Mots-Clés

K-mers, polyploids, NGS, phylogeny, yams

Description

Supervision: Hanâ Chaïr (Yam geneticist, supervisor), Bertrand Fouks and Olivier Garsmeur (Genomicists, co-supervisors) CIRAD, UMR AGAP, hana.chair@cirad.fr, bertand.fouks@cirad.fr, olivier.garsmeur@cirad.fr   

Team : UMR AGAP, Equipe DEFI- Déterminisme, Expression et Fonctionnement des traits d’intérêt chez l’Igname

Background

Yams, important tropical crops belonging to the Dioscoreaceae family, have over 650 species globally. While a few species of yams have been domesticated and are currently cultivated, many wild species are used for food or medicinal use. Among them, Dioscorea nummularia, native to Melanesia and South-East Asia Islands, is known for its role as a food source in times of scarcity. Despite being initially described as closely related to D. alata, one of the main species used as a crop throughout the tropics, recent studies show significant phenotypic differences between these species. Unlike D. alata, D. nummularia has a high dry matter content (a major trait, for yam culinary purposes) and resistance to anthracnose. These attributes make D. nummularia an important species for breeding programs that aim at enhancing the qualities of yams globally.

To take advantage of this species for breeding programs, its genome origin and architecture need to be better characterized. Yam species proved to have complex genomes, due in particular to admixture and variation of ploidy levels. D. nummularia is no stranger to this complex evolutionary history and displays great intra-specific variation of ploidy level. Recent research has shown potential hybridization between D. alata and D. nummularia, adding complexity to the phylogeny of yams. Ongoing work, including genomic in situ hybridization (GISH), reveals unequal contributions from two to three ancestral genomes in the polyploidization process.

Objectives

Therefore, the goal of this internship is: i) to identify the ancestral genomes of different D. nummularia varieties using repeated k- mers with bioinformatic tools developed at our unit AGAPi and ii) to trace phylogenetic relationships between D. nummularia, D. alata, and other yam species. For this purpose, genomic data have been produced and are available: i) long-read sequencing data (PacBio) for three polyploid varieties with different ploidy levels and ii) short-read sequencing data for 159 accessions from five yam species. This extensive dataset provides a unique opportunity to delve into the complex genetic history of yams, including understanding hybridization events, polyploidization, and genome structure.

Internship Details

The intern will work closely with a multidisciplinary research team, gaining hands-on experience in cutting-edge genomic and bioinformatics analysis techniques. This internship will contribute to advancing yam research and offer opportunities to develop new bioinformatics tools to enable complex phylogenetic reconstruction.

Skills Required

• Proficiency in scripting languages (Bash, Perl, and/or Python).
• Basic knowledge of NGS sequence data analysis methods.
• Interest in biological research, especially in genomics and phylogenetics.

Papers related to the subject:

Healey Adam, Garsmeur Olivier, et al.  2024. The complex polyploid genome architecture of sugarcane Nature, 628: 804-810. https://doi.org/10.1038/s41586-024-07231-4

Sharif B.M., Burgarella C., Cormier F., Mournet P., Causse S., Nguyen Van Kien, Kaoh J., Rajaonah M.T., Lakshan S.R., Waki J., Bhattacharjee R., Badara G., Pachakkil B., Arnau G., Chaïr H. 2020. Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata L.). Annals of Botany, 6 (2): p. 1029-1038. https://doi.org/10.1093/aob/mcaa122

Chaïr H., Sardos J., Supply A., Mournet P., Malapa R., Lebot V. 2016. Plastid phylogenetics of Oceania yams (Dioscorea spp., Dioscoreaceae) reveals natural interspecific hybridization of the greater yam (D. alata). Botanical Journal of the Linnean Society, 180 (3): p. 319-333. https://doi.org/10.1111/boj.12374