De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
| Autor: | Dutreux, Fabien, Da Silva, Corinne, d’Agata, Léo, Couloux, Arnaud, Gay, Elise J., Istace, Benjamin, Lapalu, Nicolas, Lemainque, Arnaud, Linglin, Juliette, Noel, Benjamin, Wincker, Patrick, Cruaud, Corinne, Rouxel, Thierry, Balesdent, Marie-Hélène, Aury, Jean-Marc |
|---|---|
| Přispěvatelé: | BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Genoscope, Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), France Genomique [ANR-10-INBS-09-08], PROMOSOL (Association pour la promotion de la selection des plantes oleagineuses), French National research agency (ANR) [ANR-12-ADAP-0009], Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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) |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
Statistics and Probability
Data Descriptor oilseed rape Leptosphaeria maculans Leptosphaeria biglobosa Brassica napus Leptosphaeria genomes oilseed rape canola [SDV]Life Sciences [q-bio] Library and Information Sciences canola Education Ascomycota Genome assembly algorithms [SDV.BV]Life Sciences [q-bio]/Vegetal Biology DNA sequencing Sequence Analysis RNA Comparative genomics High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Genomics Computer Science Applications [SDE]Environmental Sciences Genome Fungal Statistics Probability and Uncertainty Information Systems |
| Zdroj: | Scientific Data Scientific Data, Nature Publishing Group, 2018, 5 (180235), 11 p. ⟨10.1038/sdata.2018.235⟩ Scientific Data 180235 (5), 11 p.. (2018) |
| ISSN: | 2052-4463 |
| DOI: | 10.1038/sdata.2018.235 |
| Popis: | open; International audience; Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalization previously unsuspected following Illumina sequencing. Moreover nanopore sequencing allowed us to generate a chromosome-level assembly for the L. maculans reference isolate, JN3. The genome annotation was supported by integrating conserved proteins and RNA sequencing from Leptosphaeria-infected samples. The newly produced high-quality assemblies and annotations of those three Leptosphaeria genomes will allow further studies, notably focused on the tripartite interaction between L. maculans, L. biglobosa and oilseed rape. The discovery of as yet unknown effectors will notably allow progress in B. napus breeding towards L. maculans resistance. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|