Publications

2025

1. A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito

   Olivia V. Goldman, Alexandra E. DeFoe, Yanyan Qi, Yaoyu Jiao, Shih-Che Weng, Brittney Wick, Leah Houri-Zeevi, Priyanka Lakhiani, Takeshi Morita, Jacopo Razzauti, Adriana Rosas-Villegas, Yael N. Tsitohay, Madison M. Walker, Ben R. Hopkins, Joshua X.D. Ang, Igor Antoshechkin, Yu Cai, Fangying Chen, Yen-Chung Chen, Julien Devilliers, Linhan Dong, Roberto Feuda, Paolo Gabrieli, Artyom Kopp, Hyeogsun Kwon, Hsing-Han Li, Tzu-Chiao Lu, Thalita Lucio, João T. Marques, Marcus F. Oliveira, Roenick P. Olmo, Umberto Palatini, Zeaan M. Pithawala, Julien Pompon, Yan Reis, João Rodrigues, Ryan C. Smith, Maximilian Haeussler, Omar S. Akbari, Laura B. Duvall, Helen White-Cooper, Trevor R. Sorrells, Roshan Sharma, Hongjie Li, Leslie B. Vosshall, and Nadav Shai

   Cell, Oct 2025

   Abs DOI

   The female Aedes aegypti mosquito’s remarkable ability to hunt humans and transmit pathogens relies on her unique biology. Here, we present the Aedes aegypti Mosquito Cell Atlas, a comprehensive single-nucleus RNA sequencing dataset of more than 367,000 nuclei from 19 dissected tissues of adult female and male Aedes aegypti, providing cellular-level resolution of mosquito biology. We identify novel cell types and expand our understanding of sensory neuron organization of chemoreceptors across all sensory tissues. Our analysis uncovers male-specific cells and sexually dimorphic gene expression in the antenna and brain. In female mosquitoes, we find that glial cells, rather than neurons, undergo the most extensive transcriptional changes in the brain following blood feeding. Our findings provide insights into the cellular basis of mosquito behavior and sexual dimorphism. The Aedes aegypti Mosquito Cell Atlas resource enables systematic investigation of cell-type-specific expression across all mosquito tissues.

2. Hematophagy Generates a Convergent Genomic Signature in Mosquitoes and Sandflies

   Julien Devilliers, Ben Warren, Ezio Rosato, Charalambos P Kyriacou, and Roberto Feuda

   Genome Biology and Evolution, Mar 2025

   Abs DOI

   Blood feeding (hematophagy) is widespread across Diptera (true flies), yet the underlying genetic basis remains poorly understood. Using phylogenomics, we show that four gene families associated with neuromodulation, immune responses, embryonic development, and iron metabolism have undergone independent expansions within mosquitoes and sandflies. Our findings illuminate the underlying genetic basis for blood-feeding adaptations in these important disease vectors.

3. An Optimized SPLiT-Seq Protocol for Insects

   Julien Devilliers, Elena Emili, Virginia Vanni, Jordi Solana, and Roberto Feuda

   Mar 2025

   Abs DOI

   Single-cell RNA-sequencing revolutionized our approach of transcriptomic studies, enabling to analyze gene expression across cell type in a tissue. Here we introduce an optimized cell dissociation and a Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq) protocol to perform single-cell RNA-seq in insects. Up to 400,000 cells can be used as starting material within a single experiment.

4. Evolution of opsin genes in closely-related species of butterflies specialized in different microhabitats

   Joséphine Ledamoisel, Andrew Dang, Julien Devilliers, Tiphaine Marvillet, Sophie Lemoine, Manuela Lopez-Villavicencio, Adriana Briscoe, Vincent Debat, and Violaine Llaurens

   bioRxiv, Mar 2025

   Abs DOI

   Multiple selective pressures can shape the evolution of color vision in animals, by acting on the co- evolution of the opsin genes. How do adaptive processes shape the duplications of opsins, the evolution of their amino acids and the modification of their patterns of expression? At large phylogenetic scales, natural selection due to the contrasted light environments has been found to have a profound impact on the evolution of the opsin gene family. However, in closely-related species, species interactions due to sexual selection or competition may also influence opsin evolution. Here, we investigate the diversification of opsin sequences and their expression in closely-related blue Morpho butterfly species, living in different microhabitats, to shed light on the effect of biotic and abiotic selective pressures shaping the evolution of their opsin gene family. First, we combined genomics, transcriptomics and immunochemistry to precisely characterize the expression and the spatial distribution of the opsin proteins found in the eyes of Morpho helenor. We found unique ommatidial types compared to other butterfly species. We then investigated the evolution of opsin genes among 18 Morpho species, found signature of positive selection on two opsin genes, and identified key co-evolving amino-acids shaping the diversification of the Morpho visual system. We showed that such opsin evolution was correlated to both light environment and wing coloration, highlighting the joint effect of several selective pressures in the evolution of those proteins. Overall, our study underlines the peculiar evolution of visual systems in closely-related species specialized in divergent microhabitats.Competing Interest StatementThe authors have declared no competing interest.European Union (ERC-2022-COG - OUTOFTHEBLUE - 101088089)Human Frontier Science Program

2024

1. Molecular correlates of swarming behaviour in Aedes aegypti males

   Julien Devilliers, Hollie Marshall, Ben Warren, Charalambos P. Kyriacou, Luciana O. Araripe, Rafaela V. Bruno, Ezio Rosato, and Roberto Feuda

   Biology Letters, Mar 2024

   Abs DOI

   Mosquitoes are the deadliest vectors of diseases. They impose a huge health burden on human populations spreading parasites as disparate as protozoans (malaria), viruses (yellow fever and more) and nematodes (filariasis) that cause life-threatening conditions. In recent years, mating has been proposed as a putative target for population control. Mosquitoes mate mid-air, in swarms initiated by males and triggered by a combination of internal and external stimuli. As the number of females in a swarm is limited, there is intense competition among males, and they ‘retune’ their physiology for this demanding behaviour. There is limited knowledge on the ‘genetic reprogramming’ required to enable swarming. Interestingly, recent evidence indicates that the upregulation of circadian clock genes may be involved in the swarming of malaria mosquitoes of the genus Anopheles. Here, we use whole-head RNA-seq to identify gene expression changes in Aedes aegypti males that are engaged in swarming in a laboratory setting. Our results suggest that in preparation to swarming, males tend to lower some housekeeping functions while increasing remodelling of the cytoskeleton and neuronal connectivity; the transcription of circadian clock genes is unaffected.

2023

1. Shallow Whole-Genome Sequencing of Aedes japonicus and Aedes koreicus from Italy and an Updated Picture of Their Evolution Based on Mitogenomics and Barcoding

   Nicola Zadra, Alessia Tatti, Andrea Silverj, Riccardo Piccinno, Julien Devilliers, Clifton Lewis, Daniele Arnoldi, Fabrizio Montarsi, Paula Escuer, Giuseppe Fusco, Veronica De Sanctis, Roberto Feuda, Alejandro Sánchez-Gracia, Annapaola Rizzoli, and Omar Rota-Stabelli

   Insects, Mar 2023

   Abs DOI

   Aedes japonicus and Aedes koreicus are two invasive mosquitoes native to East Asia that are quickly establishing in temperate regions of Europe. Both species are vectors of arboviruses, but we currently lack a clear understanding of their evolution. Here, we present new short-read, shallow genome sequencing of A. japonicus and A. koreicus individuals from northern Italy, which we used for downstream phylogenetic and barcode analyses. We explored associated microbial DNA and found high occurrences of Delftia bacteria in both samples, but neither Asaia nor Wolbachia. We then assembled complete mitogenomes and used these data to infer divergence times estimating the split of A. japonicus from A. koreicus in the Oligocene, which was more recent than that previously reported using mitochondrial markers. We recover a younger age for most other nodes within Aedini and other Culicidae. COI barcoding and phylogenetic analyses indicate that A. japonicus yaeyamensis, A. japonicus amamiensis, and the two A. koreicus sampled from Europe should be considered as separate species within a monophyletic species complex. Our studies further clarify the evolution of A. japonicus and A. koreicus, and indicate the need to obtain whole-genome data from putative species in order to disentangle their complex patterns of evolution.