Current research project
Improving global food security by tracing the origin, diversity and niche conditions of cultivated bitter potatoes
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, minor/orphan 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.
The potential of locally cultivated so-called ‘bitter’ potato species as a food-crop is currently unfulfilled because of toxic alkaloids, making them more complex to process than common potatoes. Because they require freeze-drying, a process that Andean Indigenous peoples found effective, producing chuño and tanta. These bitter potatoes are drought and frost-resistant with early maturing, traits that are important in adapting agriculture to climate change. To decrease the bitterness and toxicity levels and to translate desirable traits (e.g., drought and frost resistance) into the common potato, I will i) study the genomes of these orphan crops, ii) compare their genetic and chemical diversity through the characterisation of fresh and historical material and iii) project the distribution of bitter potato species as viable crops in 30 years.
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.
As part of my PhD thesis.
In silico identification of nsSNPs in resistance genes of three wild and cultivated Oryza varieties
Rice is the staple food for a large part of the human population in the world. Pathogens threaten rice plants. However, they have developed two defence mechanisms to resist pathogens. This study focused on the resistant (R) proteins in different rice varieties encoded by NBS-LRR genes. It has been found that some motifs in the LRR domain are under strong positive selection in cultivated rice and other grass species. In this study, we aimed to determine if this feature was also present in wild rice varieties and to what extent. Material and Methods: The genome data of nine rice varieties were used as materials, including Oryza sativa japonica, Oryza sativa indica as cultivated rice and Oryza barthii, Oryza brachyantha, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctata and Oryza rufipogon as wild rice varieties. R gene identification was performed with BLAST searches and HMM approaches through PRGDB, then annotated with InterProScan, HMMPam, and Pepcoil. Ortholog analysis was done using phylogeny and sequences-based approaches (Orthofinder).
The phylogenetic analysis was performed through Fasttree using the CC-MHD region. Finally, a positive selection analysis was performed with PAML's yn00. Results: We identified the number of R genes ranging from 204 (O. meridionalis) to 551 (O. sativa indica). A common distribution trend of NBS-LRR encoding genes on chromosomes in all varieties was found; chromosomes 11 and 12 held from 26% to 40% of the total R gene amount. Additionally, we obtained 405 clades of ortholog R genes spanning the CC-MHD region in all varieties, suggesting a rapid conserved evolution and a window to improve resistance in cultivated varieties from wild ones. The results in the phylogenomic analysis confirmed previous results, showing that O. rufipogon and O. nivara are highly related to O. sativa cultivars. Oryza barthii was closely related to O. glumaepatula, while O. brachyantha was more divergent from the others. Selection pressure analyses in LRR domains among the R gene ortholog groups showed that an ortholog R gene group related to signal transduction was also found under positive selection (Ka/Ks=1.22). Additionally, its core region (xxLxLxx) was under strong positive selection (Ka/Ks=2.11), showing that R genes evolve rapidly in domesticated Oryza and wild varieties and might also be the key sites under selection in the process of rice domestication.
- Master's 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.