My scientific career extends from 2011 to present in three main stages. In 2012 I obtained an FPI fellowship to carry out a PhD in Biotechnology at the GenMic group at the Public University of Navarre. During this period, I used comparative genomics to understand the impact of Transposable Elements (TEs) in genome architecture and transcriptional profiles (Castanera et al., 2016). My scientific contributions in this stage were greatly enriched by the international collaborations emerged during four international research stays from 2012 to 2017 (University of Naples, Italy; University of California Riverside, USA; DOE-Lawrence Berkeley National Laboratory, USA and INRAE, France).  During this stage, I was funded by the DOE-Joint Genome Institute with my first project as principal investigator. In this project, we sequenced the genome of the fungus Coniophora olivacea to uncover the genomics basis of its enzymatic repertoire (Castanera et al., 2017). Between 2017 and 2018 I co-supervised a PhD thesis (Dr. A. Borgognone), leading to my first independent publication as corresponding author (Borgognone et al, 2019).

After a short postdoctoral research stay at the IKBM (Kiel, Germany), I moved to CRAG to perform a postdoctoral stage funded by two competitive fellowships, Severo Ochoa Internationalization (2018-2019) and Juan de la Cierva-Formación (2019-2021). The objective of my project was to analyze the contribution of transposon insertion polymorphisms (TIPs) to plant crop genomic and phenotypic variation and involved an international stay in 2019 (University of Perpignan, France). During this time, I also contributed to the development and evaluation of bioinformatics tools to detect TIPs (Bogaerts et al., 2020; Vendrell-Mir et al.,2020) and obtained a funded project as co-principal investigator: “Uncovering the rice transposition landscape from 1000 genomes” (Red Española de Supercomputación). In this project we deployed a strategy to uncover associations between TIPs and trait variability (Castanera et al., 2021). In addition, I participated in the assembly and annotation of several plant crop reference genomes such as almond (Alioto et al., 2020), melon (Castanera et al., 2020) or pineapple (Yow et al., 2021).

In 2021 I obtained a Juan de la Cierva-Incorporación fellowship to start a new stage on my career marked by a higher level of independence, and contributed to understand the role of TIPs on rice transcriptome variability and adaptation (Castanera et al, 2023). More recently, in 2023, I received a Ramón y Cajal fellowship to develop my research lines at IRTA (CRAG). In this stage, I am focusing my research on using pangenomes to assess the regulatory impact of structural variants (SVs) and their application to genomics assisted breeding on multiple crops. This research has been funded by two projects for which I was principal investigator, SVADAPT (funded by CRAG) and DIBGP (funded by AEI, I assumed the role of Principal Investigator after the resignation of the previous PI). Since 2024, I am the CRAG co-team leader in the COUSIN project (“Crop Wild Relatives utilisation and conservation for sustainable agriculture”), awarded by the European Commission in the HORIZON-CL6-2023-BIODIV-01 call. In this project, we aim to accelerate the use of Crop Wild Relatives (CWRs) in breeding programs, by covering the whole translational pathway from the identification and characterization of CWRs to the market-ready crops