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\begin{document}

\title{Multi-integrated genomic data for Passiflora foetida provides insights
into genome size evolution and floral development in Passiflora}



\author[1]{Yi Zou}%
\author[2]{Jie Wang}%
\author[3]{Dan Peng}%
\author[2]{Xiaoni Zhang}%
\author[4]{Luke Tembrock}%
\author[5]{Jinliang Yang}%
\author[6]{Jianli Zhao}%
\author[7]{Hong Liao}%
\author[2]{Zhiqiang Wu}%
\affil[1]{Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen}%
\affil[2]{Chinese Academy of Agricultural Sciences Agricultural Genomes Institute at Shenzhen}%
\affil[3]{Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture}%
\affil[4]{Affiliation not available}%
\affil[5]{Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln}%
\affil[6]{Yunnan University}%
\affil[7]{Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology Institute of Biodiversity}%


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  \date{May 23, 2024}


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\begin{abstract}
\emph{Passiflora} is a plant genus known for its extremely distinctive
and colorful flowers and a wide range of genome sizes (over ten-fold
variation). However, the relationship between differences in genome size
and organization and the variations in flower size and morphology among
\emph{Passiflora} species remains largely unexplored. Here, we assembled
a chromosome-scale genome of \emph{Passiflora foetida}, which is a close
relative of the commercial passionfruit \emph{P. edulis}. While the
genome of \emph{P. foetida} contains a substantial proportion of
repetitive elements (66.7\% of 424.16 Mb), it possesses significantly
fewer copies of long terminal repeat retrotransposons (LTR-RTs) compared
to P. edulis (83.94\% of 1278.14 Mb; 87.29\% of 1241.66 Mb). The
disparity in LTR-RTs is one of the main contributors to the differences
in genome sizes between these two species and possibly in floral traits.
Additionally, we observed variation in insertion times and copy numbers
of LTR-RTs across different TE lineages. Then, by integrating
transcriptomic data from 33 samples (eight floral organs and flower buds
at three developmental stages) with phylogenomic and metabolomic data,
we conducted an in-depth analysis of the expression, phylogeny, and copy
number of MIKC-type MADS-box genes and identified essential biosynthetic
genes responsible for flower color and scent. Our study provides new
insights on genome size variation and the evolution of flower
development in two important \emph{Passiflora} species.%
\end{abstract}%



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