Biography


"My long-term motivation is to become an interdisciplinary, system-scale thinker aiming to achieve a macro-level understanding of biological diversity."

I am postdoctoral researcher at the Molecular Biology Department, Max Planck Institute for Biology. I am part of the Geogenomic Archaeology Campus of Tübingen (GACT) project, mainly involved in the Biomolecules & Bioinformatics Division. The main goal of GACT is to measure the impact of humans in cave ecosystems through metagenomic characterisation of sediments and coprolites ancient DNA (aDNA). I am very happy and feel very fortunate to announce that during this new stage I will be surrounded by a big group of amazing people and scientists driven by curiosity in the DrostLab, Weigel World and Archaeo- and Paleogenetics group supervised by Hajk-Georg Drost, Detlef Weigel and Cosimo Posth, respectively.

I have done my PhD with EPIOMIDES group, lead by María Jesús Cañal, Mónica Meijón and Luis Valledor, in the Organisms and Systems Biology Department at the University of Oviedo. My thesis focused on abiotic stress responses in different species, specifically using unexplored gymnosperms as models, from a Systems Biology approach.

Beyond my professional responsabilities i am also a being half passionate half obssesed with bioinformatics and computational biology. When i have free time (wait for it xd), really enjoy trying new softwares specially those ones related with evolutionary genomics and transcriptomics.

When i am not in the lab or the batcave (home office), I dance breaking (Break Dance) and try not to become an e-boy while exchanging with other art forms.

I will add more info in the future of upcoming projects!



Publications


Journal of Integrative Plant Biology

Recent studies have documented plant responsesto climate change extensively, particularly tosingle‐stress exposures. However, critical factorsfor stress survival, such as sexual differentiation,are not often considered. The dioicous Marchantiapolymorpha stands as an evolutionary milestone,potentially preserving ancestral traits from the earlycolonizers. In this study, we employed proteomicanalyses complemented with physiological mon-itoring to investigate combined heat and droughtresponses in Tak‐1 (male) and Tak‐2 (female)accessions of this liverwort. Additionally, targetedtranscriptomics was conducted using differentnatural populations from contrasting environments.Our findings revealed sex‐biased dynamics amongnatural accessions, particularly evident undercontrol conditions and during early stress re-sponses. Although Tak‐2 exhibited greater diversitythan Tak‐1 under control conditions, male ac-cession demonstrated distinct and more rapidstress sensing and signaling. These differences instress response appeared to be strongly related tosex‐specific plasticity influenced by geoclimaticorigin. Furthermore, we established distinct proteingene ages and genomic distribution trends, un-derscoring the importance of protein diversificationover time. This study provides an evolutionaryperspective on sexual divergence and stressemergence employing a systems biology ap-proach, which allowed for the establishment ofglobal and sex‐specific interaction networks in thestress response.
PDF DOI Github
In prep

In recent decades, research on model organisms have significantly increased our understanding of core biological processes in plant science. However, this focus has created a substantial knowledge bottleneck due to the limited phylogenetic and ecological spectrum covered. Gymnosperms, especially conifers, represent a molecular and ecological diversity hotspot among seed plants. Despite their importance, research on these species is notably underrepresented, primarily due to a slower pace of investigation resulting from a lack of community-based resources and databases. To fill this gap, we developed P(inus)ra(diata)-G(ene)E(xpression)-ATLAS, which consists of several tools and two main modules: transcriptomics and proteomics, presented in this work for the forestry commercial and stress-sensitive species Pinus radiata. We summarised and centralised all the available information to provide a comprehensive view of the gene expression landscape. To illustrate how applications of the database lead to new biological insights, we integrated multiple regulatory layers across tissues and stressors. Harmonised alternative splicing analyses reveal that genes with conifers’ iconic large introns tend to be under constitutive regulation, while stress favors the retention of small introns. Furthermore, the degree of convergence between stressors differed between regulatory layers, with proteomic responses remaining highly distinctive even through intergenerational memory tolerance. Overall, Pra-GE-ATLAS aims to narrow the distance between angiosperms and gymnosperms resources, deepening our understanding of how pine intriguing features have evolved.
PDF DOI Preprint Github Web
Molecular Biology and Evolution

Evolutionary epigenomics, and more generally evolutionary functional-genomics, is an emerging field studying how non-DNA encoded alterations in gene expression regulation are an important form of plasticity and adaptation. Previous evidence analyzing plants comparative functional-genomics has mostly been focused on compare same assay matched experiments, missing the power of heterogeneous datasets for conservation inference. To fill this gap, we introduced PlantFUN(nctional)CO(nservation) database which is constitued by several tools and two main resources, inter-species chromatin states and functional genomics conservations scores, presented and analysed in this work for three well-established plant models. Overall, both resources can elucidate evolutionary information in terms of cross-species functional agreement. Therefore, PlantFUNCO could complement other comparative-genomics sources to asses evolutionary studies. In order to illustrate potential applications of the database, we replicated two previously published models predicting genetic redundancy in A. thaliana and found that chromatin states are a determinant of paralogs degree of functional divergence. These predictions were validated based on the phenotypes of mitochondrial alternative oxidases knockout mutants under two different stresses. Taken all together, PlantFUNCO aim to leverage data diversity and extrapolate molecular mechanisms findings from different model organisms to determine the extent of functional conservation, thus, deepen our understanding of how plants phenotypic plasticity has evolved.
PDF DOI Github Web
The Plant Journal

Current scenario of climate change has led to increase number of studies describing main drivers in abiotic stress. Recent findings suggest that temperature-responsive alternative splicing (AS) has a critical role in controlling plant response to high temperature at the molecular level. AS is a mechanism that allows organisms to create an assortment of RNA transcripts and proteins using single gene information. However, some of the most important insights suggested about stress AS could not be rigorously addressed because research has been focused on study model species which only covered a narrow phylogenetic and life-cycle spectrum. Thus, AS degree of diversification among more dissimilar taxa in heat response is still largely unknown. To fill this gap, the present study examines how AS landscape responds and ‘remembers’ from heat stress in the conifer Pinus radiata, a group which have received little attention even though their position can solve key evolutive and acclimation questions. Contrary to angiosperms, we found that potential intron retention may not be the most prevalent type of AS. Furthermore, our integrative analysis with metabolome and proteome data places splicing as the main source of variation during the response. Finally, we validated acquired long-term splicing-memory in a diverse subset of events and, although AS dynamics are divergent, splicing-memory seems to be conserved in seed plants. Our discoveries reveal the particular way of remembering past long-term temperature changes in conifers and open the door to include species with unique features to determine the extent of conservation in gene expression regulation.
PDF DOI Github Meta-Network IntronComp InsilicoVal
Methods Mol Biol 2139 (Plant Proteomics)

The evolution of next-generation sequencing and high-throughput technologies has created new oppor- tunities and challenges in data science. Currently, a classic proteomics analysis can be complemented by going a step beyond the individual analysis of the proteome by using integrative approaches. These integrations can be focused either on inferring relationships among proteins themselves, with other molecular levels, phenotype, or even environmental data, giving the researcher new tools to extract and determine the most relevant information in biological terms. Furthermore, it is also important the employ of visualization methods that allow a correct and deep interpretation of data. To carry out these analyses, several bioinformatics and biostatistical tools are required. In this chapter, different workflows that enable the creation of interaction networks are proposed. Resulting networks reduce the complexity of original datasets, depicting complex statistical relationships.
PDF DOI



Tools


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.

Github

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.

Github Web

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.

Github Web


EDUCATION


CD, Biology, University of Oviedo, Spain (2014-2018)
MS, Plant Biotechnology, University of Oviedo, Spain (2018-2019)
Short PhD Stay, Max Planck Institute - Biology, Computation Biology Group DrostLab-WeigelWorld, Tübingen, Germany (2023)
PhD, Biology, University of Oviedo, Spain (2019-2024)
Postdoc, Bioinformatics, Max Planck for Biology - GACT, Germany (2024-now)

GRANTS


Beca de colaboración, Min. de Educación y Formación Profesional ,2016
Formación de profesorado universitario, Mi. de Ciencia, Innovación y Universidades, 2018
Mobility grant: Formación de profesorado universitario, Mi. de Ciencia, Innovación y Universidades, 2023


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