De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

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.

Authors: Fabien Dutreux, Corinne Da Silva, Léo d’Agata, Arnaud Couloux, Elise J. Gay, Benjamin Istace, Nicolas Lapalu, Arnaud Lemainque, Juliette Linglin, Benjamin Noel, Patrick Wincker, Corinne Cruaud, Thierry Rouxel, Marie-Hélène Balesdent, Jean-Marc Aury