My research focuses upon different topics, in the fields of evolutionary and comparative genomics and ecological genomics.
Specifically, the following lines of research summarize my academic activity:
Evolutionary genomics of gene regulation: Recent advances in High Throughput DNA sequencing (NGS) revolutionized the field of genomics, opening tons of new possibilities for understanding the function and the evolution of genomes. In this context, I focus on the evolution of cis-regulatory elements, with a particular interest on enhancers and promoters in humans and other primates. Using techniques like ChIP-seq and RNA-seq, I am interested in cis-regulatory elements (CREs) active and poised in the primate genomes, trying to address some of the following questions: 1) what are the tempo and mode of cis-regulatory evolution in primates? 2) Are CREs evolving uniformly and at a steady rate across the lineage? 3) what are the genomics features determining whether a given CRE needs to be evolutionarily conserved across primates? 4) To what extent transposable elements (TEs) contribute to the primate regulatory network?
Enhancer and enhancer RNAs (eRNAs) configuration during organismal differentiation: Understanding how cell differentiate from a pluripotent progenitor is a key question in biology and evolution. Specifically, I am interested in how cis-regulatory elements reprogram and reorganize in the different steps of organismal differentiation. I take advantage of NGS approaches like GRO-seq, ATAC-seq and ChIP-seq to address these questions, in different biological systems, with a particular interest on the role of enhancer RNAs. Further, I’m investigating the contribution of a master regulator like Integrator in the above described processes.
Ecological genomics of pollen beetles: Currently, very limited data are available on the genomics of pollinator insects, and nothing is known on the genomic patterns driving host-plant selection and adaptation in pollen beetles. Within pollen beetles of the Meligethinae subfamily, some species are “monophagous” (i.e. a single beetle species is specialized on feeding on a single, species-specific, plant), while other species are “polyphagous”, since they can broadly feed on several plant species. More interestingly, within Meligethinae, the strictly specialized species are often closely related to, and recently diverged from, the broadly generalist species. Notably, Brassicogethes aeneus, the most generalist pollen beetle species (previously known as Meligethes aeneus), is a detrimental agricultural pest, feeding on any kind of Brassicaceae and causing severe damage to oilseed rape crops every year, also in the U.S. Specifically, B. aeneus can cause serious yield losses in both winter and spring oilseed rape crops, and for spring oilseed rape more than 80% yield reduction can occur. The genomes of these species are thus highly similar, and represent an optimal system in which investigating whether specific genomic features are driving the choice of the host plant. Broad questions are therefore: why are some species highly specialized whereas some others are adapted to feed and pollinate on many different plant species? Are there specific gene families driving plant selection and identification, and hence underlying the different degrees of host-plant specificity? To what extent do odorant receptor and detoxification genes contribute to this process? Is there role for gene regulation in the adaptation to different phytophagous life-styles in pollen beetles?
Evolutionary biology, phylogenetics, molecular ecology, systematics and biodiversity of water beetles (Hydraenidae): Hydraenidae (minute moss beetles) includes ca. 2000 species worldwide distributed; most moss beetles species live in freshwater habitats, a few genera live in humus. Current projects on these group see the collaboration of several international colleagues (among others: Ignacio Ribera, Institute of Evolutionary Biology, Barcelona; Philip Perkins, Harvard University; Manfred Jäch, Natural History Museum, Wien). Species belonging to this family are frequently endemic to very narrow areas, sometimes a single stream or a single valley, and hence relevant from a biogeographic standpoint. They also usually live in clean and cold waters, and are therefore good indicators of water quality. This research line has so far lead to several publications on international journals and many projects are currently running. For the next years, my intention is to employ NGS (RNA-seq, ATAC-seq) in order to study Hydraenidae evolutionary biology with a genomics approach. Several interesting questions could be addressed: why are some water beetles exclusive of freshwaters, whereas others are adapted to live in hyper-saline or even in marine environments? I would like to leverage functional genomics approaches, similar to the ones aforementioned for pollen beetles, in order to understand whether the evolution of gene regulation and expression has played a role in the adaptation to different aquatic environments.