Mots-Clés
NGS data assembly
Target Capture
Population Genomics
Agronomic-relevant genes
Genomics
Description
Nom et contact des encadrants:
Rosalía Piñeiro (CICA-UDC), rosalia.pineiro @udc.es
Laboratoire d’accueil: CICA-UDC
Lieu du stage: Integrative Centre for Chemistry and Biology, CICA. University of A Coruña, Spain
Contexte scientifique et objectifs:
This Master subject, aims to conduct research in line with the project Genomics of Tree Populations of the Genus Inga in the Amazon (AmazonPopGene; CNS2023-144710 (Research Consolidation 2023, Ministry of Science and Innovation).
The species-rich legume tree genus Inga is widely distributed and common throughout tropical America. Inga has an important history of utilization by local communities in the Amazon. Some species, notably I. edulis (pacae) and I. feuillei (ice-cream bean) have been cultivated since pre-Columbian times for their edible sweet-tasting fruits. This Master project aims to unlock the domestication history of Inga trees. Using genome-wide data (Hybrid capture) across the entire distribution of two cultivated species and six wild congeners, we intend to identify its closest wild relatives, locate its areas of domestication, and identify genes selected during the domestication process.
Genome-wide data of cultivated Inga and six wild relatives have been generated by the host team in order to investigate the origin of this tropical crop from natural tree populations in Amazonian rainforest. Sequences of specimens of cultivated and non-cultivated Inga will be analysed across their distributional ranges, with special focus on Peru, in order to understand when and where the domestication took place and if there was a single or several domestication events over the centuries. We will also estimate the date of domestication and evaluate whether it is congruent with the oldest archaeological remains around 2000 years old.
The student will gain experience in analysis of targeted capture data against a high-quality reference genome and in comparative phylogenetics and population genetics. A reference whole genome sequence of Inga is available. Software will include:
The main goals of this proposal will be subdivided into four scientific objectives:
1. Curation and analysis of genome-wide sequences (Hybrid capture). Cutting-edge bioinformatics pipelines will be used.
2. Phylogenetic analyses and inference of the date of domestication of I. feuillei
from its closest wild relative.
3. Assessment of spatial gradients of genetic diversity in order to identify ancestral populations of I. feuillei.
4. Depending on time constraints, selection of genes relevant for agriculture will be investigated. In particular, we expect that the domestication of I. feuillei implied adaptation to dry conditions, as all three wild relatives occur in rainforest environments.
The project will be supervised locally by R Pineiro, Associate Professor at CICA-UDC.
Informations additionnelles: For further information on the project and available genetic data, please send an email to the supervisor (I communicate fluently in French, too).
Exigences particulières: Interest in assembly of NGS data. The candidate will gain experience in bioinformatic analysis, phylogenetics and population genetics of genome-wide DNA sequences.
Date limite de candidature, date de retour sur les candidatures: Applications will be examined until a suitable candidate is found.