Self-presentations by each participant

Prof. Parisod "General introduction to polyploidy"

Prof. Ainouche “Historical and new questions in polyploidy research”

Prof. Leitch “Genomic plasticity in polyploids”

Prof. Parisod, Prof. Ainouche, Prof. Leitch "Null hypotheses in polyploid research"

Participants will manipulate main concepts related to the putative genomic, cytological and ecological consequences of polyploidy, and highlight hypotheses to be tested through empirical and experimental approaches.

Field excursion

Dr. Felber et al. “Field excursion: Sampling a mixed-ploidy hybrid zone”

Participants will design and implement the sampling of a hybrid zone between diploids and autotetraploids of Anthoxanthum alpinum as to enable spatially-explicit analyses and comparison with the situation twenty years ago. Participants will further learn about the many polyploid systems in the flora of the Alps

The approach to the sampling site consists of a 700 m climb on foot via marked trails (almost 3 hours), up to 2000 m asl. Provide good shoes and appropriate clothing (potentially cold and windy).

Prof. Leitch et al. “Flow cytometry”

Participants will learn to estimate the genome size and ploidy level of plants, and will practice on samples collected during the field excursion to assess the distribution of cytotypes.

Module B: Polyploid genomes

Prof. Van de Peer, Dr Li, Dr Bafort et al. “Assembly of polyploid genomes and subgenome evolution”

Participants will learn about the extra complexities of (the assembly of) polyploid genomes that consist of (very) similar or identical subgenomes. Participants will learn about how to look for evidence of subgenome dominance, and ongoing rediploidization.

Prof. Van de Peer, Dr Li, Dr Bafort et al. “Ks age distribution and genomic dot plots”

The construction of Ks age distributions and genomic dot plots are two of the most widely used and important ways to find evidence for ancient polyploidy. Where the construction of Ks distributions is not based on structural information and can be even based on extensive transcriptome information, the construction of genomic dot plots requires structural information and a well-assembled genome. 

Dr Simion, Dr Li  “Gene trees – species tree reconciliation”

Gene tree reconciliation enables to look for evidence for (very) ancient polyploidy, where this is often not possible with Ks age distributions, because of saturation of synonymous mutations for large evolutionary distances. Participants will learn to work with software to construct Ks age distributions, to make genomic dot plots, and to perform gene tree – species tree reconciliation.

Prof. Shimizu, Dr. Okada, Dr Hatakeyama et al. “Robustness of polyploid species”

Recent studies using several allopolyploid species showed that allopolyploid species inherited and combined the gene expression patterns of progenitor species. We suggest that they contributed to the environmental robustness of allopolyploid species.

Prof. Shimizu, Dr. Okada, Dr Hatakeyama et al. “RNA-seq analysis using subgenome classification methods”

For high quality RNA-seq analysis of allopolyploid species, bioinformatic workflows called subgenome classification methods were developed. We will introduce bioinformatic workflow for subgenome classification methods (HomeoRoq, EAGLE-RC) combined with RNA-seq mapping and quantification tools. We also focus on significant changes in homeolog expression ratio.

Module C: Polyploid populations

Prof. Parisod, Dr Salmon et al. “Genotyping polyploids”

Genotyping polyploids is challenging. Participants will learn about avoidable pitfalls when calling for single nucleotide polymorphisms as well as structural variants among polyploid samples and about strategies to accurately assess (fixed or partial) heterozygotes.

Prof. Parisod et al. “Autopolyploid populations”

Participants will learn how to assess tetrasomic inheritance and to compare the linkage and structure of genomic variation within and among populations of diploid-autotetraploid systems.

Prof. Lascoux, Dr Tiret et al. “Allopolyploid populations”

Participants will learn how to deal with genomic variation in allopolyploid systems that include whole-genome duplication and hybridization, with the latter that seems to matter more than the former, at least for expression.

Prof. Lascoux, Dr Tiret et al. “Demography and selection in polyploids”

Participants will learn that parental legacy plays an important role and seems to have a rather long-lasting effect. So to understand an allopolyploid we need to understand its parental species. Although allopolyploid subgenomes have been in the same individuals for a long time and therefore have had the same demography they still differ significantly.

Prof. Lascoux, Dr Tiret et al. “Signatures of selection”

Participants will learn to analyze patterns of selection and highlight selective sweeps in allopolyploids.

Prof. Lascoux, Prof. Parisod et al. “Interpretations and conclusions”

Participants will revisit hypotheses formulated at the beginning of the summer school in light of the approaches they have been practicing and highlight perspectives for polyploidy research at the population level.