Research
Current research project
Fostering agrobiodiversity in bitter potatoes by tracing their origin, diversity and niche conditions
Contemporary food systems are not diverse. In the face of climate change, they are prone to failure and have a high negative ecological impact. Agrobiodiversity is the most effective way to diversify food systems and bolster food security, positively impacting the local environment and low-income Indigenous and local families. However, local/indigenous crops are often under-explored despite their huge potential. In this project, I propose to bolster food security by studying the genetic and chemical diversity and predicting the suitable conditions for cultivating unexplored crops, such as uncommon tuber-bearing potato species.
Doña Santusa from Ocuri community, Bolivia.
Bitter potatoes owe their name to their higher glycoalkaloid content (than the common potato) making it bitter to taste. These compounds are medicinal but also toxic for consumption. Andean Indigenous peoples found an effective way to freeze-dry them, producing chuño (t'unta) and moraya. These bitter potatoes are drought and frost-resistant with early maturing, traits that are important in adapting agriculture to climate change. With this project, I dream of contributing to Andean family farmers conserving and innovating their bitter potato varieties in the wake of climate crises. Farmers can know where these bitter potatoes will thrive with the ecological models. With the genomic and metabolite data, Andean farmers can breed, if they wish to, their bitter potato varieties to better resist the effects of planetary dysregulation.
Herbarium specimen of Solanum acaule.
Past research projects
Yeast strain design
As the bioinformatician at BioPhero - FMC, I developed, implemented pipelines, and analysed multi-omic data to contribute to developing new and better pheromone products. With the main aim to disrupt insect mating to control pests, isn’t it a genius and elegant solution?
This new role allowed me to follow my dreams of using my bioinformatics skills to solve pressing issues like climate change and food security. With my passion and experience, I aimed to help to transition to a more sustainable future, where pheromones will be the main pest control method.
Palaeogenomics of Cinchona barks: On the chemical and genomic diversity of historical Fever tree barks
The fever tree (Rubiaceae: Cinchona spp.) has been widely used to treat malaria for hundreds of years due to the content of quinoline compounds that are stored in the bark. Originally from the Andes and known by indigenous peoples for its ameliorating effect on high recurrent fevers, the native Cinchona forests were heavily harvested. Later, plantations were established in other tropical countries. Despite the economic and pharmaceutical importance of the fever tree, taxonomic issues have prevented the elucidation of the evolutionary history of the Cinchona genus and its potential relation with its chemical diversity.
Furthermore, with the advent of palaeogenomics, it is now possible to obtain, analyse and authenticate DNA from historical samples, which often lack both vouchers and information about provenance. This PhD project uses historical Cinchona barks as a model of wood museomics aiming to provide new perspectives on the origin, application, and importance of the fever tree. This thesis shows that quinoline alkaloids in historical bark samples remain stable 150 years later, bringing museum specimens to life and casting new light on the fever tree's chemical diversity and selection history. A first draft genome of Cinchona pubescens is presented, and it is suggested that genome skimming may provide more accurate phylogenetic resolution than a commercial global target capture kit. Finally, it is shown how genomic approaches can be used to trace samples of unknown provenance back to their origin.
- PhD thesis.
In silico identification of nsSNPs in resistance genes of three wild and cultivated Oryza varieties
Rice serves as a global staple food and faces pathogen threats, though it has developed defence mechanisms. We examined resistant (R) proteins encoded by NBS-LRR genes across rice varieties. Scientists previously found certain LRR domain motifs under positive selection in cultivated rice and grasses. We investigated this feature in wild rice varieties using genome data from two cultivated (Oryza sativa japonica, indica) and seven wild rice species. We identified R genes using BLAST and HMM approaches, followed by annotation and ortholog analysis.
Our results revealed R gene counts ranging from 204-551, with chromosomes 11 and 12 containing 26-40% of total R genes. We found 405 ortholog R gene clades spanning all varieties, indicating conserved evolution. Our phylogenomic analysis confirmed O. rufipogon and O. nivara's close relation to cultivated varieties, while O. brachyantha showed more divergence. Our selection pressure analysis revealed positive selection in signal transduction-related R genes (Ka/Ks=1.22) and their core region (Ka/Ks=2.11), demonstrating rapid R gene evolution in both domesticated and wild varieties.
- Masters thesis
Comparative genomics of two Pasteurella strains infecting bovine and alpacas.
Pneumonia is one of the main mortality causes in alpacas; and the second one in babies’ alpacas. It might be caused by several factors like bacteria, viruses, different host conditions, or even a mixture. One of the factors mentioned is the microorganism Pasteurella multocida, which is also involved in Pasteurellosis of other domestic species, including alpacas. However, little is known about this infection, regardless of its importance. This thesis aims to compare the genomes of both strains infecting bovines and alpacas genomes, 36950 and UNMSM, respectively, to know the genomic structure of the strain isolated from alpacas and elicit which proteins are related to pathogenesis in both hosts.
For that reason, we sequenced the genome of P. multocida affecting alpaca, performed structural and functional genomics analysis, and then conducted comparative genomics analysis with P. multocida 36950. It was found that P. multocida strains UNMSM and 36950 share 1798 proteins, from which 121 were considered virulence factors. Additionally, although strain 36950 presents ICEPmu1¸ UNMSM strain does not. However, UNMSM has a unique 250 Kb region between six P. multocida multocida strains. Phylogenetic analysis showed that FUR protein is conserved between six P. multocida multocida strains. On the other hand, OMPH protein is variable between those strains. AtpD gene was also analysed, and we found that P. multocida UNMSM was highly variable among the other four subspecies’ atpD, which probably means that the UNMSM strain can be considered a new subspecies.
- Bachelor's thesis.