Our friend and colleague Sylvain Foret died in his sleep on 17 December 2016, while on a trip in Spain (read more in the Vale).
Sylvain did his undergraduate in Montpellier and Paris (France), where he studied invertebrate physiology and computer science. He obtained his PhD in 2007 from The Australian National University, working on genomics in the honeybee and in other insects such as beetles and wasps. From 2007 to 2009 he worked at the Mathematical Sciences Institute (ANU) investigating computational and statistical aspects of biological sequences comparison methods. He was then recruited to the ARC Centre of Excellence for Coral reef studies at James Cook University (2009-2011), where he worked on the transcriptomes, genomes and epigenomes of various invertebrates, with a particular focus on corals and other cnidarians. In 2012, Sylvain started his group at ANU, where his current research includes examining the mechanisms of epigenetic regulation in the honeybee and in corals, as well as comparative genomics in various invertebrates.
Interactions between genome and environment
Over evolutionary time scales, selection shapes the genes, gene families and other functional genomic elements that play adaptive roles. We seek to characterise these genomic adaptation in the context of the life history of their organisms. We are particularly interested in fast evolving gene families and lineage specific expansions, such as the insect odorant binding proteins (OBPs) and chemosensory proteins (CSPs).
Within the lifetime of an organism, genomes can also respond to changes in the environment and produce different phenotypic outputs. We are interested in the molecular bases of this phenotypic plasticity. In particular we study the roles played by epigenetic regulation in mediating responses to environmental changes. The main models that we use for this purpose are the European honeybee (Apis mellifera) and scleractinian corals such as the staghorn coral (Acropora millepora).
Evolution of epigenetic regulation
The epigenetic regulatory mechanisms have evolved and diversified. For instance, DNA methylation varies greatly between species. At one end of the spectrum, DNA methylation is absent from the fly (Drosophila melanogaster) or the worm (Caenorhabditis elegans). At the other end of the spectrum, mammalian genomes display very high methylation levels (up to 80%). Various intermediate situations can be found in invertebrates. We seek to understand how these various DNA methylation landscapes evolved, and the roles that they play.
The rapid advances in molecular techniques allow us to tackle the above comparative genomics and epigenomics questions at the whole genome level, producing an unprecedented amount of data. We are interested in developing new methods for the analysis of such large datasets. This includes genome assembly algorithms, and statistical inference methods for differental gene expression and differential methylation patterns.
- A. Moya, L. Huisman, E. E. Ball, D. C. Hayward, L. C. Grasso, C. M. Chua, H. N. Woo, J-P. Gattuso, S. Foret, and D. J. Miller. Whole transcriptome analysis of the coral Acropora millepora reveals complex response to -driven acidification during the initiation of calcification. Molecular Ecology, 2012
- S. Foret, R. Kucharski, M. Pellegrini, S. Feng, S. E. Jacobsen, G. E. Robinson, and R. Maleszka. DNA methylation dynamics, metabolic fluxes, gene splicing and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A, 2012.
- S. Foret, F. Seneca, D. de Jong, A. Bieller, G. Hemmrich, R Augustin, D. C. Hayward, E. E. Ball, T. C. G. Bosch, K. Agata, M. Hassel, and D. J. Miller. Phylogenomics reveals an anomalous distribution of usp genes in metazoans. Mol Biol Evol, 28(1):153–161, Jan 2011.
- F. Lyko, S. Foret, R. Kucharski, S. Wolf, C. Falckenhayn, and R. Maleszka. The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol, 8(11):e1000506, 2010.
- S. Foret, B. Knack, E. Houliston, T. Momose, M. Manuel, E. Queinnec, D. C. Hayward, E. E. Ball, and D. J. Miller. New tricks with old genes: the genetic bases of novel cnidarian traits. Trends Genet, 26(4):154–8, 2010.
- S. Foret, R. Kucharski, Y. Pittelkow, G. A. Lockett, and R. Maleszka. Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes. BMC Genomics, 10:472, 2009.
- S. Forêt, S. R. Wilson, and C. J. Burden. Empirical distribution of k-word matches in biological sequences.Pattern Recognition, 42(4):539–548, 2009.
- R. Kucharski, J. Maleszka, S. Foret, and R. Maleszka. Nutritional control of reproductive status in honeybees via DNA methylation. Science, 319(5871):1827–30, 2008.
- G. Weinstock, ..., S. Forêt, ..., and R.A. Gibbs. Insights into social insects from the genome of the honeybee Apis mellifera. Nature, 443(7114):931–49, 2006.
- S. Forêt and R. Maleszka. Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera). Genome Res, 16(11):1404–13, 2006.