At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions.

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria

The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II)2Cys6 transcription factor BcBot6

Botrydial (BOT) is a non-host specific phytotoxin produced by the polyphagous phytopathogenic fungus Botrytis cinerea. The genomic region of the BOT biosynthetic gene cluster was investigated and revealed two additional genes named Bcbot6 and Bcbot7. Analysis revealed that the G + C/A + T-equilibrated regions that contain the Bcbot genes alternate with A + T-rich regions made of relics of transposable elements that have undergone repeat-induced point mutations (RIP). Furthermore, BcBot6, a Zn(II)2Cys6 putative transcription factor was identified as a nuclear protein and the major positive regulator of BOT biosynthesis. In addition, the phenotype of the DBcbot6 mutant indicated that BcBot6 and therefore BOT are dispensable for the development, pathogenicity and response to abiotic stresses in the B. cinerea strain B05.10. Finally, our data revealed that B. pseudocinerea, that is also polyphagous and lives in sympatry with B. cinerea, lacks the ability to produce BOT. Identification of BcBot6 as the major regulator of BOT synthesis is the first step towards a comprehensive understanding of the complete regulation network of BOT synthesis and of its ecological role in the B. cinerea life cycle

A gene coding for a monomeric form of cucumber mosaic virus satellite RNA confers tolerance to CMV

International audienceA gene whose transcript bears a monomeric form of cucumber mosaic virus (CMV) satellite RNA was introduced into tobacco (Nicotiana tabacum ‘Xanthi’ nc) plants by using an Ri plasmid-based vector system. On CMV infection, the transcript of the satellite RNA gene was used as a template to yield unit-length satellite RNA, which was efficiently amplified by the virus. Plants bearing the satellite RNA gene displayed long-term tolerance to CMV infection and were also tolerant to CMV infection by aphids, the natural vector of CMV. Implications of these results concerning the mechanism of satellite RNA replication are discussed

Comportement de plantes transgeniques exprimant un gene codant pour une forme monomerique de l'ARN satellite du virus de la mosaique du concombre face au virus

National audienc

RepetDB: a unified resource for transposable element references

International audienceTransposable elements (TEs) are major players in the structure and evolution of eukaryote genomes. Thanksto their ability to move around and replicate within genomes, they are probably the most important contributorsto genome plasticity. The insertion of TEs close to genes can affect gene structure, expression and function,contributing to the genetic diversity underlying species adaptation. Many studies have shown that TEs aregenerally silenced through epigenetic defense mechanisms, and that these elements play an important role inepigenetic genome regulation. Their detection and annotation are considered essential and must be undertakenin the frame of any genome sequencing project.Here, we will present the new version of RepetDB [1] (Amselem et al., Mobile DNA, 2019),(https://urgi.versailles.inrae.fr/repetdb) our TE database developed to store and retrieve detected, classifiedand annotated TEs in a standardized manner. This RepetDB v2 new version was updated with 31 more speciesof plants and fungi and provides TE consensi with evidences able to justify their classification.RepetDB v2 is a customized implementation of InterMine [2,3], an open-source data warehouse frameworkused here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence.InterMine provides powerful capabilities to query and visualize all biological information on TE. It allows tomake simple search on the database using the QuickSearch (‘google like search’) or make more complexqueries using the Querybuilder to display various desired information.RepetDB v2 is designed to be a TE knowledge base populated with full de novo TE annotations of complete(or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates theexploration of specific TE families, superfamilies or orders across a large range of species. It also makespossible cross-species searches and comparisons of TE family content between genomes.References1. Amselem, J., Cornut, G., Choisne, N., Alaux, M., Alfama-Depauw, F., Jamilloux, V., Maumus, F., Letellier, T.,Luyten, I., Pommier, C., Adam-Blondon, A. F., & Quesneville, H. (2019). RepetDB: a unified resource fortransposable element references. Mobile DNA, 10, 6. https://doi.org/10.1186/s13100-019-0150-y2. InterMine: extensive web services for modern biology. Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M,Heimbach J, Hu F, Smith R, Stˇepán R, Sullivan J, Micklem G. Nucleic Acids Res. 2014 Jul; 42 (Web Serverissue): W468-723. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, StepanR, Sullivan J, Wakeling M, Watkins X, Micklem G. Bioinformatics (2012) 28 (23): 3163-3165

Toward phloem deciphering : a transcriptome analysis of the phloem of apium graveolens in arabidopsis thaliana

International audienc

RepetDB: a unified resource for transposable element references

International audienceTransposable elements (TEs) are major players in the structure and evolution of eukaryote genomes. Thanksto their ability to move around and replicate within genomes, they are probably the most important contributorsto genome plasticity. The insertion of TEs close to genes can affect gene structure, expression and function,contributing to the genetic diversity underlying species adaptation. Many studies have shown that TEs aregenerally silenced through epigenetic defense mechanisms, and that these elements play an important role inepigenetic genome regulation. Their detection and annotation are considered essential and must be undertakenin the frame of any genome sequencing project.Here, we will present the new version of RepetDB [1] (Amselem et al., Mobile DNA, 2019),(https://urgi.versailles.inrae.fr/repetdb) our TE database developed to store and retrieve detected, classifiedand annotated TEs in a standardized manner. This RepetDB v2 new version was updated with 31 more speciesof plants and fungi and provides TE consensi with evidences able to justify their classification.RepetDB v2 is a customized implementation of InterMine [2,3], an open-source data warehouse frameworkused here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence.InterMine provides powerful capabilities to query and visualize all biological information on TE. It allows tomake simple search on the database using the QuickSearch (‘google like search’) or make more complexqueries using the Querybuilder to display various desired information.RepetDB v2 is designed to be a TE knowledge base populated with full de novo TE annotations of complete(or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates theexploration of specific TE families, superfamilies or orders across a large range of species. It also makespossible cross-species searches and comparisons of TE family content between genomes.References1. Amselem, J., Cornut, G., Choisne, N., Alaux, M., Alfama-Depauw, F., Jamilloux, V., Maumus, F., Letellier, T.,Luyten, I., Pommier, C., Adam-Blondon, A. F., & Quesneville, H. (2019). RepetDB: a unified resource fortransposable element references. Mobile DNA, 10, 6. https://doi.org/10.1186/s13100-019-0150-y2. InterMine: extensive web services for modern biology. Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M,Heimbach J, Hu F, Smith R, Stˇepán R, Sullivan J, Micklem G. Nucleic Acids Res. 2014 Jul; 42 (Web Serverissue): W468-723. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, StepanR, Sullivan J, Wakeling M, Watkins X, Micklem G. Bioinformatics (2012) 28 (23): 3163-3165

Systemic response to aphid infestation by Myzus persicae in the phloem of apuim graveolens

International audienc

Transcriptome analysis of the phloem in the plant response to virus, bacteria or fungi pathogens

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