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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. 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 i5K Webinar Series
Presented on February 1st 2017
BIPAA Apollo Training
Presented on March 22nd 2017
(NB: this recording has not been captioned or edited) 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:
​" Tiny, Unseeing Mite Defies Expectations ".
"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 Unige, Le Journal de UNIGE, Le Temps and a video on "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.