Research
Amazing Arthropods | Incredible Insects
  
As the most successful terrestrial animals, they demonstrate countless evolutionary adaptations exploiting many ecological niches, making them ideal for investigating how conservation or divergence and gains or losses of functional genomic elements give rise to the splendour of animal biology. This diversity makes insects and other arthropods fascinating to study, as models for processes like ageing and sociality, and also because of their roles in human, livestock, and crop health as disease vectors, in agriculture as pests, pollinators, or biological control agents, and more generally in ecology and environmental conservation.
My doctoral studies detailed the computational comparative analysis of insect genomes applied to the characterisation of trends and features that distinguish this diverse animal group. The research focused on the innate immune system of disease-vector mosquitoes as a key factor determining the transmission of some of the most devastating diseases of mankind, and was complemented by broader comparative genomic analyses with additional insect species. Pioneered by the fruit fly, sequenced genomes have come to represent a logical framework for building comprehensive biological knowledgebases. However, these cannot exist in isolation, as cross-species comparisons detail the evolutionary histories of genomic elements and so inform their putative functions.
During my research I have developed comparative approaches to explore evolutionary-functional correspondences with an early focus on disease-vector mosquitoes. As insect genome sequencing has progressed I have played an active role in the comparative analyses of many diverse species including beetles, wasps, lice, ants, bees, bumblebees, butterflies, flies, ticks, mites, and of course, more mosquitoes. With more than 100 arthropod genomes already having been sequenced, and many more projects planned or already under way, e.g. as part of the i5K initiative, the field of insect genomics is expanding rapidly. I believe that with the growing body of data we can move towards an enhanced understanding of insect biology through integrative evolutionary systems biology approaches.
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Resources
Benchmarking Universal Single-Copy Orthologs - BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.      http://busco.ezlab.org
The Hierarchical Catalog of Orthologs - OrthoDB classifies protein-coding genes into groups of orthologs descended from a single gene of the last common ancestor.      www.orthodb.org

Presented on February 1st 2017
Clustering and mapping of i5K species to OrthoDB8 - all ortho-group and protein alignment data for the 28 arthropods sequenced and annotated as part of the  i5K pilot project .  
Codon Alignment Viewer for each of the anopheline genomes - whole genome alignments available for browsing (developed with Irwin Jungreis at MIT) .      http://www.broadinstitute.org/compbio1/cav.php
Anopheles Alignment Locator - Gene Identifier Search. Quickly and easily look up your favourite gene view the whole-genome alignments.
Orthology for the Anopheles genomes project - orthology delineation across the anophelines, other mosquitoes, and outgroup species linked to annotations and VectorBase.  
Orthology for the seven ant genomes project - orthology delineation across the ants and five outgroup species linked to annotations and source databases.     http://cegg.unige.ch/orthodbants
Insect immune-related genes and gene families - access to gene family assignments, annotations and phylogenetic data from the mosquito immunogenomics projects.    http://cegg.unige.ch/Insecta/immunodb

Research Highlights

"Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface." 

Featured in University of Geneva's

' Le Journal ' & ' Le Campus ':

UNIGE Le Journal article "Le papillon «Manduca sexta» est, sous sa forme larvaire, un amateur des cultures de tabac et de pommes de terre. La connaissance de son génome permettra de comprendre comment
il  parvient à résister à
un poison aussi nocif
que la nicotine." 
"Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomised Hox genes and super-dynamic intron evolution." 

Featured in GBE Highlight article by Danielle Venton:
  
 
"Coauthor Stephen Richards, from the Baylor College of Medicine in Texas, says his “mind is still blown” when he reflects on this finding."
"Genomic insights into the Ixodes scapularis tick vector of Lyme disease."  featured in Le Matin -
"Des Suisses décodent le génome de la tique".

Lead on Radio Télévision Suisse CQFD:
"la tique est enfin décortiquée".

GenomeWeb - "Tick Genome Provides Resource for Understanding Bloodsucker's Biology, Disease Transmission".
"Unique features of a global human ectoparasite identified through sequencing of the bed bug genome." featured in The New Yorker -
"Crosstown Traffic: The Bedbug Genome". And BBC News -
"Bed-bug DNA scanned for vulnerabilities".
Newsweek - "Ick Factor"
"Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection" featured in TechTimes - "Study Of Blood Sucking Kissing Bugs Could Help Control Chagas Disease".
"Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions" featured in Sydney Morning Herald - "Genome mapping could find a way to finally give blowflies the flick".
"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" CEGMA, the most widely-used software for assessing assembly completeness, announced on their website that they will no longer support CEGMA development and instead encourage researchers to use BUSCO: “ Goodbye CEGMA, hello BUSCO! ”.
"Genomic signatures of evolutionary transitions from solitary to group living" in Science’s Highlights - "For bees, many roads lead to social harmony" - Nature’s Outlooks - "The beeline" - and  The Scientist - "The Evolution of Social Bees: Scientists describe the genetic changes associated with solitary-to-social transitions throughout bee evolution".
"The genomes of two key bumblebee species with primitive eusocial organisation"  & "A depauperate immune repertoire precedes evolution of sociality in bees" featured in Genome Biology’s Research Highlights - "The making of eusociality: insights from two bumblebee genomes" - BMC Blogs - "Disease, drugs and a social life: insights from humble bee genomes" - The Scientist - "Genome Digest: The social genes of bees" - Handelszeitung - "Schweizer entschlüsseln wichtiges Hummel-Erbgut" - The International Business Times - "Pollination interrupted: How the bumblebee genome study can help" - and Actualités Unige - "Les génomes des bourdons créent le buzz dans le domaine de la pollinisation".
"Evolution of sexual traits influencing vectorial capacity in anopheline mosquitoes" featured in Science’s Perspectives - "An unexpected cost of sex", The Economist - "Plugging away: A mosquito’s ability to transmit disease depends on its sexual behaviour" - and ScienceNews - "Sexual conflict in mosquitoes may have worsened spread of malaria".
"Mosquito sex and malaria" - on
The Economist's cover
"Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes" & "Extensive introgression in a malaria vector species complex revealed by phylogenomics" Science issue cover, featured in Science’s Perspectives - "Conundrum of jumbled mosquito genomes", Nature Genetics’ Research Highlights, Trends in Parasitology’s Spotlight - "Evolving the world's most dangerous animal", The Economist, The Scientist - "Mosquito Genomes Galore", Neue Zürcher Zeitung, Marie Curie Actions News, and Actualités Unige.
"The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera" featured in The Scientist - "Genome Digest: Checkered history".
"Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality" featured in The Scientist - "The Genetics of Society".
"Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics" & "Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens" featured in Science’s Editor’s Choice - "Closing the Vector Circle" - and Nature Genetics’ Research Highlights, the Tribune de Genève, Television Suisse Romande, Actualités UnigeLe Journal de UNIGE, Le Temps and a video on 
  1. LeTempsCulex1
  2. LeTempsCulex2
"Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle" featured at Nature News - "Sequencing Napoleon's nemesis" - and the Tribune de Genève, and the Association des Médecins du canton de Genève.
"Functional and evolutionary insights from the genomes of three parasitoid Nasonia species" featured in Nature’s Editor’s Summary - "Parasitic wasps' DNA laid bare" - and a news item on Leman Bleu and Radio Suisse Romande, and an article in the Tribune de Genève.
"Leucine-rich repeat protein complex activates mosquito complement in defence against Plasmodium parasites" featured in Science’s Editor’s Choice - "Mosquito Immune Mediation".
"The genome of the model beetle and pest Tribolium castaneum" featured in Nature’s Editor’s Summary - "Cereal offender".
"Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes" featured in Science’s Editor’s Choice, and at Scitizen, bringing science closer to society.
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
    This element represents the description field.
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    NAME OF PRODUCT
    This element represents the description field.
  108. Managing Director
    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
    This element represents the description field.
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    NAME OF PRODUCT
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    NAME OF PRODUCT
    This element represents the description field.
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
    This element represents the description field.
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    NAME OF PRODUCT
    This element represents the description field.
  124. Managing Director
    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
    This element represents the description field.
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    NAME OF PRODUCT
    This element represents the description field.
  129. Managing Director
    NAME OF PRODUCT
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  130. Managing Director
    NAME OF PRODUCT
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  131. Managing Director
    NAME OF PRODUCT
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  132. Managing Director
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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  137. Managing Director
    NAME OF PRODUCT
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  138. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  139. Managing Director
    NAME OF PRODUCT
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    NAME OF PRODUCT
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    NAME OF PRODUCT
    This element represents the description field.
  143. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  144. Managing Director
    NAME OF PRODUCT
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  145. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  146. Managing Director
    NAME OF PRODUCT
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  149. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  150. Managing Director
    NAME OF PRODUCT
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  151. Managing Director
    NAME OF PRODUCT
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    NAME OF PRODUCT
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  153. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
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    NAME OF PRODUCT
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    NAME OF PRODUCT
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  156. Managing Director
    NAME OF PRODUCT
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  157. Managing Director
    NAME OF PRODUCT
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  158. Managing Director
    NAME OF PRODUCT
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  159. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  160. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  161. Managing Director
    NAME OF PRODUCT
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    NAME OF PRODUCT
    This element represents the description field.
  164. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  165. Managing Director
    NAME OF PRODUCT
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  166. Managing Director
    NAME OF PRODUCT
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  167. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  168. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
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    NAME OF PRODUCT
    This element represents the description field.
  170. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  171. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  172. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  173. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  174. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  175. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  176. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  177. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  178. Managing Director
    NAME OF PRODUCT
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  179. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  180. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  181. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  182. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  183. Managing Director
    NAME OF PRODUCT
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  184. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  185. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  186. Managing Director
    NAME OF PRODUCT
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  187. Managing Director
    NAME OF PRODUCT
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  188. Managing Director
    NAME OF PRODUCT
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  189. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  190. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  191. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  192. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  193. Managing Director
    NAME OF PRODUCT
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  194. Managing Director
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  195. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  196. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  197. Managing Director
    NAME OF PRODUCT
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  198. Managing Director
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  199. Managing Director
    NAME OF PRODUCT
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  200. Managing Director
    NAME OF PRODUCT
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  201. Managing Director
    NAME OF PRODUCT
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  202. Managing Director
    NAME OF PRODUCT
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  203. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  204. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  205. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  206. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  207. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  208. Managing Director
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  210. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  211. Managing Director
    NAME OF PRODUCT
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  212. Managing Director
    NAME OF PRODUCT
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  213. Managing Director
    NAME OF PRODUCT
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  214. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  215. Managing Director
    NAME OF PRODUCT
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  216. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  217. Managing Director
    NAME OF PRODUCT
    This element represents the description field.
  218. Managing Director
    Title 218
  219. Managing Director
    Title 219
  220. Managing Director
    Title 220
  221. Managing Director
    Title 221
    Description
  222. Managing Director
    Title 222
    Description
  223. Managing Director
    Title 223
    Description
  224. Managing Director
    Title 224
    Description
  225. Managing Director
    Title 225
    Description
  226. Managing Director
    Title 226
    Description
  227. Managing Director
    Title 227
    Description
  228. Managing Director
    Title 228
    Description
  229. Managing Director
    Title 229
    Description
  230. Managing Director
    Title 230
    Description
  231. Managing Director
    Title 231
    Description
  232. Managing Director
    Title 232
    Description
  233. Managing Director
    Title 233
    Description
  234. Managing Director
    Title 234
    Description
  235. Managing Director
    Title 235
    Description
  236. Managing Director
    Title 236
    Description
  237. Managing Director
    Title 237
    Description
  238. Managing Director
    Title 238
    Description
  239. Managing Director
    Title 239
    Description
  240. Managing Director
    Title 240
    Description
  241. Managing Director
    Title 241
    Description
  242. Managing Director
    Title 242
    Description
  243. Managing Director
    Title 243
    Description
  244. Managing Director
    Title 244
    Description
  245. Managing Director
    Title 245
    Description
  246. Managing Director
    Title 246
    Description
  247. Managing Director
    Title 247
    Description
  248. Managing Director
    Title 248
    Description
  249. Managing Director
    Title 249
    Description
  250. Managing Director
    Title 250
    Description
  251. Managing Director
    Title 251
    Description
  252. Managing Director
    Title 252
    Description
  253. Managing Director
    Title 253
    Description
  254. Managing Director
    Title 254
    Description
  255. Managing Director
    Title 255
    Description
  256. Managing Director
    Title 256
    Description
  257. Managing Director
    Title 257
    Description
  258. Managing Director
    Title 258
    Description
  259. Managing Director
    Title 259
    Description
  260. Managing Director
    Title 260
    Description
  261. Managing Director
    Title 261
    Description
  262. Managing Director
    Title 262
    Description
  263. Managing Director
    Title 263
    Description
  264. Managing Director
    Title 264
    Description
  265. Managing Director
    Title 265
    Description
  266. Managing Director
    Title 266
    Description
  267. Managing Director
    Title 267
    Description
  268. Managing Director
    Title 268
    Description
  269. Managing Director
    Title 269
    Description
  270. Managing Director
    Title 270
    Description
  271. Managing Director
    Title 271
    Description
  272. Managing Director
    Title 272
    Description
  273. Managing Director
    Title 273
    Description
  274. Managing Director
    Title 274
    Description
  275. Managing Director
    Title 275
    Description
  276. Managing Director
    Title 276
    Description
  277. Managing Director
    Title 277
    Description
  278. Managing Director
    Title 278
    Description
  279. Managing Director
    Title 279
    Description
  280. Managing Director
    Title 280
    Description
  281. Managing Director
    Title 281
    Description
  282. Managing Director
    Title 282
    Description
  283. Managing Director
    Title 283
    Description
  284. Managing Director
    Title 284
    Description
  285. Managing Director
    Title 285
    Description
  286. Managing Director
    Title 286
    Description
  287. Managing Director
    Title 287
    Description
  288. Managing Director
    Title 288
    Description
  289. Managing Director
    Title 289
    Description
  290. Managing Director
    Title 290
    Description
  291. Managing Director
    Title 291
    Description
  292. Managing Director
    Title 292
    Description
  293. Managing Director
    Title 293
    Description
  294. Managing Director
    Title 294
    Description
  295. Managing Director
    Title 295
    Description
  296. Managing Director
    Title 296
    Description
  297. Managing Director
    Title 297
    Description