Chlamytina: displaying Chlamydomonas reinhardtii epipotreomic landscape

Chlamytina is a project focused in this well-known green-alage model try to answer a common question in some proteomic/transcriptomic studies: Are my molecules of interest epigenetically regulated?

To fill this gap, we collected all epigenectic files published until the date and developed a new chromatin states model (ChromHMM) including 6mA, 5mC and nucleosome-profile for the first time. Additionally, an epigenome-browser was conducted focusing on the site-specific approach. This tool engage the link-up between proteomic/transcriptomic changes and epigenetic patterns, thus displaying the Chlamydomonas reinhardtii epi-proteogenomic landscape.

P(inus)ra(diata)-G(ene)E(expression) Atlas

In the current context of global warming, the study of stress in plants becomes a priority. Conifers have received little attention even though their phylogenetic position can solve several key evolutionary and environmental acclimation questions. Pinus, the largest genus of conifers and arguably the most important genus of trees in the world, provides an ideal example to explore gene regulation differentiation due to its long evolutionary history and potentially unique genomic features. We focused in Pinus radiata the most stress-sensitive species in the genus and widely used for contanst production of forest services. Pra-GE Atlas tries to answer the next questions: Where and when are all genes identified till the date expressed? , Which is the regulatory signals defining tissue identity? Specific and conserved responses to environmental stress?

This is a challenge because P.radiata as a non-model organism does not have public reference genome, despite its industrial interest. This tool will generate a large amount of basic knowledge about this organism and will make applied research easier in the future.

PlantFUNCO: integrative functional-genomics to allow the detection of functional constraints

Many comparative-genomics studies interrogate sequence-conserved loci of interest across a wide range of species and its function is determined by perturbing their homologous in a single model organism. In this context, a maze of opportunities and challenges appeared to systematically and confidently determine the extent of conservation at the functional genomics level between model species. PlantFUNCO is constituted by various tools and two main resources, inter-species chromatin states and functional genomics conservation scores, for three well known plant model organisms (A.thaliana, Z.mays and O.sativa).

PlantFUNCO aim to leverage data diversity and extrapolate findings from different models to determine the extent of functional constraint, thus, deepen our understanding of how plants phenotypic plasticity has fascinatingly evolved.