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\begin{document}

\title{First chromosome scale genomes of ithomiine butterflies (Nymphalidae:
Ithomiini): comparative models for mimicry genetic studies}



\author[1]{Jérémy GAUTHIER}%
\author[2]{Joana Meier}%
\author[3]{Fabrice Legeai}%
\author[4]{Melanie McClure}%
\author[5]{Annabel Whibley}%
\author[3]{Anthony Bretaudeau}%
\author[6]{Hélène Boulain}%
\author[7]{Hugues Parrinello}%
\author[8]{Sam Mugford}%
\author[2]{Richard Durbin}%
\author[2]{Chenxi Zhou}%
\author[2]{Shane McCarthy}%
\author[9]{Christopher Wheat}%
\author[4]{Florence Piron-Prunier}%
\author[10]{Christelle Monsempes}%
\author[10]{Marie-Christine François}%
\author[11]{Paul Jay}%
\author[12]{Camille Nous}%
\author[10]{Emma Persyn}%
\author[10]{Emmanuelle  Jacquin-Joly}%
\author[10]{Camille Meslin}%
\author[10]{Nicolas Montagné}%
\author[13]{Claire Lemaitre}%
\author[4]{Marianne Elias}%
\affil[1]{Muséum d'histoire naturelle de la Ville de Genève}%
\affil[2]{University of Cambridge}%
\affil[3]{BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes}%
\affil[4]{Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 – CNRS MNHN UPMC EPHE, Muséum national d’Histoire naturelle, Sorbonne Universités}%
\affil[5]{The University of Auckland School of Biological Sciences}%
\affil[6]{University of Lausanne Department of Ecology and Evolution}%
\affil[7]{CNRS}%
\affil[8]{John Innes Centre}%
\affil[9]{Stockholm University}%
\affil[10]{Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris}%
\affil[11]{Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay}%
\affil[12]{Laboratoire Cogitamus}%
\affil[13]{Univ Rennes, Inria, CNRS, IRISA}%


\vspace{-1em}



  
  \date{May 23, 2024}


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\begin{abstract}
The ithomiine butterflies (Nymphalidae: Danainae) represent the largest
known radiation of Mullerian mimetic butterflies. They dominate by
number the mimetic butterfly communities, which include species such as
the iconic neotropical \emph{Heliconius} genus. Despite recent studies
carried out on ithomiine ecology and genetic structure, no reference
genome was available for the tribe. Here, we generated high-quality,
chromosome-scale genome assemblies of two \emph{Melinaea} species,
\emph{Melinaea marsaeus} and \emph{Melinaea menophilus}, and a draft
genome of \emph{Ithomia salapia}. We obtained genomes with a size
ranging from 396 Mb to 503 Mb across the three species and scaffold N50
of 40.5 Mb and 23.2 Mb for the two chromosome-scale assemblies. Using
collinearity analyses we identified massive rearrangements between the
two closely related \emph{Melinaea} species. A detailed annotation of
transposable elements and genes was performed, resulting in the
identification of 24,341, 31,081 and 31,976 genes in \emph{I. salapia},
\emph{M. marsaeus} and \emph{M. menophilus}, respectively. We used 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 of
mimicry, such as \emph{Heliconius}, and will enable further
understanding of the mechanisms of adaptation and the genetic bases
underpinning mimicry.%
\end{abstract}%



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