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11. The genome of Eucalyptus grandis

Author

Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Hellsten, Uffe, Hayes, Richard D., Grimwood, Jane, Jenkins, Jerry, Lindquist, Erika, Tice, Hope, Bauer, Diane, Goodstein, David M., Dubchak, Inna, Poliakov, Alexandre, Mizrachi, Eshchar, Kullan, Anand R. K., Hussey, Steven G., Pinard, Desre, van der Merwe, Karen, Singh, Pooja, van Jaarsveld, Ida, Silva-Junior, Orzenil B., Togawa, Roberto C., Pappas, Marilia R., Faria, Danielle A., Sansaloni, Carolina P., Petroli, Cesar D., Yang, Xiaohan, Ranjan, Priya, Tschaplinski, Timothy J., Ye, Chu-Yu, Li, Ting, Sterck, Lieven, Vanneste, Kevin, Murat, Florent, Soler, Marçal, Clemente, Hélène San, Saidi, Naijib, Cassan-Wang, Hua, Dunand, Christophe, Hefer, Charles A., Bornberg-Bauer, Erich, Kersting, Anna R., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Boyd, Alexander E., Liston, Aaron, Spatafora, Joseph W., Dharmwardhana, Palitha, Raja, Rajani, Sullivan, Christopher, Romanel, Elisson, Alves-Ferreira, Marcio, Külheim, Carsten, Foley, William, Carocha, Victor, Paiva, Jorge, Kudrna, David, Brommonschenkel, Sergio H., Pasquali, Giancarlo, Byrne, Margaret, Rigault, Philippe, Tibbits, Josquin, Spokevicius, Antanas, Jones, Rebecca C., Steane, Dorothy A., Vaillancourt, René E., Potts, Brad M., Joubert, Fourie, Barry, Kerrie, Pappas, Georgios J., Strauss, Steven H., Jaiswal, Pankaj, Grima-Pettenati, Jacqueline, Salse, Jérôme, Van de Peer, Yves, Rokhsar, Daniel S., and Schmutz, Jeremy

Published
2014
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13. Additional file 1 of Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

Author

Boher, Pau, Soler, Marçal, Fernández-Piñán, Sandra, Torrent, Xènia, Müller, Sebastian Y., Kelly, Krystyna A., Serra, Olga, and Figueras, Mercè

Abstract

Additional file 1: Fig. S1 Amino acid alignment of the potato (S. tuberosum Group Tuberosum) StRIK protein with the most homologous proteins of S. tuberosum Group Phureja (PGSC0003DMP400043638), S. lycopersicum and S. pennellii (XP_004233384.1 and XP_015065578.1), Arabidopsis (AAY24687.1) and maize (AAY24682.1). The Arabidopsis splicing factor 1 SF1-like, At5g51300, identified by Lorkovic and Barta (2002) as KH domain protein, and the two most homologous proteins in potato PGSC0003DMP40003285 and PGSC0003DMP400012836 (designated as S.tubPhurSF1_1 and S.tubPhurSF1_2, respectively) are also included. The two predicted SF1_like-KH conserved protein domains and the highly conserved KH domain core consensus sequence IIGxxGxxI described by Burd and Dreyfuss [21] are indicated. The proline-rich region identified is also shown. The amino acids that are identical are shaded in black and the ones that are similar in grey. The following abbreviations were used for the RIK and SF1 sequences: S.tub, S. tuberosum Group Tuberosum; S.tubPhur, S. tuberosum Group Phureja; S.lyc, S. lycopersicum; S.pen, S. pennellii; Arab, Arabidopsis; Z.may, Z. mays.

Published
2021
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14. Additional file 3 of Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

Author

Boher, Pau, Soler, Marçal, Fernández-Piñán, Sandra, Torrent, Xènia, Müller, Sebastian Y., Kelly, Krystyna A., Serra, Olga, and Figueras, Mercè

Abstract

Additional file 3: Fig. S3 Genomic StRIK sequence. Nucleotide sequence used for StRIK silencing is shown in red characters. The 12 exons of StRIK gene are shadowed in grey. The start initiation and the STOP codons are highlighted in green.

Published
2021
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18. Silencing against the conserved NAC domain of the potato StNAC103 reveals new NAC candidates to repress the suberin associated waxes in phellem

Author

Ministerio de Educación y Ciencia (España), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), European Commission, Generalitat de Catalunya, Universidad de Girona, Soler, Marçal, Verdaguer, Roger, Fernández-Piñán, Sandra, Company-Arumí, Dolors, Boher, Pau, Góngora-Castillo. Elsa, Valls, Marc, Anticó, Enriqueta, Molinas, Marisa, Serra, Olga, Figueras, Mercè, Ministerio de Educación y Ciencia (España), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), European Commission, Generalitat de Catalunya, Universidad de Girona, Soler, Marçal, Verdaguer, Roger, Fernández-Piñán, Sandra, Company-Arumí, Dolors, Boher, Pau, Góngora-Castillo. Elsa, Valls, Marc, Anticó, Enriqueta, Molinas, Marisa, Serra, Olga, and Figueras, Mercè

Abstract

Both suberin and its associated waxes contribute to the formation of apoplastic barriers that protect plants from the environment. Some transcription factors have emerged as regulators of the suberization process. The potato StNAC103 gene was reported as a repressor of suberin polyester and suberin-associated waxes deposition because its RNAi-mediated downregulation (StNAC103-RNAi) over-accumulated suberin and associated waxes in the tuber phellem concomitantly with the induction of representative biosynthetic genes. Here, to explore if other genes of the large NAC gene family participate to this repressive function, we extended the silencing to other NAC members by targeting the conserved NAC domain of StNAC103 (StNAC103-RNAi-c). Transcript profile of the StNAC103-RNAi-c phellem indicated that StNAC101 gene was an additional potential target. In comparison with StNAC103-RNAi, the silencing with StNAC103-RNAi-c construct resulted in a similar effect in suberin but yielded an increased load of associated waxes in tuber phellem, mainly alkanes and feruloyl esters. Globally, the chemical effects in both silenced lines are supported by the transcript accumulation profile of genes involved in the biosynthesis, transport and regulation of apoplastic lipids. In contrast, the genes of polyamine biosynthesis were downregulated. Altogether these results point out to StNAC101 as a candidate to repress the suberin-associated waxes.

Published
2020

19. Oak genome reveals facets of long lifespan

Author

Leroy, Thibault, Murat, Florent, Duplessis, Sébastien, Faye, Sébastien, Francillonne, Nicolas, Labadie, Karine, Le Provost, Grégoire, Lesur Kupin, Isabelle, Bartholome, Jérôme, Faivre-Rampant, Patricia, Kohler, Annegret, Leplé, Jean-Charles, Chantret, Nathalie, Chen, Jun, Dievart, Anne, Alaeitabar, Tina, Barbe, Valérie, Belser, Caroline, Berges, Helene, Bodenes, Catherine, Bogeat-Triboulot, Marie-Béatrice, Bouffaud, Marie-Lara, Brachi, Benjamin, Chancerel, Emilie, Cohen, David, Couloux, Arnaud, Da Silva, Corinne, Dossat, Carole, Ehrenmann, François, Gaspin, Christine, Grima-Pettenati, Jacqueline, Guichoux, Erwan, Hecker, Arnaud, Herrmann, Sylvie, Hugueney, Philippe, Hummel, Iréne, Klopp, Christophe, Lalanne, Céline, Lascoux, Martin, Lasserre, Eric, Lemainque, Arnaud, Desprez-Loustau, Marie Laure, Luyten, Isabelle, Madoui, Mohammed-Amin, Mangenot, Sophie, Marchal, Clémence, Maumus, Florian, Mercier, Jonathan, Michotey, Célia, Panaud, Olivier, Picault, Nathalie, Rouhier, Nicolas, Rué, Olivier, Rustenholz, Camille, Salin, Franck, Soler, Marçal, Tarkka, Mika, Velt, Amandine, Zanne, Amy E., Martin, Francis, Wincker, Patrick, Quesneville, Hadi, Kremer, Antoine, Salse, Jerome, Plomion, Christophe, Aury, Jean-Marc, and Amselem, Joelle

Subjects
Forestry, Genomics, Plant evolution, Plant Immunity, Sequencing
Abstract

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Published
2018

20. Oak genome reveals facets of long lifespan

Author

Plomion, Christophe, Aury, Jean-Marc, Amselem, Joelle, Leroy, Thibault, Murat, Florent, Duplessis, Sébastien, Faye, Sébastien, Francillonne, Nicolas, Labadie, Karine, Le Provost, Grégoire, Lesur Kupin, Isabelle, Bartholome, Jérôme, Faivre-Rampant, Patricia, Kohler, Annegret, Leplé, Jean-Charles, Chantret, Nathalie, Chen, Jun, Dievart, Anne, Alaeitabar, Tina, Barbe, Valérie, Belser, Caroline, Berges, Helene, Bodenes, Catherine, Bogeat-Triboulot, Marie-Béatrice, Bouffaud, Marie-Lara, Brachi, Benjamin, Chancerel, Emilie, Cohen, David, Couloux, Arnaud, da Silva, Corinne, Dossat, Carole, Ehrenmann, François, Gaspin, Christine, Grima Pettenati, Jacqueline, Guichoux, Erwan, Hecker, Arnaud, Herrmann, Sylvie, Hugueney, Philippe, Hummel, Irène, Klopp, Christophe, Lalanne, Céline, Lascoux, Martin, Lasserre, Eric, Lemainque, Arnaud, Desprez-Loustau, Marie Laure, Luyten, Isabelle, Madoui, Mohammed-Amin, Mangenot, Sophie, Marchal, Clémence, Maumus, Florian, Mercier, Jonathan, Michotey, Célia, Panaud, Olivier, Picault, Nathalie, Rouhier, Nicolas, Rué, Olivier, Rustenholz, Camille, Salin, Franck, Soler, Marçal, Tarkka, Mika, Velt, Amandine, Zanne, Amy E., Martin, Francis, Wincker, Patrick, Quesneville, Hadi, Kremer, Antoine, Salse, Jerome, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Etude du Polymorphisme des Génomes Végétaux (EPGV), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Centre National de Ressources Génomiques Végétales (CNRGV), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Department of Soil Ecology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Régulation et Dynamique de la Formation du Bois, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), German Centre for Integrative Biodiversity Research, Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratori del Suro, Universitat de Girona (UdG), Department of Biological Sciences, University at Albany [SUNY], State University of New York (SUNY)-State University of New York (SUNY), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université d'Evry Val d'Essonne, Université Paris-Saclay, European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), German Centre for Integrative Biodiversity Research (iDiv), The George Washington University (GW), Université d'Évry-Val-d'Essonne (UEVE), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Strasbourg (UNISTRA)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Biodiversité, Gènes et Communautés, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), SILVA (SILVA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Lorraine (UL), Helmholtz Centre for Environmental Research (UFZ), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)-AgroParisTech

Subjects
Evolutionary Biology, DNA, Plant, [SDV]Life Sciences [q-bio], Longevity, Genetic Variation, Forestry, Sequence Analysis, DNA, Genomics, Biological Evolution, Article, Evolutionsbiologi, Quercus, Plant evolution, Mutation, Genetics, Sequencing, Plant Immunity, Genetik, Genome, Plant, Phylogeny
Abstract

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Published
2018
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21. Long cold exposure induces transcriptional and biochemical remodelling of xylem secondary cell wall in Eucalyptus

Author

Ployet, Raphael, primary, Soler, Marçal, additional, Carocha, Victor, additional, Ladouce, Nathalie, additional, Alves, Ana, additional, Rodrigues, José-Carlos, additional, Harvengt, Luc, additional, Marque, Christiane, additional, Teulières, Chantal, additional, Grima-Pettenati, Jacqueline, additional, and Mounet, Fabien, additional

Published
2017
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22. The Eucalyptus linker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation

Author

Soler, Marçal, Plasencia, Anna, Larbat, Romain, Pouzet, Cécile, Jauneau, Alain, Rivas, Susana, Pesquet, Edouard, Lapierre, Catherine, Truchet, Isabelle, Grima-Pettenati, Jacqueline, Soler, Marçal, Plasencia, Anna, Larbat, Romain, Pouzet, Cécile, Jauneau, Alain, Rivas, Susana, Pesquet, Edouard, Lapierre, Catherine, Truchet, Isabelle, and Grima-Pettenati, Jacqueline

Abstract

Wood, also called secondary xylem, is a specialized vascular tissue constituted by different cell types that undergo a differentiation process involving deposition of thick, lignified secondary cell walls. The mechanisms needed to control the extent of lignin deposition depending on the cell type and the differentiation stage are far from being fully understood. We found that the Eucalyptus transcription factor EgMYB1, which is known to repress lignin biosynthesis, interacts specifically with a linker histone variant, EgH1.3. This interaction enhances the repression of EgMYB1' s target genes, strongly limiting the amount of lignin deposited in xylem cell walls. The expression profiles of EgMYB1 and EgH1.3 overlap in xylem cells at early stages of their differentiation as well as in mature parenchymatous xylem cells, which have no or only thin lignified secondary cell walls. This suggests that a complex between EgMYB1 and EgH1.3 integrates developmental signals to prevent premature or inappropriate lignification of secondary cell walls, providing a mechanism to fine-tune the differentiation of xylem cells in time and space. We also demonstrate a role for a linker histone variant in the regulation of a specific developmental process through interaction with a transcription factor, illustrating that plant linker histones have other functions beyond chromatin organization.

Published
2017
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23. The Woody-Preferential Gene EgMYB88 Regulates the Biosynthesis of Phenylpropanoid-Derived Compounds in Wood

Author

Soler, Marçal, Plasencia, Anna, Lepikson-Neto, Jorge, Camargo, Eduardo L. O., Dupas, Annabelle, Ladouce, Nathalie, Pesquet, Edouard, Mounet, Fabien, Larbat, Romain, Grima-Pettenati, Jacqueline, Soler, Marçal, Plasencia, Anna, Lepikson-Neto, Jorge, Camargo, Eduardo L. O., Dupas, Annabelle, Ladouce, Nathalie, Pesquet, Edouard, Mounet, Fabien, Larbat, Romain, and Grima-Pettenati, Jacqueline

Abstract

Comparative phylogenetic analyses of the R2R3-MYB transcription factor family revealed that five subgroups were preferentially found in woody species and were totally absent from Brassicaceae and monocots (Soler et al., 2015). Here, we analyzed one of these subgroups (WPS-I) for which no gene had been yet characterized. Most Eucalyptus members of WPS-I are preferentially expressed in the vascular cambium, the secondary meristem responsible for tree radial growth. We focused on EgMYB88, which is the most specifically and highly expressed in vascular tissues, and showed that it behaves as a transcriptional activator in yeast. Then, we functionally characterized EgMYB88 in both transgenic Arabidopsis and poplar plants overexpressing either the native or the dominant repression form (fused to the Ethylene-responsive element binding factor-associated Amphiphilic Repression motif, EAR). The transgenic Arabidopsis lines had no phenotype whereas the poplar lines overexpressing EgMYB88 exhibited a substantial increase in the levels of the flavonoid catechin and of some salicinoid phenolic glycosides (salicortin, salireposide, and tremulacin), in agreement with the increase of the transcript levels of landmark biosynthetic genes. A change in the lignin structure (increase in the syringyl vs. guaiacyl, S/G ratio) was also observed. Poplar lines overexpressing the EgMYB88 dominant repression form did not show a strict opposite phenotype. The level of catechin was reduced, but the levels of the salicinoid phenolic glycosides and the S/G ratio remained unchanged. In addition, they showed a reduction in soluble oligolignols containing sinapyl p-hydroxybenzoate accompanied by a mild reduction of the insoluble lignin content. Altogether, these results suggest that EgMYB88, and more largely members of the WPS-I group, could control in cambium and in the first layers of differentiating xylem the biosynthesis of some phenylpropanoid-derived secondary metabolites including lignin.

Published
2016
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26. The Eucalyptus linker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation

Author

Soler, Marçal, primary, Plasencia, Anna, additional, Larbat, Romain, additional, Pouzet, Cécile, additional, Jauneau, Alain, additional, Rivas, Susana, additional, Pesquet, Edouard, additional, Lapierre, Catherine, additional, Truchet, Isabelle, additional, and Grima‐Pettenati, Jacqueline, additional

Published
2016
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27. Breeding grasses for capacity to biofuel production or silage feeding value: an updated list of genes involved in maize secondary cell wall biosynthesis and assembly

Author

Courtial, Audrey, Soler, Marçal, Chateigner Boutin, Anne Laure, Reymond, Matthieu, Méchin, Valérie, Cassan-Wang, Hua, Grima Pettenati, Jacqueline, Barrière, Yves, Unité de recherche Génétique et Amélioration des Plantes Fourragères (UGAPF), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), INRA, Advanta, Caussade Semences, Limagrain Genetics, MaisAdour, Monsanto SAS, Pioneer Genetique, Pau Euralis, R2n RAGT Semences, SDME KWS France, and Syngenta seeds

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, s-methylmethionine cycle, degradability, bio-ethanol, identifies candidate genes, transcription factor family, lignin, vascular tissue-development, maize, ferulate cross-linking, innamyl alcohol-dehydrogenase, brown-midrib mutant, biogas, cell wall, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, acid o-methyltransferase, silage, caffeoyl-coa 3-o-methyltransferase, cobra-like protein
Abstract

International audience; In the near future, maize, sorghum, or switchgrass stovers and cereal straws will be a significant source of carbohydratesfor sustainable biofuel production, in addition to the current use of grass silage in cattle feeding. However, cell wall properties, including the enzymatic degradability of structural polysaccharides in industrial fermenters or animal rumen, is greatly influenced by the embedding of cell wall carbohydrates in lignin matrix, and the linkages between lignins, p-hydroxycinnamic acids, and arabinoxylans. Breeding for higher and cheaper biofuelor silage production will thus be based on the discovery of genetic traits involved in each cell wall component biosynthesis and deposition in each lignified tissue. Due to its considerable genetic and genomic backgrounds, maize is the relevant model species for identifying traits underlying cell wall degradability variations in grasses. Maize genes involved or putatively involved in the biosynthesis of cell wall phenolic compounds, cell wall carbohydratesand regulation factors were therefore searched for using data available in grass, Arabidopsis, and woody species (mostly poplar and eucalyptus). All maize ortholog genes were searched for using protein sequences and a “blastp” strategy against data available in the www.maizesequence.org database. Genes were also mapped in silico considering their physical position in the same database. Finally, 409 candidate genes putatively involved in secondary cell wall biosynthesis and assembly were shown in the maize genome, out of which 130 were related to phenolic compound biosynthesis, 81 were related to cell wall carbohydrate biosynthesis, and 198 were involved in more or less known regulation mechanisms. Most probable candidate genes involved in regulation and assembly of secondary cell wall belonged to the MYB (45 genes) and NAC (38 genes) families, but also included zinc finger and HDZipIII encoding genes. While genes involved in ferulic acid cross-linkages with other cell wall components were little known, several families putatively involved in (arabino)-xylan chain biosynthesis and in feruloyl transferwere shown, including especially arabinosyl-CoA-acyltransferases, feruloyl-AX b-1,2-xylosyl transferases, and xylan-O-3-arabinosyl transferases. This candidate gene list, which focused on genes and orthologs known to be involved in cell wall component biosynthesis and regulation, cannot be considered as exhaustive. Other genes, whose role in cell wall lignification and deposition have not yet been defined, should very likely be added to the list of candidates required for secondary cell wall assembly. Genes encoding proteins of still unknown function should also be added to the list, as several of the latter are probably involved in lignified tissue biosynthesis and deposition.

Published
2013

28. Eucalyptus hairy roots, a fast, efficient and versatile tool to explore function and expression of genes involved in wood formation

Author

Plasencia, Anna, primary, Soler, Marçal, additional, Dupas, Annabelle, additional, Ladouce, Nathalie, additional, Silva‐Martins, Guilherme, additional, Martinez, Yves, additional, Lapierre, Catherine, additional, Franche, Claudine, additional, Truchet, Isabelle, additional, and Grima‐Pettenati, Jacqueline, additional

Published
2015
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30. Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandis

Author

Yu, Hong, primary, Soler, Marçal, additional, Mila, Isabelle, additional, San Clemente, Hélène, additional, Savelli, Bruno, additional, Dunand, Christophe, additional, Paiva, Jorge A. P., additional, Myburg, Alexander A., additional, Bouzayen, Mondher, additional, Grima-Pettenati, Jacqueline, additional, and Cassan-Wang, Hua, additional

Published
2014
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31. Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus

Author

Camargo, Eduardo Leal Oliveira, primary, Nascimento, Leandro Costa, additional, Soler, Marçal, additional, Salazar, Marcela Mendes, additional, Lepikson-Neto, Jorge, additional, Marques, Wesley Leoricy, additional, Alves, Ana, additional, Teixeira, Paulo José Pereira Lima, additional, Mieczkowski, Piotr, additional, Carazzolle, Marcelo Falsarella, additional, Martinez, Yves, additional, Deckmann, Ana Carolina, additional, Rodrigues, José Carlos, additional, Grima-Pettenati, Jacqueline, additional, and Pereira, Gonçalo Amarante Guimarães, additional

Published
2014
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32. The Eucalyptus grandis R2R3‐MYB transcription factor family: evidence for woody growth‐related evolution and function

Author

Soler, Marçal, primary, Camargo, Eduardo Leal Oliveira, additional, Carocha, Victor, additional, Cassan‐Wang, Hua, additional, San Clemente, Hélène, additional, Savelli, Bruno, additional, Hefer, Charles A., additional, Paiva, Jorge A. Pinto, additional, Myburg, Alexander A., additional, and Grima‐Pettenati, Jacqueline, additional

Published
2014
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33. Eucalyptus hairy roots, a fast, efficient and versatile tool to explore function and expression of genes involved in wood formation.

Author

Plasencia, Anna, Soler, Marçal, Dupas, Annabelle, Ladouce, Nathalie, Silva‐Martins, Guilherme, Martinez, Yves, Lapierre, Catherine, Franche, Claudine, Truchet, Isabelle, and Grima‐Pettenati, Jacqueline

Subjects
*EUCALYPTUS, *PLANT roots, *GENE expression in plants, *WOODY plants, *HARDWOODS, *ECONOMICS
Abstract

Eucalyptus are of tremendous economic importance being the most planted hardwoods worldwide for pulp and paper, timber and bioenergy. The recent release of the Eucalyptus grandis genome sequence pointed out many new candidate genes potentially involved in secondary growth, wood formation or lineage-specific biosynthetic pathways. Their functional characterization is, however, hindered by the tedious, time-consuming and inefficient transformation systems available hitherto for eucalypts. To overcome this limitation, we developed a fast, reliable and efficient protocol to obtain and easily detect co-transformed E. grandis hairy roots using fluorescent markers, with an average efficiency of 62%. We set up conditions both to cultivate excised roots in vitro and to harden composite plants and verified that hairy root morphology and vascular system anatomy were similar to wild-type ones. We further demonstrated that co-transformed hairy roots are suitable for medium-throughput functional studies enabling, for instance, protein subcellular localization, gene expression patterns through RT- qPCR and promoter expression, as well as the modulation of endogenous gene expression. Down-regulation of the Eucalyptus cinnamoyl-CoA reductase1 ( Eg CCR1) gene, encoding a key enzyme in lignin biosynthesis, led to transgenic roots with reduced lignin levels and thinner cell walls. This gene was used as a proof of concept to demonstrate that the function of genes involved in secondary cell wall biosynthesis and wood formation can be elucidated in transgenic hairy roots using histochemical, transcriptomic and biochemical approaches. The method described here is timely because it will accelerate gene mining of the genome for both basic research and industry purposes. [ABSTRACT FROM AUTHOR]

Published
2016
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34. Effects of nitrogen fertilization on global xylem transcript profiling of Eucalyptus urophylla x grandisevaluated by RNA-seq technology

Author

Camargo, Eduardo, primary, Costa, Leandro, additional, Soler, Marçal, additional, Salazar, Marcela, additional, Lepikson, Jorge, additional, Gonçalves, Danieli, additional, Marques, Wesley, additional, Carazzolle, Marcelo, additional, Martinez, Yves, additional, Grima-Pettenati, Jacqueline, additional, and Pereira, Gonçalo, additional

Published
2011
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37. The Eucalyptus grandis R2 R3- MYB transcription factor family: evidence for woody growth-related evolution and function.

Author

Soler, Marçal, Camargo, Eduardo Leal Oliveira, Carocha, Victor, Cassan‐Wang, Hua, San Clemente, Hélène, Savelli, Bruno, Hefer, Charles A., Paiva, Jorge A. Pinto, Myburg, Alexander A., and Grima‐Pettenati, Jacqueline

Subjects
*EUCALYPTUS grandis, *PLANT chemical analysis, *PLANT cell walls, *CHROMOSOME duplication, *ARABIDOPSIS thaliana, *LIGNIN structure
Abstract

The R2 R3- MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide., A total of 141 predicted R2 R3- MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR., We found some R2 R3- MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed., In Eucalyptus, R2 R3- MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth. [ABSTRACT FROM AUTHOR]

Published
2015
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38. Comprehensive Genome-Wide Analysis of the Aux/IAA Gene Family in Eucalyptus: Evidence for the Role of EgrIAA4 in Wood Formation.

Author

Hong Yu, Soler, Marçal, Clemente, Hélène San, Mila, Isabelle, Paiva, Jorge A. P., Myburg, Alexander A., Bouzayen, Mondher, Grima-Pettenati, Jacqueline, and Hua Cassan-Wang

Subjects
*EUCALYPTUS grandis, *AUXIN, *PLANT growth, *PLANT development, *CAMBIUM, *PLANT genomes
Abstract

Auxin plays a pivotal role in various plant growth and development processes, including vascular differentiation. The modulation of auxin responsiveness through the auxin perception and signaling machinery is believed to be a major regulatory mechanism controlling cambium activity and wood formation. To gain more insights into the roles of key Aux/IAA gene regulators of the auxin response in these processes, we identified and characterized members of the Aux/IAA family in the genome of Eucalyptus grandis, a tree of worldwide economic importance. We found that the gene family in Eucalyptus is slightly smaller than that in Populus and Arabidopsis, but all phylogenetic groups are represented. High-throughput expression profiling of different organs and tissues highlighted several Aux/IAA genes expressed in vascular cambium and/or developing xylem, some showing differential expression in response to developmental (juvenile vs. mature) and/or to environmental (tension stress) cues. Based on the expression profiles, we selected a promising candidate gene, EgrIAA4, for functional characterization. We showed that EgrIAA4 protein is localized in the nucleus and functions as an auxin-responsive repressor. Overexpressing a stabilized version of EgrIAA4 in Arabidopsis dramatically impeded plant growth and fertility and induced auxin-insensitive phenotypes such as inhibition of primary root elongation, lateral root emergence and agravitropism. Interestingly, the lignified secondary walls of the interfascicular fibers appeared very late, whereas those of the xylary fibers were virtually undetectable, suggesting that EgrIAA4 may play crucial roles in fiber development and secondary cell wall deposition. [ABSTRACT FROM AUTHOR]

Published
2015
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39. Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus.

Author

Oliveira Camargo, Eduardo Leal, Nascimento, Leandro Costa, Soler, Marçal, Salazar, Marcela Mendes, Lepikson-Neto, Jorge, Marques, Wesley Leoricy, Alves, Ana, Lima Teixeira, Paulo José Pereira, Mieczkowski, Piotr, Carazzolle, Marcelo Falsarella, Martinez, Yves, Deckmann, Ana Carolina, Rodrigues, José Carlos, Grima-Pettenati, Jacqueline, and Guimarães Pereira, Gonçalo Amarante

Subjects
NITROGEN fertilizers, EUCALYPTUS, GENE expression in plants, XYLEM, PLANT cell walls, RNA sequencing, PHENYLPROPANOIDS
Abstract

Background Nitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns. Results Histological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RTqPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants. Conclusions This work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels. [ABSTRACT FROM AUTHOR]

Published
2014
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40. Seasonal variation in transcript abundance in cork tissue analyzed by real time RT-PCR.

Author

SOLER, MARÇAL, SERRA, OLGA, MOLINAS, MARISA, GARCÍA-BERTHOU, EMILI, CARITAT, ANTÒNIA, and FIGUERAS, MERCÈ

Subjects
*BIOSYNTHESIS, *BIOCHEMICAL engineering, *GENES, *CORK oak, *REVERSE transcriptase polymerase chain reaction, *POLYMERASE chain reaction
Abstract

The molecular processes underlying cork biosynthesis and differentiation are mostly unknown. Recently, a list of candidate genes for cork biosynthesis and regulation was made available opening new possibilities for molecular studies in cork oak (Quercus suber L.). Based on this list, we analyzed the seasonal variation in mRNA abundance in cork tissue of selected genes by real time reverse-transcriptase polymerase chain reaction (RT-PCR). Relative transcript abundance was evaluated by principal component analysis and genes were clustered in several functional subgroups. Structural genes of suberin pathways such as CYP86A1, GPAT and HCBT, and regulatory genes of the NAM and WRKY families showed highest transcript accumulation in June, a crucial month for cork development. Other cork structural genes, such as FAT and F5H, were significantly correlated with temperature and relative humidity. The stress genes HSP17.4 and ANN were strongly positively correlated to temperature, in accord with their protective role. [ABSTRACT FROM AUTHOR]

Published
2008
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41. Effects of nitrogen fertilization on global xylem transcript profiling of Eucalyptus urophylla x grandis evaluated by RNA-seq technology.

Author

Camargo, Eduardo, Costa, Leandro, Soler, Marçal, Salazar, Marcela, Lepikson, Jorge, Gonçalves, Danieli, Marques, Wesley, Carazzolle, Marcelo, Martinez, Yves, Grima-Pettenati, Jacqueline, and Pereira, Gonçalo

Subjects
EUCALYPTUS grandis
Abstract

An abstract of the conference paper "Effects of nitrogen fertilization on global xylem transcript profiling of Eucalyptus urophylla x grandis evaluated by RNA-seq technology," by Eduardo Camargo and colleagues is presented.

Published
2011
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42. Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

Author

Mercè Figueras, Olga Serra, Marçal Soler, Pau Boher, Xènia Torrent, Krystyna A. Kelly, Sandra Fernández-Piñán, Sebastian Müller, Boher, Pau [0000-0002-1558-0779], Soler, Marçal [0000-0002-9138-9394], Fernández-Piñán, Sandra [0000-0002-4300-0778], Müller, Sebastian Y [0000-0002-0148-7020], Serra, Olga [0000-0002-1678-0932], Figueras, Mercè [0000-0002-6288-1830], Apollo - University of Cambridge Repository, Müller, Sebastian Y. [0000-0002-0148-7020], MEC, MICINN, and Ministerio de Economía y Competitividad (Espanya)

Subjects
Arabidopsis, Plant Science, Flowers, KH-domain RNA-binding protein, Flowering, Transcriptome, RS2-INTERACTING KH PROTEIN, RNA interference, Gene Expression Regulation, Plant, Stress, Physiological, Gene silencing, Coding region, Gene Regulatory Networks, Gene Silencing, Potato tuber periderm, Gene, Plant Proteins, Solanum tuberosum, Cell Nucleus, biology, Patates -- Genètica, fungi, Wild type, Botany, RNA, food and beverages, Genomics, biology.organism_classification, Plants, Genetically Modified, Development and cell biology, Cell biology, Genòmica, Plant Tubers, RNA, Plant, QK1-989, RNA regulation, DNA Transposable Elements, Potatoes -- Genetics, Research Article
Abstract

Background The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. Results To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue. Conclusions The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm This work was supported by the Ministerio de Educación y Ciencia (AGL2006–07342: identification of the gene and obtention of the transgenic lines), the Ministerio de Innovación y Ciencia [AGL2009–13745, FPI grant to P.B.: Transcript profile of the gene in potato, selection of the transgenic lines], the Ministerio de Economía y Competitividad [AGL2012–36725; AGL2015–67495-C2–1-R: analysis of the periderm anatomy, periderm transcriptome and cell localization of the protein], Departament d’Universitats, Investigació i Societat de la Informació de Catalunya [PhD grant to M.S.], the University of Girona [PhD grant to S.F.-P] and The European Regional Development Fund (ERDF)

Published
2021

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