey
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Sébastien Aubourg
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Patrick Houben
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Jiri Sedlak
- Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czechia
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Charles Poncet
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Anthony Théron
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Shigeki Moriya
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Marco C. A. M. Bink
- Wageningen UR, Biometris, Wageningen, Netherlands
- Hendrix Genetics, Boxmeer, Netherlands
| | - François Laurens
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Charles-Eric Durel
| |
Collapse
|
16
|
Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V. GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. Nucleic Acids Res 2014; 43:D1010-7. [PMID: 25392409 PMCID: PMC4383956 DOI: 10.1093/nar/gku1155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein–protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17 264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource.
Collapse
Affiliation(s)
- Rim Zaag
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean Philippe Tamby
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Cécile Guichard
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Zakia Tariq
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Guillem Rigaill
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Etienne Delannoy
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean-Pierre Renou
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Sandrine Balzergue
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Tristan Mary-Huard
- INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France UMRGV, INRA, Université Paris-Sud, CNRS, F-91190 Gif-sur-Yvette, Paris, France
| | - Sébastien Aubourg
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Marie-Laure Martin-Magniette
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France
| | - Véronique Brunaud
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| |
Collapse
|
17
|
Lange H, Zuber H, Sement FM, Chicher J, Kuhn L, Hammann P, Brunaud V, Bérard C, Bouteiller N, Balzergue S, Aubourg S, Martin-Magniette ML, Vaucheret H, Gagliardi D. The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana. PLoS Genet 2014; 10:e1004564. [PMID: 25144737 PMCID: PMC4140647 DOI: 10.1371/journal.pgen.1004564] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [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: 08/02/2013] [Accepted: 06/28/2014] [Indexed: 11/19/2022] Open
Abstract
The RNA exosome is the major 3'-5' RNA degradation machine of eukaryotic cells and participates in processing, surveillance and turnover of both nuclear and cytoplasmic RNA. In both yeast and human, all nuclear functions of the exosome require the RNA helicase MTR4. We show that the Arabidopsis core exosome can associate with two related RNA helicases, AtMTR4 and HEN2. Reciprocal co-immunoprecipitation shows that each of the RNA helicases co-purifies with the exosome core complex and with distinct sets of specific proteins. While AtMTR4 is a predominantly nucleolar protein, HEN2 is located in the nucleoplasm and appears to be excluded from nucleoli. We have previously shown that the major role of AtMTR4 is the degradation of rRNA precursors and rRNA maturation by-products. Here, we demonstrate that HEN2 is involved in the degradation of a large number of polyadenylated nuclear exosome substrates such as snoRNA and miRNA precursors, incompletely spliced mRNAs, and spurious transcripts produced from pseudogenes and intergenic regions. Only a weak accumulation of these exosome substrate targets is observed in mtr4 mutants, suggesting that MTR4 can contribute, but plays rather a minor role for the degradation of non-ribosomal RNAs and cryptic transcripts in Arabidopsis. Consistently, transgene post-transcriptional gene silencing (PTGS) is marginally affected in mtr4 mutants, but increased in hen2 mutants, suggesting that it is mostly the nucleoplasmic exosome that degrades aberrant transgene RNAs to limit their entry in the PTGS pathway. Interestingly, HEN2 is conserved throughout green algae, mosses and land plants but absent from metazoans and other eukaryotic lineages. Our data indicate that, in contrast to human and yeast, plants have two functionally specialized RNA helicases that assist the exosome in the degradation of specific nucleolar and nucleoplasmic RNA populations, respectively.
Collapse
Affiliation(s)
- Heike Lange
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - François M. Sement
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Johana Chicher
- Platforme Protéomique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Platforme Protéomique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Platforme Protéomique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France
| | - Véronique Brunaud
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France
| | | | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Sandrine Balzergue
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France
| | - Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France
| | - Marie-Laure Martin-Magniette
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France
- UMR AgroParisTech-INRA MIA 518, Paris, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| |
Collapse
|
18
|
Celton JM, Gaillard S, Bruneau M, Pelletier S, Aubourg S, Martin-Magniette ML, Navarro L, Laurens F, Renou JP. Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control. New Phytol 2014; 203:287-99. [PMID: 24690119 DOI: 10.1111/nph.12787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 01/29/2014] [Accepted: 02/26/2014] [Indexed: 05/04/2023]
Abstract
Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined. Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3'UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants.
Collapse
Affiliation(s)
- Jean-Marc Celton
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 49071, Beaucouzé, France
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Frei dit Frey N, Garcia AV, Bigeard J, Zaag R, Bueso E, Garmier M, Pateyron S, de Tauzia-Moreau ML, Brunaud V, Balzergue S, Colcombet J, Aubourg S, Martin-Magniette ML, Hirt H. Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences. Genome Biol 2014; 15:R87. [PMID: 24980080 PMCID: PMC4197828 DOI: 10.1186/gb-2014-15-6-r87] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [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: 11/15/2013] [Accepted: 06/30/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but the specific and cooperative contributions of the MAPKs in these signalling events are largely unclear. RESULTS In this work, we analyse the behaviour of MPK3, MPK4 and MPK6 mutants in early and late immune responses triggered by the MAMP flg22 from bacterial flagellin. A genome-wide transcriptome analysis reveals that 36% of the flg22-upregulated genes and 68% of the flg22-downregulated genes are affected in at least one MAPK mutant. So far MPK4 was considered as a negative regulator of immunity, whereas MPK3 and MPK6 were believed to play partially redundant positive functions in defence. Our work reveals that MPK4 is required for the regulation of approximately 50% of flg22-induced genes and we identify a negative role for MPK3 in regulating defence gene expression, flg22-induced salicylic acid accumulation and disease resistance to Pseudomonas syringae. Among the MAPK-dependent genes, 27% of flg22-upregulated genes and 76% of flg22-downregulated genes require two or three MAPKs for their regulation. The flg22-induced MAPK activities are differentially regulated in MPK3 and MPK6 mutants, both in amplitude and duration, revealing a highly interdependent network. CONCLUSIONS These data reveal a new set of distinct functions for MPK3, MPK4 and MPK6 and indicate that the plant immune signalling network is choreographed through the interplay of these three interwoven MAPK pathways.
Collapse
Affiliation(s)
- Nicolas Frei dit Frey
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
- Present address: Laboratoire de Recherche en Sciences Végétales (LRSV), UMR 5546, Université Paul Sabatier/CNRS, 24, chemin de Borde Rouge B.P. 42617 Auzeville, Castanet-Tolosan 31326, France
| | - Ana Victoria Garcia
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean Bigeard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Rim Zaag
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eduardo Bueso
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Marie Garmier
- Institut de Biologie des Plantes (IBP), CNRS-Université Paris-Sud - UMR 8618 - Saclay Plant Sciences, Orsay, Cedex 91405, France
| | - Stéphanie Pateyron
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
- Unité de Recherche en Génomique Végétale (URGV), Plateforme Transcriptome, UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196, 2 rue Gaston Crémieux, Evry 91057, France
| | - Marie-Ludivine de Tauzia-Moreau
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Véronique Brunaud
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sandrine Balzergue
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
- Unité de Recherche en Génomique Végétale (URGV), Plateforme Transcriptome, UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean Colcombet
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
| | - Marie-Laure Martin-Magniette
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
- AgroParisTech, UMR 518 MIA, Paris 75005, France
- INRA, UMR 518 MIA, Paris 75005, France
| | - Heribert Hirt
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d’Evry Val d’Essonne - ERL CNRS 8196 - Saclay Plant Sciences, 2 rue Gaston Crémieux, Evry 91057, France
- Center for Desert Agriculture, 4700 King Abdullah University of Sciences and Technology, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
20
|
Abstract
Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps.
Collapse
Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität München (TUM), 85354 Freising-Weihenstephan, Germany.
| | | | | | | | | |
Collapse
|
21
|
Parage C, Tavares R, Réty S, Baltenweck-Guyot R, Poutaraud A, Renault L, Heintz D, Lugan R, Marais GA, Aubourg S, Hugueney P. Structural, functional, and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine. Plant Physiol 2012; 160:1407-19. [PMID: 22961129 PMCID: PMC3490603 DOI: 10.1104/pp.112.202705] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/30/2012] [Indexed: 05/04/2023]
Abstract
Stilbenes are a small family of phenylpropanoids produced in a number of unrelated plant species, including grapevine (Vitis vinifera). In addition to their participation in defense mechanisms in plants, stilbenes, such as resveratrol, display important pharmacological properties and are postulated to be involved in the health benefits associated with a moderate consumption of red wine. Stilbene synthases (STSs), which catalyze the biosynthesis of the stilbene backbone, seem to have evolved from chalcone synthases (CHSs) several times independently in stilbene-producing plants. STS genes usually form small families of two to five closely related paralogs. By contrast, the sequence of grapevine reference genome (cv PN40024) has revealed an unusually large STS gene family. Here, we combine molecular evolution and structural and functional analyses to investigate further the high number of STS genes in grapevine. Our reannotation of the STS and CHS gene families yielded 48 STS genes, including at least 32 potentially functional ones. Functional characterization of nine genes representing most of the STS gene family diversity clearly indicated that these genes do encode for proteins with STS activity. Evolutionary analysis of the STS gene family revealed that both STS and CHS evolution are dominated by purifying selection, with no evidence for strong selection for new functions among STS genes. However, we found a few sites under different selection pressures in CHS and STS sequences, whose potential functional consequences are discussed using a structural model of a typical STS from grapevine that we developed.
Collapse
Affiliation(s)
| | | | - Stéphane Réty
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Raymonde Baltenweck-Guyot
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Anne Poutaraud
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Lauriane Renault
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Dimitri Heintz
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Raphaël Lugan
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Gabriel A.B. Marais
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Sébastien Aubourg
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| | - Philippe Hugueney
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (C.P., R.B.-G., A.P., L.R., P.H.); Centre National de la Recherche Scientifique, Université Lyon 1, Unité Mixte de Recherche 5558 Laboratoire de Biométrie et Biologie Evolutive, F–69622 Villeurbanne, France (R.T., G.A.B.M.); Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165 Unité de Recherche en Génomique Végétale, Université d’Evry-Val-d’Essonne, Equipe de Recherche Labellisée 8196 Centre National de la Recherche Scientifique, F–91057 Evry, France (S.A.); Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357 Institut de Biologie Moléculaire des Plantes, F–67084 Strasbourg, France (D.H., R.L.); Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Faculte de Pharmacie, Université Paris Descartes, F–75270 Paris, France (S.R.); Université de Strasbourg, F–67081 Strasbourg, France (C.P., R.B.-G., A.P., L.R., D.H., R.L., P.H.); Instituto Gulbenkian de Ciência, P–2780–156 Oeiras, Portugal (R.T., G.A.B.M.)
| |
Collapse
|
22
|
Dèrozier S, Samson F, Tamby JP, Guichard C, Brunaud V, Grevet P, Gagnot S, Label P, Leplé JC, Lecharny A, Aubourg S. Exploration of plant genomes in the FLAGdb++ environment. Plant Methods 2011; 7:8. [PMID: 21447150 PMCID: PMC3073958 DOI: 10.1186/1746-4811-7-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/29/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. RESULTS The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). CONCLUSION Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.
Collapse
Affiliation(s)
- Sandra Dèrozier
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Unité Mathématique Informatique et Génome (MIG), UR INRA 1077, Domaine de Vilvert, F-78352 Jouy-en-Josas Cedex, France
| | - Franck Samson
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Unité Mathématique Informatique et Génome (MIG), UR INRA 1077, Domaine de Vilvert, F-78352 Jouy-en-Josas Cedex, France
| | - Jean-Philippe Tamby
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Cécile Guichard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Véronique Brunaud
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Philippe Grevet
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Séverine Gagnot
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
- Laboratoire de Chimie Bactérienne (LCB), UPR CNRS 9043 - IFR 88, 31 Chemin Joseph Aiguier, F-13009 Marseille, France
| | - Philippe Label
- Unité Amélioration, Génétique et Physiologie Forestières (UAGPF), UR INRA 588, 2163 avenue de la Pomme de Pin, CS 4001 Ardon, F-45075 Orléans, France
| | - Jean-Charles Leplé
- Unité Amélioration, Génétique et Physiologie Forestières (UAGPF), UR INRA 588, 2163 avenue de la Pomme de Pin, CS 4001 Ardon, F-45075 Orléans, France
| | - Alain Lecharny
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | - Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| |
Collapse
|
23
|
Martin DM, Aubourg S, Schouwey MB, Daviet L, Schalk M, Toub O, Lund ST, Bohlmann J. Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays. BMC Plant Biol 2010; 10:226. [PMID: 20964856 PMCID: PMC3017849 DOI: 10.1186/1471-2229-10-226] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 10/21/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS) were predicted by in silico analysis of the grapevine (Vitis vinifera) genome assembly 1. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. RESULTS We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. CONCLUSIONS The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information about gene structure and phylogeny for the entire currently known VvTPS gene family.
Collapse
Affiliation(s)
- Diane M Martin
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C, V6T 1Z4, Canada
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, B.C., V6T 1Z4, Canada
| | - Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV) UMR INRA 1165 - Université d'Evry Val d'Essonne - ERL CNRS 8196, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France
| | | | - Laurent Daviet
- Firmenich SA, Corporate R&D Division, Geneva, CH-1211, Switzerland
| | - Michel Schalk
- Firmenich SA, Corporate R&D Division, Geneva, CH-1211, Switzerland
| | - Omid Toub
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C, V6T 1Z4, Canada
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, B.C., V6T 1Z4, Canada
| | - Steven T Lund
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, B.C., V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C, V6T 1Z4, Canada
| |
Collapse
|
24
|
Benhamed M, Martin-Magniette ML, Taconnat L, Bitton F, Servet C, De Clercq R, De Meyer B, Buysschaert C, Rombauts S, Villarroel R, Aubourg S, Beynon J, Bhalerao RP, Coupland G, Gruissem W, Menke FLH, Weisshaar B, Renou JP, Zhou DX, Hilson P. Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J 2008; 56:493-504. [PMID: 18644002 DOI: 10.1111/j.1365-313x.2008.03606.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We have assembled approximately 20 000 Arabidopsis thaliana promoter regions, compatible with functional studies that require cloning and with microarray applications. The promoter fragments can be captured as modular entry clones (MultiSite Gateway format) via site-specific recombinational cloning, and transferred into vectors of choice to investigate transcriptional networks. The fragments can also be amplified by PCR and printed on glass arrays. In combination with immunoprecipitation of protein-DNA complexes (ChIP-chip), these arrays enable characterization of binding sites for chromatin-associated proteins or the extent of chromatin modifications at genome scale. The Arabidopsis histone acetyltransferase GCN5 associated with 40% of the tested promoters. At most sites, binding did not depend on the integrity of the GCN5 bromodomain. However, the presence of the bromodomain was necessary for binding to 11% of the promoter regions, and correlated with acetylation of lysine 14 of histone H3 in these promoters. Combined analysis of ChIP-chip and transcriptomic data indicated that binding of GCN5 does not strictly correlate with gene activation. GCN5 has previously been shown to be required for light-regulated gene expression and growth, and we found that GCN5 targets were enriched in early light-responsive genes. Thus, in addition to its transcriptional activation function, GCN5 may play an important role in priming activation of inducible genes under non-induced conditions.
Collapse
Affiliation(s)
- Moussa Benhamed
- Institut de Biotechnologie des Plantes, UMR 8618, Centre National de la Recherche Scientifique, Université de Paris Sud 11, 91405 Orsay, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Armisén D, Lecharny A, Aubourg S. Unique genes in plants: specificities and conserved features throughout evolution. BMC Evol Biol 2008; 8:280. [PMID: 18847470 PMCID: PMC2576244 DOI: 10.1186/1471-2148-8-280] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Accepted: 10/10/2008] [Indexed: 11/10/2022] Open
Abstract
Background Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications. These duplications lead up to the formation of gene families, which are the usual material for many evolutionary studies. However, all characterized genomes include single-copy (unique) genes that have not received much attention. Unlike gene duplication, gene loss is not an unspecific mechanism but is rather influenced by a functional selection. In this context, we have established and used stringent criteria in order to identify suitable sets of unique genes present in plant proteomes. Comparisons of unique genes in the green phylum were used to characterize the gene and protein features exhibited by both conserved and species-specific unique genes. Results We identified the unique genes within both A. thaliana and O. sativa genomes and classified them according to the number of homologs in the alternative species: none (U{1:0}), one (U{1:1}) or several (U{1:m}). Regardless of the species, all the genes in these groups present some conserved characteristics, such as small average protein size and abnormal intron number. In order to understand the origin and function of unique genes, we further characterized the U{1:1} gene pairs. The possible involvement of sequence convergence in the creation of U{1:1} pairs was discarded due to the frequent conservation of intron positions. Furthermore, an orthology relationship between the two members of each U{1:1} pair was strongly supported by a high conservation in the protein sizes and transcription levels. Within the promoter of the unique conserved genes, we found a number of TATA and TELO boxes that specifically differed from their mean number in the whole genome. Many unique genes have been conserved as unique through evolution from the green alga Ostreococcus lucimarinus to higher plants. Plant unique genes may also have homologs in bacteria and we showed a link between the targeting towards plastids of proteins encoded by plant nuclear unique genes and their homology with a bacterial protein. Conclusion Many of the A. thaliana and O. sativa unique genes are conserved in plants for which the ancestor diverged at least 725 million years ago (MYA). Half of these genes are also present in other eukaryotic and/or prokaryotic species. Thus, our results indicate that (i) a strong negative selection pressure has conserved a number of genes as unique in genomes throughout evolution, (ii) most unique genes are subjected to a low divergence rate, (iii) they have some features observed in housekeeping genes but for most of them there is no functional annotation and (iv) they may have an ancient origin involving a possible gene transfer from ancestral chloroplasts or bacteria to the plant nucleus.
Collapse
Affiliation(s)
- David Armisén
- Unité de Recherche en Génomique Végetale , UMR INRA 1165 - CNRS 8114 - Université d'Evry Val d'Essonne, 2 rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France.
| | | | | |
Collapse
|
26
|
Chantret N, Salse J, Sabot F, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Leroy P, Bernard M, Chalhoub B. Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species. J Mol Evol 2008; 66:138-50. [PMID: 18274696 DOI: 10.1007/s00239-008-9066-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 09/06/2007] [Accepted: 01/02/2008] [Indexed: 11/25/2022]
Abstract
We study here the evolution of genes located in the same physical locus using the recently sequenced Ha locus in seven wheat genomes in diploid, tetraploid, and hexaploid species and compared them with barley and rice orthologous regions. We investigated both the conservation of microcolinearity and the molecular evolution of genes, including coding and noncoding sequences. Microcolinearity is restricted to two groups of genes (Unknown gene-2, VAMP, BGGP, Gsp-1, and Unknown gene-8 surrounded by several copies of ATPase), almost conserved in rice and barley, but in a different relative position. Highly conserved genes between wheat and rice run along with genes harboring different copy numbers and highly variable sequences between close wheat genomes. The coding sequence evolution appeared to be submitted to heterogeneous selective pressure and intronic sequences analysis revealed that the molecular clock hypothesis is violated in most cases.
Collapse
|
27
|
Aubourg S, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Lecharny A, Renou JP. Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. BMC Genomics 2007; 8:401. [PMID: 17980019 PMCID: PMC2174955 DOI: 10.1186/1471-2164-8-401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 11/02/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the finishing of the sequencing of the Arabidopsis thaliana genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis transcriptome to search for genes missed by different annotation processes. Probes on the CATMA microarrays are specific gene sequence tags (GSTs) based on the CDS models predicted by the Eugene software. Among the 24 576 CATMA v2 GSTs, 677 are in regions considered as intergenic by the TAIR annotation. We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models. RESULTS The statistical analysis of the results of more than 500 hybridized samples distributed among 12 organs provides an experimental validation for 465 novel genes. The hybridization evidence was confirmed by RT-PCR approaches for 88% of the 465 novel genes. Comparisons with the current annotation show that these novel genes often encode small proteins, with an average size of 137 aa. Our approach has also led to the improvement of pre-existing gene models through both the extension of 16 CDS and the identification of 13 gene models erroneously constituted of two merged CDS. CONCLUSION This work is a noticeable step forward in the improvement of the Arabidopsis genome annotation. We increased the number of Arabidopsis validated genes by 465 novel transcribed genes to which we associated several functional annotations such as expression profiles, sequence conservation in plants, cognate transcripts and protein motifs.
Collapse
Affiliation(s)
- Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Aubourg S, Renou JP, Lecharny A, Brunaud V. CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. Nucleic Acids Res 2007; 36:D986-90. [PMID: 17940091 PMCID: PMC2238931 DOI: 10.1093/nar/gkm757] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [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] [Indexed: 11/14/2022] Open
Abstract
CATdb is a free resource available at http://urgv.evry.inra.fr/CATdb that provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform. CATMA probes consist of gene-specific sequence tags (GSTs) of 150–500 bp. The v2 version of CATMA contains 24 576 GST probes representing most of the predicted A. thaliana genes, and 615 probes tiling the chloroplastic and mitochondrial genomes. Data in CATdb are entirely processed with the same standardized protocol, from microarray printing to data analyses. CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental conditions, 45 mutants and 63 environmental conditions. All the data contained in CATdb can be downloaded from the web site and subsets of data can be sorted out and displayed either by keywords, by experiments, genes or lists of genes up to 100. CATdb gives an easy access to the complete description of experiments with a picture of the experiment design.
Collapse
Affiliation(s)
- Séverine Gagnot
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Jean-Philippe Tamby
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Marie-Laure Martin-Magniette
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Frédérique Bitton
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Ludivine Taconnat
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Sandrine Balzergue
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Jean-Pierre Renou
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Alain Lecharny
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
| | - Véronique Brunaud
- Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France
- *To whom correspondence should be addressed.+33 1 60 87 45 14+33 1 60 87 45 49 The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
| |
Collapse
|
29
|
Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Clepet C, Aubourg S, Rameau C, Caboche M, Bendahmane A. Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. Plant J 2007; 51:1116-25. [PMID: 17651368 DOI: 10.1111/j.1365-313x.2007.03201.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Scanning DNA sequences for mutations and polymorphisms has become one of the most challenging, often expensive and time-consuming obstacles in many molecular genetic applications, including reverse genetic and clinical diagnostic applications. Enzymatic mutation detection methods are based on the cleavage of heteroduplex DNA at the mismatch sites. These methods are often limited by the availability of a mismatch-specific endonuclease, their sensitivity in detecting one allele in a pool of DNA and their costs. Here, we present detailed biochemical analysis of five Arabidopsis putative mismatch-specific endonucleases. One of them, ENDO1, is presented as the first endonuclease that recognizes and cleaves all types of mismatches with high efficiency. We report on a very simple protocol for the expression and purification of ENDO1. The ENDO1 system could be exploited in a wide range of mutation diagnostic tools. In particular, we report the use of ENDO1 for discovery of point mutations in the gibberellin 3beta-hydrolase gene of Pisum sativum. Twenty-one independent mutants were isolated, five of these were characterized and two new mutations affecting internodes length were identified. To further evaluate the quality of the mutant population we screened for mutations in four other genes and identified 5-21 new alleles per target. Based on the frequency of the obtained alleles we concluded that the pea population described here would be suitable for use in a large reverse-genetics project.
Collapse
Affiliation(s)
- Karine Triques
- URGV, Unité de Recherche en Génomique Végétale, UMR INRA CNRS. 2, Rue Gaston Crémieux, 91057 Evry Cedex, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007; 449:463-7. [PMID: 17721507 DOI: 10.1038/nature06148] [Citation(s) in RCA: 2177] [Impact Index Per Article: 128.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 08/07/2007] [Indexed: 01/12/2023]
Abstract
The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Collapse
Affiliation(s)
- Olivier Jaillon
- Genoscope (CEA) and UMR 8030 CNRS-Genoscope-Université d'Evry, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Aubourg S, Brunaud V, Bruyère C, Cock M, Cooke R, Cottet A, Couloux A, Déhais P, Deléage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlné G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J, Risler JL, Rivière S, Rombauts S, Rouzé P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M, Lecharny A. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Res 2005; 33:D641-6. [PMID: 15608279 PMCID: PMC540069 DOI: 10.1093/nar/gki115] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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] [Indexed: 11/29/2022] Open
Abstract
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.
Collapse
Affiliation(s)
- Sébastien Aubourg
- Unité de Recherche en Génomique Végétale (INRA/CNRS/UEVE) 2 Rue Gaston Crémieux, CP 5708, 91057 Evry Cedex, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B. Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 2005; 17:1033-45. [PMID: 15749759 PMCID: PMC1087984 DOI: 10.1105/tpc.104.029181] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The Hardness (Ha) locus controls grain hardness in hexaploid wheat (Triticum aestivum) and its relatives (Triticum and Aegilops species) and represents a classical example of a trait whose variation arose from gene loss after polyploidization. In this study, we investigated the molecular basis of the evolutionary events observed at this locus by comparing corresponding sequences of diploid, tertraploid, and hexaploid wheat species (Triticum and Aegilops). Genomic rearrangements, such as transposable element insertions, genomic deletions, duplications, and inversions, were shown to constitute the major differences when the same genomes (i.e., the A, B, or D genomes) were compared between species of different ploidy levels. The comparative analysis allowed us to determine the extent and sequences of the rearranged regions as well as rearrangement breakpoints and sequence motifs at their boundaries, which suggest rearrangement by illegitimate recombination. Among these genomic rearrangements, the previously reported Pina and Pinb genes loss from the Ha locus of polyploid wheat species was caused by a large genomic deletion that probably occurred independently in the A and B genomes. Moreover, the Ha locus in the D genome of hexaploid wheat (T. aestivum) is 29 kb smaller than in the D genome of its diploid progenitor Ae. tauschii, principally because of transposable element insertions and two large deletions caused by illegitimate recombination. Our data suggest that illegitimate DNA recombination, leading to various genomic rearrangements, constitutes one of the major evolutionary mechanisms in wheat species.
Collapse
Affiliation(s)
- Nathalie Chantret
- Institut National de la Recherche Agronomique-Centre de Cooperation Internationale en Recherche Agronomique pour le Développement, Biotrop, F-34398 Montpellier Cedex 5, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, Bhalerao RP, Bitton F, Caboche M, Cannoot B, Chardakov V, Cognet-Holliger C, Colot V, Crowe M, Darimont C, Durinck S, Eickhoff H, de Longevialle AF, Farmer EE, Grant M, Kuiper MTR, Lehrach H, Léon C, Leyva A, Lundeberg J, Lurin C, Moreau Y, Nietfeld W, Paz-Ares J, Reymond P, Rouzé P, Sandberg G, Segura MD, Serizet C, Tabrett A, Taconnat L, Thareau V, Van Hummelen P, Vercruysse S, Vuylsteke M, Weingartner M, Weisbeek PJ, Wirta V, Wittink FRA, Zabeau M, Small I. Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res 2004; 14:2176-89. [PMID: 15489341 PMCID: PMC528935 DOI: 10.1101/gr.2544504] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.
Collapse
Affiliation(s)
- Pierre Hilson
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Gent, Belgium.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 2004; 16:2089-103. [PMID: 15269332 PMCID: PMC519200 DOI: 10.1105/tpc.104.022236] [Citation(s) in RCA: 933] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Accepted: 04/22/2004] [Indexed: 05/18/2023]
Abstract
The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.
Collapse
Affiliation(s)
- Claire Lurin
- Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique/Université d'Evry Val d'Essone, CP 5708, 91057 Evry Cedex, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Lescot M, Rombauts S, Zhang J, Aubourg S, Mathé C, Jansson S, Rouzé P, Boerjan W. Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements. Theor Appl Genet 2004; 109:10-22. [PMID: 15085260 DOI: 10.1007/s00122-004-1621-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2003] [Accepted: 01/29/2004] [Indexed: 05/24/2023]
Abstract
Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/ copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.
Collapse
Affiliation(s)
- M Lescot
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Samson F, Brunaud V, Duchêne S, De Oliveira Y, Caboche M, Lecharny A, Aubourg S. FLAGdb++: a database for the functional analysis of the Arabidopsis genome. Nucleic Acids Res 2004; 32:D347-50. [PMID: 14681431 PMCID: PMC308868 DOI: 10.1093/nar/gkh134] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
FLAGdb++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis. FLAGdb++ displays the predicted or experimental data in a position-dependent way and displays correlations and relationships between different features. FLAGdb++ provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and specificities having an impact upon the confidence we will put in the experimental results. A selected subset of the available information is linked to a locus represented on an easy-to-interpret and memorable graphical display. Data are curated, processed and formatted before their integration into FLAGdb++. FLAGdb++ contains different options for easy back and forth navigation through many loci selected at the start of a session. It includes an original two-component visualization of the data, a genome-wide and a local view, which are permanently linked and display complementary information. Density curves along the chromosomes may be displayed in parallel for suggesting correlations between different structural and functional data. FLAGdb++ is fully accessible at http://genoplante-info.infobiogen.fr/FLAGdb/.
Collapse
Affiliation(s)
- Franck Samson
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, CNRS 8114, Université d'Evry Val d'Essonne, 2 rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | | | | | | | | | | | | |
Collapse
|
37
|
Abstract
MOTIVATION The availability of complete genome sequences allows the identification of short DNA segments that are specific to each annotated gene. Such unique gene sequence tags (GSTs) replace advantageously cDNAs in microarray transcript profiling experiments. In particular, probes corresponding to individual members of multigene families can be chosen carefully to avoid cross-hybridization events. RESULTS The Specific Primer and Amplicon Design Software (SPADS) was constructed to delineate the more divergent regions in each gene by comparing them with a completely annotated genome sequence and to select optimal primer pairs for the polymerase chain reaction amplification of one divergent region per gene. SPADS is a unique integrated tool to design specific GSTs from any public or private genome sequences and allows the user to fine-tune GST size and specificity. SPADS has been used to obtain probes for whole genome and family-wide transcript profiling, as well as inserts for gene-specific knock-out experiments. AVAILABILITY The GENOPLANTE SPADS source code and web interface are available upon request. The online version is accessible via http://genoplante-info.infobiogen.fr/spads and via http://oberon.fvms.ugent.be:8080/SPADS/
Collapse
Affiliation(s)
- Vincent Thareau
- Laboratoire Associé de l'Institut National de Recherche Agronomique, France
| | | | | | | | | | | |
Collapse
|
38
|
Crowe ML, Serizet C, Thareau V, Aubourg S, Rouzé P, Hilson P, Beynon J, Weisbeek P, van Hummelen P, Reymond P, Paz-Ares J, Nietfeld W, Trick M. CATMA: a complete Arabidopsis GST database. Nucleic Acids Res 2003; 31:156-8. [PMID: 12519971 PMCID: PMC165518 DOI: 10.1093/nar/gkg071] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as well as primer sequences for GST amplification and a wide range of supplementary information. All CATMA GST sequences are specific to the gene for which they were designed, and all gene models were predicted from a complete reannotation of the genome using uniform parameters. The database is searchable by sequence name, sequence homology or direct SQL query, and is available through the CATMA website at http://www.catma.org/.
Collapse
Affiliation(s)
- Mark L Crowe
- The John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Lecharny A, Boudet N, Gy I, Aubourg S, Kreis M. Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure. J Struct Funct Genomics 2003. [PMID: 12836690 DOI: 10.1023/a:1022614001371] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Gene duplication is considered to be a source of genetic information for the creation of new functions. The Arabidopsis thaliana genome sequence revealed that a majority of plant genes belong to gene families. Regarding the problem of genes involved in the genesis of novel organs or functions during evolution, the reconstitution of the evolutionary history of gene families is of critical importance. A comparison of the intron/exon gene structure may provide clues for the understanding of the evolutionary mechanisms underlying the genesis of gene families. An extensive study of A. thaliana genome showed that families of duplicated genes may be organized according to the number and/or density of intron and the diversity in gene structure. In this paper, we propose a genomic classification of several A. thaliana gene families based on introns in an evolutionary perspective.
Collapse
Affiliation(s)
- Alain Lecharny
- Institut de Biotechnologie des Plantes, Unité Mixte de Recherche-Centre National de la Recherche Scientifique 8618, Université de Paris-Sud, Bât. 630, F-91405 Orsay Cedex, France.
| | | | | | | | | |
Collapse
|
40
|
Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Cruaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A. T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep 2002; 3:1152-7. [PMID: 12446565 PMCID: PMC1308325 DOI: 10.1093/embo-reports/kvf237] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A statistical analysis of 9000 flanking sequence tags characterizing transferred DNA (T-DNA) transformants in Arabidopsis sheds new light on T-DNA insertion by illegitimate recombination. T-DNA integration is favoured in plant DNA regions with an A-T-rich content. The formation of a short DNA duplex between the host DNA and the left end of the T-DNA sets the frame for the recombination. The sequence immediately downstream of the plant A-T-rich region is the master element for setting up the DNA duplex, and deletions into the left end of the integrated T-DNA depend on the location of a complementary sequence on the T-DNA. Recombination at the right end of the T-DNA with the host DNA involves another DNA duplex, 2-3 base pairs long, that preferentially includes a G close to the right end of the T-DNA.
Collapse
Affiliation(s)
- Véronique Brunaud
- URGV, UMR en Génomique Végétale (INRA/CNRS/Université Evry-Val d'Essonne), F-91057 Evry, France
| | - Sandrine Balzergue
- URGV, UMR en Génomique Végétale (INRA/CNRS/Université Evry-Val d'Essonne), F-91057 Evry, France
| | - Bertrand Dubreucq
- Laboratoire de Biologie des Semences, INRA, F-78026, Versailles, France
| | - Sébastien Aubourg
- URGV, UMR en Génomique Végétale (INRA/CNRS/Université Evry-Val d'Essonne), F-91057 Evry, France
| | - Franck Samson
- URGV, UMR en Génomique Végétale (INRA/CNRS/Université Evry-Val d'Essonne), F-91057 Evry, France
| | - Stéphanie Chauvin
- URGV, UMR en Génomique Végétale (INRA/CNRS/Université Evry-Val d'Essonne), F-91057 Evry, France
| | - Nicole Bechtold
- Station de Génétique et Amélioration des Plantes, INRA, F-78026, Versailles, France
- Usine des molécules recombinantes, 1020 route de l'église, bureau 600, Sainte Foy, Canada G1V 3V9
| | | | | | - Georges Pelletier
- Station de Génétique et Amélioration des Plantes, INRA, F-78026, Versailles, France
| | - Loïc Lepiniec
- Laboratoire de Biologie des Semences, INRA, F-78026, Versailles, France
| | - Michel Caboche
- URGV, UMR en Génomique Végétale (INRA/CNRS/Université Evry-Val d'Essonne), F-91057 Evry, France
| | - Alain Lecharny
- URGV, UMR en Génomique Végétale (INRA/CNRS/Université Evry-Val d'Essonne), F-91057 Evry, France
- Tel: +33 1 60 87 45 18; Fax: +33 1 60 87 45 10;
| |
Collapse
|
41
|
Aubourg S, Lecharny A, Bohlmann J. Genomic analysis of the terpenoid synthase ( AtTPS) gene family of Arabidopsis thaliana. Mol Genet Genomics 2002; 267:730-45. [PMID: 12207221 DOI: 10.1007/s00438-002-0709-y] [Citation(s) in RCA: 247] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2002] [Accepted: 05/27/2002] [Indexed: 11/25/2022]
Abstract
A family of 40 terpenoid synthase genes ( AtTPS) was discovered by genome sequence analysis in Arabidopsis thaliana. This is the largest and most diverse group of TPS genes currently known for any species. AtTPS genes cluster into five phylogenetic subfamilies of the plant TPS superfamily. Surprisingly, thirty AtTPS closely resemble, in all aspects of gene architecture, sequence relatedness and phylogenetic placement, the genes for plant monoterpene synthases, sesquiterpene synthases or diterpene synthases of secondary metabolism. Rapid evolution of these AtTPS resulted from repeated gene duplication and sequence divergence with minor changes in gene architecture. In contrast, only two AtTPS genes have known functions in basic (primary) metabolism, namely gibberellin biosynthesis. This striking difference in rates of gene diversification in primary and secondary metabolism is relevant for an understanding of the evolution of terpenoid natural product diversity. Eight AtTPS genes are interrupted and are likely to be inactive pseudogenes. The localization of AtTPS genes on all five chromosomes reflects the dynamics of the Arabidopsis genome; however, several AtTPS genes are clustered and organized in tandem repeats. Furthermore, some AtTPS genes are localized with prenyltransferase genes ( AtGGPPS, geranylgeranyl diphosphate synthase) in contiguous genomic clusters encoding consecutive steps in terpenoid biosynthesis. The clustered organization may have implications for TPS gene evolution and the evolution of pathway segments for the synthesis of terpenoid natural products. Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of the TPS gene family.
Collapse
Affiliation(s)
- S Aubourg
- Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique (INRA), FRE-CNRS, 2 Rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France
| | | | | |
Collapse
|
42
|
Boudet N, Aubourg S, Toffano-Nioche C, Kreis M, Lecharny A. Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila. Genome Res 2001; 11:2101-14. [PMID: 11731501 PMCID: PMC311229 DOI: 10.1101/gr.200801] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The DEAD box RNA helicase (RH) proteins are homologs involved in diverse cellular functions in all of the organisms from prokaryotes to eukaryotes. Nevertheless, there is a lack of conservation in the splicing pattern in the 53 Arabidopsis thaliana (AtRHs), the 32 Caenorhabditis elegans (CeRHs) and the 29 Drosophila melanogaster (DmRHs) genes. Of the 153 different observed intron positions, 4 are conserved between AtRHs, CeRHs, and DmRHs, and one position is also found in RHs from yeast and human. Of the 27 different AtRH structures with introns, 20 have at least one predicted ancient intron in the regions coding for the catalytic domain. In all of the organisms examined, we found at least one gene with most of its intron predicted to be ancient. In A. thaliana, the large diversity in RH structures suggests that duplications of the ancestral RH were followed by a high number of intron deletions and additions. The very high bias toward phase 0 introns is in favor of intron addition, preferentially in phase 0. Results from this comparative study of the same gene family in a plant and in two animals are discussed in terms of the general mechanisms of gene family evolution.
Collapse
Affiliation(s)
- N Boudet
- Institut de Biotechnologie des Plantes, Unité Mixte de Recherche-Centre National Recherche Scientifique 8618, Université de Paris-Sud, Bât. 630, F-91405 Orsay Cedex, France
| | | | | | | | | |
Collapse
|
43
|
Aubourg S, Boudet N, Kreis M, Lecharny A. In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants. Plant Mol Biol 2000; 42:603-13. [PMID: 10809006 DOI: 10.1023/a:1006352315928] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In the sequences released by the Arabidopsis Genome Initiative (AGI), we discovered a new and unexpectedly large family of orphan genes (127 genes by 01.08.99), named AtPCMP. The distribution of the AtPCMP genes on the five chromosomes suggests that the genome of Arabidopsis thaliana contains more than 200 genes of this family (1% of the whole genome). The deduced AtPCMP proteins are characterized by a surprising combinatorial organization of sequence motifs. The amino-terminal domain is made of a succession of three conserved motifs which generate an important diversity. These proteins are classified into three subfamilies based on the length and nature of their carboxy-terminal domain constituted by 1-6 motifs. All the motifs characterized have an important level of conservation in both sequence and spacing. A specific signature of this large family is defined. The presence of ESTs in databases and the detection of clones in A. thaliana cDNA libraries indicate that most of the genes of this family are expressed. The absence of similar sequences outside the plant kingdom strongly suggests that this unusually large orphan family is unique to plants. Features, the genesis, the potential function and the evolution of this plant combinatorial and modular protein family are discussed.
Collapse
Affiliation(s)
- S Aubourg
- Institut de Biotechnologie des Plantes, UMR CNRS 8618, Laboratoire de Biologie du Développement des Plantes, Université de Paris-Sud, Orsay, France
| | | | | | | |
Collapse
|
44
|
Tavares R, Aubourg S, Lecharny A, Kreis M. Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2. Plant Mol Biol 2000; 42:703-717. [PMID: 10809443 DOI: 10.1023/a:1006368316413] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Arabidopsis Genome Initiative has released up to now more than 80% of the genome sequence of Arabidopsis thaliana. About 70% of the identified genes have at least one paralogue. In order to understand the biological function of individual genes, it is essential to study the structure, expression and organization of the entire multigene family. A systematic analysis of multigene families, made possible by the amount of genomic sequence data available, provides important clues for the understanding of genome evolution and plasticity. In this paper, four multigene families of A. thaliana are characterized, namely LCAD, HD-GL2, LGT and MYST. Members of HD-GL2 and LCAD have already been reported in plants. The LGT genes specify proteins containing motifs of glycosyl transferase. No plant genes similar to the LGT genes have been reported to date. The novel MYST family, most likely plant-specific, encodes proteins with no identified function. Sequencing and in silico analysis led to the characterization of 29 novel genes belonging to these four gene families. The organization, structure and evolution of all the members of the four families are discussed, as well as their chromosome location. Expression data of some of the paralogues of each family are also presented.
Collapse
Affiliation(s)
- R Tavares
- Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Université de Paris-Sud, Orsay France
| | | | | | | |
Collapse
|
45
|
Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kötter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream MA, Lyne M, Benes V, Rechmann S, Borkova D, Blöcker H, Scharfe M, Grimm M, Löhnert TH, Dose S, de Haan M, Maarse A, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mündlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby IK, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 1999; 402:769-77. [PMID: 10617198 DOI: 10.1038/47134] [Citation(s) in RCA: 313] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
Collapse
Affiliation(s)
- K Mayer
- GSF-Forschungszentrum f. Umwelt u. Gesundheit, Munich Information Center for Protein Sequences am Max-Planck-Institut f. Biochemie, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Aubourg S, Picaud A, Kreis M, Lecharny A. Structure and expression of three src2 homologues and a novel subfamily of flavoprotein monooxygenase genes revealed by the analysis of a 25kb fragment from Arabidopsis thaliana chromosome IV. Gene 1999; 230:197-205. [PMID: 10216258 DOI: 10.1016/s0378-1119(99)00073-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Biological and computer-assisted analyses of a 25kb fragment from Arabidopsis thaliana chromosome IV led to the characterization of two multigene families and three novel orphan genes, not previously described. The first gene family named AtMO1-4 encodes monooxygenases, related to the prokaryotic salicylate hydroxylases. The second gene family contains three members, two on the analysed 25kb fragment and one on chromosome I. The latter three genes lack introns and are homologous to the previously studied Glycine max src2 gene which is overexpressed at low temperature. Gene expression and primary structure of the deduced proteins are described and compared. Three genes of unknown function, showing tissue specific expressions, are characterized on the 25kb fragment. Full length or partial cognate cDNAs have been sequenced for all the genes studied.
Collapse
Affiliation(s)
- S Aubourg
- Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud, ERS/CNRS 569, F-91405, Orsay Cedex, France
| | | | | | | |
Collapse
|
47
|
Abstract
The numerous genomic sequences and ESTs released by the Arabidopsis thaliana Genome Initiative (AGI) have allowed a systematic and functional study of the DEAD box RNA helicase family. Sequencing and in silico analysis led to the characterization of 28 novel A. thaliana DEAD box RNA helicases forming a family of 32 members, named AtRH. Fourteen AtRH genes with an unexpected heterogeneous mosaic structure are described and compared bringing new information about the genesis of the gene family. The mapping of the AtRH genes shows their repartition on the five chromosomes without clustering and therefore AtRH s have been estimated to 60 genes per A.thaliana haploid genome. Sequence comparisons revealed a very conserved catalytic central domain flanked or not by four classes of extensions in the N- and/or C- extremities. The global amino acid composition of the extensions are tentatively correlated to specific functions such as targeting, protein interaction or RNA binding. The expression of the 32 AtRH genes has been recorded in different tissues. Separate patterns of expression and alternative polyadenylation sites have been shown. Based on the integration of all this information, we propose a classification of the AtRH proteins into subfamilies with associated functions.
Collapse
Affiliation(s)
- S Aubourg
- Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud-ERS/CNRS 569, F-91405 Orsay Cedex, France
| | | | | |
Collapse
|
48
|
Aubourg S, Chéron A, Kreis M, Lecharny A. Structure and expression of an asparaginyl-tRNA synthetase gene located on chromosome IV of Arabidopsis thaliana and adjacent to a novel gene of 15 exons. Biochim Biophys Acta 1998; 1398:225-31. [PMID: 9655910 DOI: 10.1016/s0167-4781(98)00068-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The gene AtNS1 coding for an asparaginyl-tRNA synthetase and located on chromosome IV of Arabidopsis thaliana has been characterized. AtNS1 is the first asparaginyl-tRNA synthetase gene described in higher plants. The genomic environment of AtNS1 has been studied, as well as a partial cDNA of a second homologous asparaginyl-tRNA synthetase gene, AtNS2. Both AtNS1 and AtNS2 exhibit the highest similarity with prokaryotic homologues. A large novel gene of 15 exons, named AtG2484-1, is located adjacent to AtNS1. AtG2484-1 shows features rarely described in plants including large exons and one 3' non-coding exon. PCR and Northern analyses were carried out to obtain information about the expression of these genes in various A. thaliana tissues.
Collapse
Affiliation(s)
- S Aubourg
- Institut de Biotechnologie des Plantes, ERS/CNRS 569, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud, F-91405 Orsay Cedex, France
| | | | | | | |
Collapse
|
49
|
Gy I, Aubourg S, Sherson S, Cobbett CS, Cheron A, Kreis M, Lecharny A. Analysis of a 14-kb fragment containing a putative cell wall gene and a candidate for the ARA1, arabinose kinase, gene from chromosome IV of Arabidopsis thaliana. Gene 1998; 209:201-10. [PMID: 9524266 DOI: 10.1016/s0378-1119(98)00049-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An Arabidopsis thaliana genomic DNA fragment of 14kb has been characterized in the framework of the E.S.S.A. programme. Computational and molecular approaches identified three novel gene sequences coding, respectively, for a protein of unknown function, a putative membrane-anchored cell wall protein and an arabinose kinase gene corresponding to the locus ARA1. The latter two genes named AtSEB1 and AtISA1 have been characterized in detail. They are very different in their organization, codon usage and level of expression. Homologues of AtSEB1 and AtISA1 have been identified. Sequence comparisons showed that the former genes contained a long 5' extension coding for an N-terminal domain probably specifying subcellular localization. Cloning and sequencing of the cognate cDNA for the AtISA1 homologue in A. thaliana, named GAL1, indicate that it encodes for a galactokinase-like protein. Our results highlight the integrative outcome of a systematic sequencing project in which links between biochemically and genetically characterized mutants, ESTs and genomic sequence data are generated.
Collapse
Affiliation(s)
- I Gy
- Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud, CNRS-ERS 569, F-91405, Orsay, Cedex, France
| | | | | | | | | | | | | |
Collapse
|
50
|
Aubourg S, Takvorian A, Chéron A, Kreis M, Lecharny A. Structure, organization and putative function of the genes identified within a 23.9-kb fragment from Arabidopsis thaliana chromosome IV. Gene 1997; 199:241-53. [PMID: 9358062 DOI: 10.1016/s0378-1119(97)00374-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the framework of the complete genome sequencing programme of the crucifer Arabidopsis thaliana, a 23.9-kb fragment from the long arm of chromosome IV has been analysed. This paper presents a methodological approach, integrating computerized predictions, database screening, the sequencing of cognate cDNAs and a PCR-based detection of expression that allows the accumulation of an important amount of information from an anonymous sequence. This work revealed the organization of novel genes and the vestige of a copia-like retrotransposon. The gene AtRH1 encodes the first member of a new subfamily of the plant DEAD box RNA helicases. A recurrent and complete search of dbEST has been used to evaluate the number of different RNA helicases expressed in A. thaliana. On the 18 discriminated members of the family, only a small number seems to be expressed at a relatively high level. The putative gene AtTS1 encodes a novel terpene synthase in A. thaliana, and the genes G14587-5 and G14587-6 encode unknown proteins. This study illustrates most of the situations that could be encountered during the analysis of an anonymous sequence from A. thaliana.
Collapse
Affiliation(s)
- S Aubourg
- Laboratoire de Biologie du Développement des Plantes, Institut de Biotechnologie des Plantes, ERS/CNRS 569, Université de Paris-Sud, Orsay, France
| | | | | | | | | |
Collapse
|