Mots-Clés
bioinformatics
genomics
assembly
annotation
pangenome
Description
Scientific context
In 2025, France harvested more than 158,000 tons of pears, making it the fifth-largest pear producer in Europe (FAO, 2026; Agreste, 2026). However, domestic production does not meet national demand. With an annual consumption of approximately 2.8 kg of pears per capita, France imports almost as many pears as it produces (Agreste, 2025).
Climate change, political uncertainty, and plant health issues are creating new challenges for the French pear industry. Strengthening food sovereignty has therefore become a priority for policymakers. As part of this effort, a report was commissioned to assess the future of the sector up to 2040 (Ceresco, AgroClimat, 2025).
The report highlights the major challenges posed by climate change. Depending on the region, pear production will need to adapt to shorter, milder winters, late spring frosts, and hotter, drier summers. At the same time, the use of pesticides and other agricultural inputs must be reduced. Competition for water between irrigation and other human activities may also become an increasing source of conflict. These challenges are already affecting the industry, with both the area under pear cultivation and yields declining between 2010 and 2020 (Ceresco, AgroClimat, 2025).
Developing new pear varieties is therefore essential to address these challenges. These varieties should be more resistant to pathogens, reducing the need for plant protection treatments, and better adapted to changing climatic conditions. However, the genetic resources currently available for breeding programs remain limited. One promising way to broaden this diversity is to study wild relatives of cultivated fruit trees, which may carry valuable traits that are not found in commercial varieties.
The European research project FruitDiv (http://fruitdiv.eu) aims to characterize, conserve, and make use of the genetic diversity found in wild relatives of cultivated fruit trees. The project focuses on wild pear trees (Pyrus), while other research teams study apples (Malus) and stone fruits (Prunus).
Field surveys have been conducted across Europe to investigate the genetic diversity of wild populations of these species. However, no reference genome is currently available for European wild relatives of the cultivated pear. As a result, structural variations within the genus Pyrus—such as insertions, deletions, and translocations—remain largely unexplored. Studying these variations will help reveal the genetic diversity of wild pears and identify resources that could support future breeding programs.
Work Environment and Internship Tasks
You will join the Research Institute for Horticulture and Seeds (Institut de Recherche en Horticulture et Semences, IRHS), a joint research unit involving INRAE, the University of Angers, and Institut Agro Rennes-Angers.
The institute studies the genetics, health, and diversity of cultivated plants. Its research teams combine approaches from genomics, bioinformatics, and statistics to better understand plant species and help develop more sustainable agricultural systems.
Your internship is part of the European FruitDiv project and focuses on wild pear trees belonging to the genus Pyrus. Three wild species have already been sequenced, providing the data needed to assemble and compare their genomes.
Your work will help characterize the genetic diversity of these species and lay the foundations for developing a pangenome. A pangenome brings together the genetic information from multiple individuals or related species, providing a broader picture of their shared and unique genetic features.
You will work on assembling the genomes of three wild pear species: Pyrus spinosa, P. pyraster, and P. salicifolia.
Your tasks will include:
• Assembling the existing PacBio HiFi sequencing data for the three species.
• Using the bioinformatics tools and scripts already available within the research team.
• Adapting, where necessary, genome assembly methods developed by the project partners.
• Using existing genome assemblies from cultivated pears to help guide and improve the assembly process.
Once the genomes have been assembled, you will help identify and analyze the different elements they contain. This process, known as genome annotation, will provide information about their genetic content and allow comparisons between species.
Your tasks will include:
• Annotating the assembled genomes to identify their genetic features and compare them across species.
• Using locally generated RNA sequencing data to support genome annotation.
• Contributing to the initial stages of pangenome development, depending on the progress of the internship.
• Using the bioinformatics tools and analysis pipelines developed within the FruitDiv and AgroDiv projects.
Expected Background and Skills
You are currently completing your second year of a Master’s degree (M2), or an equivalent qualification, in bioinformatics, plant biology, or evolutionary biology. You have a strong interest in bioinformatics and/or statistics.
Previous experience with computing clusters, UNIX environments, or command-line tools would be an advantage.
Technical skills
• Basic knowledge of genetics and genomics.
• Ability to develop or use scripts and bioinformatics and/or statistical analysis pipelines.
• Understanding of the main principles of biological data analysis.
• Ability to communicate in English, both orally and in writing, particularly during meetings with European project partners.
• No knowledge of French is mandatory, as work can be conducted entirely in English, but some basic knowledge will help you in your everyday life.
Personal qualities
• Enjoy working in a team and collaborating with scientific partners.
• Be able to organize and carry out tasks independently.
• Demonstrate attention to detail and rigor when analyzing data and monitoring computational workflows.