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14 results on '"Antonios Zambounis"'

1. Targeted plant improvement through genome editing: from laboratory to field

Author

Hilde-Gunn Opsahl-Sorteberg, Ana Marjanović Jeromela, Antonios Zambounis, Dragana Miladinović, Sandra Cvejić, Allah Bakhsh, Ankica Kondić-Špika, Dulce Antunes, Zoe Hilioti, and Kubilay Yıldırım

Subjects
0106 biological sciences, 0301 basic medicine, Review, Plant Science, Breeding, Biology, 01 natural sciences, 03 medical and health sciences, Genome editing, Improvement, Production (economics), Adaptation (computer science), Productivity, Disease resistance, Food security, business.industry, General Medicine, Plants, Traits, Toolbox, 030104 developmental biology, Risk analysis (engineering), Agriculture, Food processing, business, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Key message This review illustrates how far we have come since the emergence of GE technologies and how they could be applied to obtain superior and sustainable crop production. Abstract The main challenges of today’s agriculture are maintaining and raising productivity, reducing its negative impact on the environment, and adapting to climate change. Efficient plant breeding can generate elite varieties that will rapidly replace obsolete ones and address ongoing challenges in an efficient and sustainable manner. Site-specific genome editing in plants is a rapidly evolving field with tangible results. The technology is equipped with a powerful toolbox of molecular scissors to cut DNA at a pre-determined site with different efficiencies for designing an approach that best suits the objectives of each plant breeding strategy. Genome editing (GE) not only revolutionizes plant biology, but provides the means to solve challenges related to plant architecture, food security, nutrient content, adaptation to the environment, resistance to diseases and production of plant-based materials. This review illustrates how far we have come since the emergence of these technologies and how these technologies could be applied to obtain superior, safe and sustainable crop production. Synergies of genome editing with other technological platforms that are gaining significance in plants lead to an exciting new, post-genomic era for plant research and production. In previous months, we have seen what global changes might arise from one new virus, reminding us of what drastic effects such events could have on food production. This demonstrates how important science, technology, and tools are to meet the current time and the future. Plant GE can make a real difference to future sustainable food production to the benefit of both mankind and our environment.

Published
2021

2. Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species

Author

Athanassios Molassiotis, Antonios Zambounis, Christos Kissoudis, Chrysanthi Polychroniadou, Anna-Maria Farsakoglou, Athanasios Tsaftaris, Christos Bazakos, Konstantinos Kazantzis, Ioannis Ganopoulos, Evangelos Karagiannis, Michail Michailidis, Filippos A. Aravanopoulos, Aliki Xanthopoulou, Maria Manioudaki, and Panagiotis Madesis

Subjects
0106 biological sciences, 0301 basic medicine, Comparative genomics, Genetics, Germplasm, Linkage disequilibrium, food and beverages, Plant Science, Horticulture, Biology, Plant disease resistance, 01 natural sciences, Biochemistry, 03 medical and health sciences, Prunus, 030104 developmental biology, Genetic variation, Cultivar, 010606 plant biology & botany, Biotechnology, Reference genome
Abstract

Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of ‘Satonishiki’ cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.

Published
2020

3. Adaptive response of Pinus monticola driven by positive selection upon resistance gene analogs (RGAs) of the TIR-NBS-LRR subfamily

Author

I. Arzimanoglou, Evangelos Barbas, Filippos A. Aravanopoulos, Antonios Zambounis, Athanasios Tsaftaris, Evangelia V. Avramidou, Panagiotis Madesis, and A. Papadima

Subjects
0106 biological sciences, 0301 basic medicine, Subfamily, White Pines, Biology, Plant disease resistance, Genomics-assisted Breeding, 01 natural sciences, 03 medical and health sciences, Phylogenetics, lcsh:Forestry, Clade, Gene, Positive Selection, Nature and Landscape Conservation, Genetics, Ecology, Fungal Diseases, Forestry, R gene, biology.organism_classification, Resistance Gene Analogs (RGAs), 030104 developmental biology, Cronartium ribicola, GenBank, lcsh:SD1-669.5, Non-synonymous Nucleotide Substitution, 010606 plant biology & botany
Abstract

Western white pine (Pinus monticola Dougl.) is an important forest tree species, which is intensively plagued by the fungus Cronartium ribicola. Resistance gene analogs (RGAs) are the most highly abundant class of potential resistance (R) genes sharing greatly conserved domains and structures. Hence RGAs are crucial components for disease resistance breeding programs on P. monticola serving as useful functional markers. A total of 33 P. monticola RGAs gene homologues were mined from GenBank, encoding for R gene members of the TIR-NBS-LRR subfamily. The existence of positive selection acting upon RGAs was determined using a series of maximum likelihood analyses. Robust evidence of positive selection was showed to be acting widely in three clades across RGA gene phylogeny, both on terminal and ancestral lineages. Furthermore, our analysis revealed that the majority of positively selected residues sites are localized widely across these RGAs sequences, putatively affecting the structures of their ligand-binding domains and offering novel specificities. These results may find immediate application in ongoing disease resistance breeding programs.

Published
2017

4. Forewarned is forearmed: harmonized approaches for early detection of potentially invasive pests and pathogens in sentinel plantings

Author

Maarten de Groot, Alberto Santini, Richard O'Hanlon, Daiva Burokienė, Amani Bellahirech, Alain Roques, H. Tuğba Doğmuş Lehtijärvi, Johanna Witzell, Dmitry L. Musolin, Michelle Cleary, Leho Tedersoo, Simone Prospero, Iva Franić, Carmen Morales-Rodríguez, Marc Kenis, Antonios Zambounis, Natalia Kirichenko, Ejup Çota, Milka Glavendekić, Marie-Anne Auger-Rozenberg, Andrea Vannini, Justyna A. Nowakowska, Iryna Matsiakh, Dovilė Čepukoit, Venche Talgø, Tiia Drenkhan, Kateryna Davydenko, Sylvie Augustin, Sten Anslan, Yuri N. Baranchikov, Magdalena Kacprzyk, Anne Uimari, René Eschen, Rein Drenkhan, Steve Woodward, Department for Innovation in Biological, Agro-Food and Forest Systems, Tuscia University, Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Sukachev Institute of Forest, Russian Academy of Sciences [Moscow] (RAS), Institut National de Recherche en Génie Rural Eaux et Forêts (INRGREF), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institution de la Recherche et de l'Enseignement Supérieur Agricoles [Tunis] (IRESA), Institute of Botany of Nature Research Centre, Agricultural University of Tirana, Ukrainian Research Institute of Forestry and Forest Melioration (URIFFM), Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences (SLU), Isparta Applied Science University, Partenaires INRAE, Estonian University of Life Sciences (EMU), CABI Europe Switzerland, Faculty of forestry, University of Belgrade [Belgrade], Slovenian Forestry Institute, University of Agriculture in Krakow, Siberian Federal University (SibFU), Ukrainian National Forestry University (UNFU), St. Petersburg State Forest Technical University, Cardinal Stefan Wyszynski University in Warsaw, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche [Roma] (CNR), Norwegian Institute of Bioeconomy Research (NIBIO), Institute of Ecology and Earth Sciences [Tartu], University of Tartu, Natural Resources Institute Finland (LUKE), Department of Plant and Soil Science, University of Aberdeen, and Hellenic Agricultural Organization Demeter (HAO Demeter)

Subjects
0106 biological sciences, 0301 basic medicine, insecte nuisible, Plant Science, 01 natural sciences, Basic research, alien invasive pests and pathogens, Cost action, Milieux et Changements globaux, sampling techniques, lcsh:QH301-705.5, udc:630*4, 2. Zero hunger, early warning, napovedovanje, Ecology, alien invasive pests, Ecological Modeling, Pest Risk Analysis, pest risk analysis, analiza tveganja, commodity risk analysis, sentinel plants, prediction, détection précoce, Christian ministry, agent pathogène, analyse de risque, tuji invazivni patogeni, risque phytosanitaire, Higher education, alien invasive pathogens, méthode de prédiction, tuji invazivni škodljivci, [SDE.MCG]Environmental Sciences/Global Changes, VDP::Landbruks- og Fiskerifag: 900::Landbruksfag: 910::Planteforedling, hagebruk, plantevern, plantepatologi: 911, Early detection, Library science, modèle prédictionnel de risque, Aquatic Science, 03 medical and health sciences, Political science, espèce exotique invasive, organisme nuisible, Ecology, Evolution, Behavior and Systematics, business.industry, fungi, 15. Life on land, zgodnje opozarjanje, analiza tveganja škodljivcev, 030104 developmental biology, lcsh:Biology (General), 13. Climate action, Insect Science, tehnike vzorčenja, Animal Science and Zoology, arbre sentinelle, évaluation des risques, business, Sentinel Plants, 010606 plant biology & botany
Abstract

International audience; The number of invasive alien pest and pathogen species affecting ecosystem functioning, human health and economies has increased dramatically over the last decades. Discoveries of invasive pests and pathogens previously unknown to science or with unknown host associations yet damaging on novel hosts highlights the necessity of developing novel tools to predict their appearance in hitherto naive environments. The use of sentinel plant systems is a promising tool to improve the detection of pests and pathogens before introduction and to provide valuable information for the development of preventative measures to minimize economic or environmental impacts. Though sentinel plantings have been established and studied during the last decade, there still remains a great need for guidance on which tools and protocols to put into practice in order to make assessments accurate and reliable. The sampling and diagnostic protocols chosen should enable as much information as possible about potential damaging agents and species identification. Consistency and comparison of results are based on the adoption of common procedures for sampling design and sample processing. In this paper, we suggest harmonized procedures that should be used in sentinel planting surveys for effective sampling and identification of potential pests and pathogens. We also review the benefits and limitations of various diagnostic methods for early detection in sentinel systems, and the feasibility of the results obtained supporting National Plant Protection Organizations in pest and commodity risk analysis.

Published
2019

5. Phenotypic and molecular characterization of apple (Malus × domestica Borkh) genetic resources in Greece

Author

Thomas Sotiropoulos, Nikolaos Tourvas, Athanasios Tsaftaris, Ioannis Ganopoulos, Aliki Xanthopoulou, Filippos A. Aravanopoulos, Euaggelia Avramidou, Nikolaos Koutinas, Panagiotis Madesis, and Antonios Zambounis

Subjects
0106 biological sciences, 0301 basic medicine, Genetics, Malus, Genetic diversity, phenotyping, fungi, food and beverages, genetic diversity, Biology, microsatellite markers, biology.organism_classification, 01 natural sciences, Phenotype, lcsh:S1-972, 03 medical and health sciences, 030104 developmental biology, multivariate analysis, genotyping, Genetic resources, lcsh:Agriculture (General), Genotyping, 010606 plant biology & botany
Abstract

The phenotypic and genetic analysis of apple (Malus × domestica Borkh) genotypes is essential for breeding species. Information on the morphology and genetic structure of apple offers significant help for germplasm maintenance and selection of suitable material to breed superior cultivars. This study shows the results of an investigation on the morphology and the genetic diversity for 19 apple cultivars, which are preserved in an ex situ collection in Naoussa, Central Macedonia, Greece. Information was recorded over a 5-year period for 47 traits describing plant morphology and phenotype, as well as leaf and fruit quality. Data were analyzed using the principal component analysis (PCA) method. The Euclidean distance metric and the Ward’s agglomeration method were used in an unsupervised hierarchical cluster analysis of all cultivars. The cultivars were grouped into four main clusters, suggesting that the characterized apple collection has a high potential for specific breeding goals. Furthermore, the cultivars were genotyped using seven microsatellite primers. Moderate levels of polymorphism were detected, and 38 distinctive alleles (5.4 alleles per primer pair) were identified. Both multivariate clustering approach (phenotypic data) and the genetic distance clustering approach (genetic data) grouped the apple cultivars according to their type. Hence, these data could be used for protection or patenting processes of existing or new apple cultivars carried out by the EU-Community Plant Variety Office.

Published
2018

6. Genetic Diversity and Structure of Tobacco in Greece on the Basis of Morphological and Microsatellite Markers

Author

Ioannis Ganopoulos, Evangelia V. Avramidou, Athanasios Tsaftaris, Antonios Zambounis, Theodoros Moysiadis, Irene Bosmali, Maslin Osathanunkul, Irini Nianiou-Obeidat, Apostolos Kalivas, Panagiotis Madesis, Ioannis Grigoriadis, Eleni Tsaliki, and Aliki Xanthopoulou

Subjects
0106 biological sciences, 0301 basic medicine, Genetics, Genetic diversity, Biology, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Plant morphology, Genetic marker, Genetic variation, Microsatellite, Crop quality, Allele, Agronomy and Crop Science, 010606 plant biology & botany
Published
2016

7. Morpho-physiological diversity in the collection of sour cherry (Prunus cerasus) cultivars of the Fruit Genebank in Naoussa, Greece using multivariate analysis

Author

Theodoros Moysiadis, Konstantinos Kazantzis, Panagiotis Madesis, Athanasios Tsaftaris, Ioannis Chatzicharisis, Thomas Sotiropoulos, Antonios Zambounis, Maslin Osathanunkul, Evangelia V. Avramidou, Ioannis Ganopoulos, Aliki Xanthopoulou, and Filippos A. Aravanopoulos

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, Pomology, biology, Phenology, food and beverages, Titratable acid, Horticulture, biology.organism_classification, 01 natural sciences, Prunus cerasus, 03 medical and health sciences, 030104 developmental biology, Plant morphology, Principal component analysis, Cultivar, 010606 plant biology & botany
Abstract

The phenotypic characterization of sour cherry cultivars provides important information on their attributes, which is of paramount importance for their breeding and germplasm management. This study examined the Hellenic Sour Cherry Genebank, which consists of 27 sour cherry cultivars, located in the Institute of Pomology Fruit Genebank, Naoussa, Greece. The data analyzed in this study were obtained after a ten-year consecutive monitoring of 38 morpho-physiological descriptors of phenology, plant morphology, yield and fruit quality. For the statistical analysis were applied hierarchical cluster analysis and principal component analysis (PCA). According to the analysis, the descriptors demonstrated a high degree of variability, especially, yield, ratio of titratable acidity and soluble solids, number of flower buds, and pit weight. Moreover, the variables fruit equatorial diameter, fruit width, fruit weight, fruit size, fruit shape and lamella shape characters exhibited high discriminating power. Significant positive and negative correlations were detected as well among the studied quantitative traits. The highest significant positive correlation was found between the fruit equatorial diameter and the fruit width (0.974). Whereas, the highest significant negative correlation was found between the ratio of pit volume to fruit volume and the fruit weight (−0.737). An unsupervised hierarchical cluster analysis was performed using the Euclidean distance and the Ward's agglomeration method. The sour cherry cultivars were classified into three main clusters, suggesting that the characterized sour cherry collection has a high potential for specific breeding goals. We discuss the usefulness of the identified correlations among the traits, for potential breeding projects regarding fruit size and quality.

Published
2016

8. RNA sequencing-based transcriptome analysis of kiwifruit infected by Botrytis cinerea

Author

Ioannis Ganopoulos, Lefkothea Karapetsi, Antonios Zambounis, Panagiotis Madesis, and Dimitris Valasiadis

Subjects
0106 biological sciences, 0301 basic medicine, Genetics, RNA, Plant Science, Biology, biology.organism_classification, 01 natural sciences, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Plant defense against herbivory, Gene, Cell wall modification, Pathogen, Transcription factor, 010606 plant biology & botany, Botrytis cinerea
Abstract

An RNA sequencing (RNA-Seq) approach was employed to determine the induced responses of mature kiwifruits infected with Botrytis cinerea, the second most important phytopathogen in commercial crops. In total, we identified 2795 differentially expressed genes (DEGs) across a broad and time-dependent transcriptional reprogramming during infection. Suppression of photosynthesis-related pathways occurred within 12 h after infection (HAI), whereas DEGs involved in particular cell wall modification processes may have facilitated early pathogen colonization. A shift towards defense responses was triggered in delay and not earlier than 24 HAI. The majority of DEGs were up-regulated mainly at 48 HAI and were predominately involved in the induction of pathogen recognition and signaling transduction cascades, biosynthesis of secondary metabolites, activation of pathogenesis-related proteins, transcription factors, and various sorts of transporters. Additionally, a set of B, cinerea genes that are linked to pathogen growth or manipulation of specific plant defense responses were also detected. Overall, our data provide novel insights into the compatible kiwifruit-B. cinerea interaction.

Published
2020

9. The Top 10 oomycete pathogens in molecular plant pathology

Author

M. Shahid Mukhtar, Ronaldo J. D. Dalio, Guido Van den Ackerveken, Gul Shad Ali, Howard S. Judelson, Leonardo Schena, Sophien Kamoun, Mahmut Tör, Niklaus J. Grünwald, Jonathan D. G. Jones, John M. McDowell, Mark Gijzen, Franck Panabières, Jon Hulvey, Daniel F. A. Tomé, Brett M. Tyler, Jean B. Ristaino, Antonios Zambounis, David J. Cahill, Remco Stam, Michelina Ruocco, Xiao-Ren Chen, Andreia Figueiredo, Paul R. J. Birch, S. Roy, Hannele Lindqvist-Kreuze, Francine Govers, Harold J. G. Meijer, William E. Fry, Kurt Lamour, Kentaro Yoshida, Fouad Daayf, Benjamin Petre, and Oliver J. Furzer

Subjects
2. Zero hunger, 0106 biological sciences, Oomycete, 0303 health sciences, biology, Ecology, Soil Science, Albugo candida, Plant Science, 15. Life on land, Phytophthora cinnamomi, biology.organism_classification, 01 natural sciences, Pythium ultimum, 03 medical and health sciences, Phytophthora capsici, Phytophthora ramorum, Phytophthora infestans, Botany, Phytophthora sojae, Agronomy and Crop Science, Molecular Biology, 030304 developmental biology, 010606 plant biology & botany
Abstract

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

Published
2014

10. Chronic stress and disease resistance in the genome model marine seaweed Ectocarpus siliculosus

Author

Antonios Zambounis, Claire M. M. Gachon, and Martina Strittmatter

Subjects
0106 biological sciences, chemistry.chemical_classification, Oomycete, 0303 health sciences, Ectocarpus siliculosus, Plant Science, Aquatic Science, Biology, Plant disease resistance, biology.organism_classification, Laminaria digitata, 01 natural sciences, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Glutathione S-transferase, chemistry, Botany, biology.protein, Arachidonic acid, Pathogen, 030304 developmental biology, 010606 plant biology & botany, Polyunsaturated fatty acid
Abstract

In order to test the capacity of the genome model seaweed Ectocarpus siliculosus to acquire disease resistance, plantlets were repeatedly treated with the polyunsaturated fatty acids (PUFAs) linolenic and arachidonic acid in conditions known to increase the resistance of the kelp Laminaria digitata against the endophytic parasite Laminariocolax tomentosoides. Hydrogen peroxide, a well documented inducer of antioxidative defenses, was also applied as a positive control. Real-time PCR transcriptional profiling revealed an induction of a vanadium-bromoperoxidase, a heat-shock protein, a glutaredoxin and a glutathione S transferase, suggesting a transcriptional remodelling during chronic stress. We further assessed the resistance of E. siliculosus against the oomycete pathogen Eurychasma dicksonii following repeated exposure to arachidonic and linolenic acids. In contrast to observations made on L. digitata, we did not evidence any significant change in resistance compared to mock-treated control E. siliculosus. Altogether, our observations imply that E. siliculosus does react transcriptionally to chronic PUFA exposure. However, these inducible defenses may not be as potent as the ones of L. digitata, or they might be efficiently bypassed by Eu. dicksonii.

Published
2013

11. Highly Dynamic Exon Shuffling in Candidate Pathogen Receptors … What if Brown Algae Were Capable of Adaptive Immunity?

Author

Antonios Zambounis, Marek Eliáš, Claire M. M. Gachon, Lieven Sterck, Florian Maumus, University of Thessaly, University of Ostrava, Dept Plant Syst Biol, Flanders Institute for Biotechnology, Dept Plant Biotechnol & Bioinformat, Universiteit Gent = Ghent University [Belgium] (UGENT), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Scottish Association for Marine Sciences, Natural Environment Research Council [NE/F012705/1, NE/J00460X/1], FP7 Marie Curie award [PERG03-GA-2008-230865], Czech Science Foundation [P305/10/0205], ASSEMBLE [227799], and Scottish Association for Marine Science

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], PROTEIN, Leucine-Rich Repeat Proteins, 01 natural sciences, NONSYNONYMOUS SUBSTITUTION, Exon, REPEAT, brown alga, PHYLOGENETIC ANALYSIS, MAXIMUM-LIKELIHOOD, innate immunity, Phylogeny, Genetics, Recombination, Genetic, 0303 health sciences, biology, Ectocarpus siliculosus, Ectocarpus, adaptive immunity, Exons, Acquired immune system, DNA shuffling, Tetratricopeptide, VARIABLE LYMPHOCYTE RECEPTORS, RESISTANCE GENES, Research Article, Protein Binding, Molecular Sequence Data, chemical and pharmacologic phenomena, Exon shuffling, Phaeophyta, Evolution, Molecular, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, PLANT, Selection, Genetic, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Repetitive Sequences, Nucleic Acid, Innate immune system, Models, Genetic, fungi, Algal Proteins, RECOGNITION, Biology and Life Sciences, Proteins, DNA Shuffling, biology.organism_classification, EVOLUTION, Protein Structure, Tertiary, resistance gene analogue, exon shuffling, Sequence Alignment, 010606 plant biology & botany
Abstract

International audience; Pathogen recognition is the first step of immune reactions. In animals and plants, direct or indirect pathogen recognition is often mediated by a wealth of fast-evolving receptors, many of which contain ligand-binding and signal transduction domains, such as leucine-rich or tetratricopeptide repeat (LRR/TPR) and NB-ARC domains, respectively. In order to identify candidates potentially involved in algal defense, we mined the genome of the brown alga Ectocarpus siliculosus for homologues of these genes and assessed the evolutionary pressures acting upon them. We thus annotated all Ectocarpus LRR-containing genes, in particular an original group of LRR-containing GTPases of the ROCO family, and 24 NB-ARC-TPR proteins. They exhibit high birth and death rates, while a diversifying selection is acting on their LRR (respectively TPR) domain, probably affecting the ligand-binding specificities. Remarkably, each repeat is encoded by an exon, and the intense exon shuffling underpins the variability of LRR and TPR domains. We conclude that the Ectocarpus ROCO and NB-ARC-TPR families are excellent candidates for being involved in recognition/transduction events linked to immunity. We further hypothesize that brown algae may generate their immune repertoire via controlled somatic recombination, so far only known from the vertebrate adaptive immune systems.

Published
2011

12. First Report of Penicillium expansum (Link) Thom. Causing Postharvest Fruit Rot of Kiwifruit in Northern Greece

Author

Thomas Thomidis, I. Prodromou, and Antonios Zambounis

Subjects
0106 biological sciences, biology, 04 agricultural and veterinary sciences, Plant Science, Fruit rot, biology.organism_classification, 01 natural sciences, 040501 horticulture, Horticulture, Postharvest, Penicillium expansum, 0405 other agricultural sciences, Agronomy and Crop Science, 010606 plant biology & botany
Published
2018

13. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Author

Tristan Barbeyron, Wilfrid Carré, Michael Katinka, Loraine Brillet, Klaus Valentin, Karine Labadie, Betina M. Porcel, Zofia Nehr, Francisco Cabello-Hurtado, Mirjam Czjzek, Benjamin Noel, Philippe Deschamps, Susana M. Coelho, John H. F. Bothwell, Pascal J. Lopez, Marek Eliáš, François Artiguenave, François-Yves Bouget, Thierry Tonon, Jean Weissenbach, Christophe Colleoni, Deirdre H. McLachlan, Ahmed A. Moustafa, Cécile Hervé, Olivier Panaud, Catherine Boyen, Jonas Collén, Antonios Zambounis, Frédéric Partensky, Cristian Chaparro, Ludovic Delage, Jose Fernandes Barbosa-Neto, Salvador Capella-Gutierrez, Bernard Kloareg, Nathalie Kowalczyk, Gaelle Samson, Gurvan Michel, Simon M. Dittami, Jean-Marc Aury, J. Mark Cock, Patrick Wincker, Agnès Groisillier, Pi Nyvall Collén, Bénédicte Charrier, Corinne Da Silva, Catherine Leblanc, Lionel Cladière, Alok Arun, Laurence Meslet-Cladiere, Claire M. M. Gachon, Sylvie Rousvoal, Kamel Jabbari, Stefan A. Rensing, Toni Gabaldón, Steven G. Ball, Aikaterini Symeonidi, Julie Poulain, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), 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)-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 Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Department of Plant Physiology, Faculty of Sciences, Charles University [Prague] (CU), Belfast e-Science Centre [Belfast] (BESC), Queen's University [Belfast] (QUB), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Scottish Association for Marine Science (SAMS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, University of Freiburg [Freiburg], Freiburg Initiative in Systems Biology, Centre for Research and Technology Hellas (CERTH), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Charles University [Prague], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona], Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Center for Research and Technology Hellas, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Transposable element, Genome evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Bacterial genome size, Biology, Chondrus, MESH: Base Sequence, MESH: RNA, Plant, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, MESH: Genes, Plant, 14. Life underwater, Gene, Genome size, MESH: Evolution, Molecular, 030304 developmental biology, Plant Proteins, Genetics, 0303 health sciences, Multidisciplinary, MESH: Molecular Sequence Data, Base Sequence, MESH: Plant Proteins, Archaeplastida, Biological Sciences, biology.organism_classification, MicroRNAs, RNA, Plant, MESH: MicroRNAs, MESH: Chondrus, 010606 plant biology & botany
Abstract

Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.

Published
2013

14. Occurrence of a Postharvest Fruit Rot Disease of Apples Caused by Boeremia exigua var. exigua in Ptolemaida Kozani, Greece

Author

Antonios Zambounis, I. Prodromou, and Thomas Thomidis

Subjects
0106 biological sciences, 0301 basic medicine, Boeremia exigua, Plant Science, 030108 mycology & parasitology, Biology, Fruit rot, biology.organism_classification, 01 natural sciences, 03 medical and health sciences, Botany, Exigua, Postharvest, Agronomy and Crop Science, 010606 plant biology & botany
Published
2016

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