First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies

Gauthier Jérémy, Meier Joana, Legeai Fabrice, McClure Melanie, Whibley Annabel, Bretaudeau Anthony, Boulain Hélène, Parrinello Hugues, Mugford Sam T., Durbin Richard, Zhou Chenxi, McCarthy Shane, Wheat Christopher W., Piron-Prunier Florence, Monsempès Christelle, François Marie-Christine, Jay Paul, Noûs Camille, Persyn Emma, Jacquin-Jolyb Emmanuelle, Meslin Camille, Montagné Nicolas, Lemaitre Claire, Elias Marianne. 2023. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies. Molecular Ecology Resources, 23 (4) : 872-885.

Url - autres données associées : https://github.com/JeremyLGauthier/scripts_Ithomiine_genomes

Résumé : The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.

Mots-clés Agrovoc : génome, phylogénie, génomique, Nymphalidae, Lepidoptera

Mots-clés libres : Chromosome-level genome, Hi-C, Ithomiine butterflies, Mimicry, Olfaction

Classification Agris : L10 - Génétique et amélioration des animaux

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Agences de financement hors UE : Agence Nationale de la Recherche

Projets sur financement : (FRA) Organisation et montée en puissance d'une Infrastructure Nationale de Génomique, (FRA) Répétabilité du processus de spéciation chez les papillons: replications naturelles dans une zone de suture, (FRA) La transparence : origine physique, fonctions adaptatives et évolution chez les papillons transparents

Auteurs et affiliations

• Gauthier Jérémy, Natural History Museum (CHE) - auteur correspondant
• Meier Joana, University of Cambridge (GBR)
• Legeai Fabrice, INRAE (FRA)
• McClure Melanie, CNRS (FRA)
• Whibley Annabel, University of Auckland (NZL)
• Bretaudeau Anthony, INRAE (FRA)
• Boulain Hélène, UNIL (CHE)
• Parrinello Hugues, CNRS (FRA)
• Mugford Sam T., John Innes Centre (GBR)
• Durbin Richard, University of Cambridge (GBR)
• Zhou Chenxi, University of Cambridge (GBR)
• McCarthy Shane, University of Cambridge (GBR)
• Wheat Christopher W., Stockholm University (SWE)
• Piron-Prunier Florence, CNRS (FRA)
• Monsempès Christelle, INRAE (FRA)
• François Marie-Christine, INRAE (FRA)
• Jay Paul, CNRS (FRA)
• Noûs Camille, Sorbonne université (FRA)
• Persyn Emma, CIRAD-BIOS-UMR PVBMT (REU)
• Jacquin-Jolyb Emmanuelle, INRAE (FRA)
• Meslin Camille, INRAE (FRA)
• Montagné Nicolas, INRAE (FRA)
• Lemaitre Claire, INRIA (FRA)
• Elias Marianne, CNRS (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/608013/)

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