Are there rules to the game? Patterns of Genome Evolution in Paleopolyploid Plants

Project Information

PGEPP

Grant agreement ID: 660742

DOI

10.3030/660742

Project closed

EC signature date 12 March 2015

Start date 1 April 2015

End date 28 July 2017

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 177 598,80

EU contribution

€ 177 598,80

Coordinated by

WAGENINGEN UNIVERSITY
Netherlands

Periodic Reporting for period 1 - PGEPP (Are there rules to the game? Patterns of Genome Evolution in Paleopolyploid Plants)

Reporting period: 2015-04-01 to 2017-03-31

Summary of the context and overall objectives of the project

"In our project, ""Are there rules to the game? Patterns of Genome Evolution in Paleopolyploid Plants"" or PGEPP we investigated evolution of genomes after whole genome duplications (WGD) or polyploidy.

Polyploidy events (i.e. the process of genome doubling that gives rise to organisms with multiple sets of chromosomes) have had a strong impact on land plants diversification, adaptation and speciation. Genomic investigations have found that polyploidy is ubiquitous among angiosperms and have identified independent lineage-specific ancient polyploidizations. Traces of these polyploidy events are still present, although duplication events are followed by massive gene loss and chromosome structural rearrangements. However, the mechanisms/principles that govern these genomic changes following polyploidization are still poorly understood. Our project aims to overcome this limitation by analyzing genomic changes following polyploidization in three plant families among which two are of particular agricultural and economical importance. Specifically I will test if common mechanisms (e.g. presence of repetitive elements) are involved in chromosomal rearrangements. I will combine physical mapping approaches (molecular cytogenetic and optical mapping) and sequence analysis to characterize and compare genomic collinearity (synteny) between genomes of Brassicaceae, Cleomaceae and Solanaceae species. This work will improve our understanding of genome evolution by looking mechanisms of chromosomal changes and will improve synteny analysis between model plants such as Arabidopsis and more distant crops for homolog identification."

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

A key-out of our work was the analysis of ancient genome triplication for the important plant family Solanaceae done by the analysis of the Petunia genome. This led to our inclusion on the genome paper in Nature Plants and including a detailed supplemental publication on our analysis and conclusions:

https://www.nature.com/articles/nplants201674
https://images.nature.com/original/nature-assets/nplants/2016/nplants201674/extref/nplants201674-s5.pdf

We also undertook the detailed analysis of ancient polyploidy in the Brassicaceae family by analysis of the the Aethionema genome and genetic map to understand. The manuscript for this work is now in preparation.

Finally, as part of the project we analyzed chromosome evolution in tomato and potato by performing the genome sequencing and optical mapping in the outgroup species Solanum etuberosum. The manuscript for this work is nearly completed and will be submitted soon. The main applicant, Dr. Grandont, was also able to present the results of this work at important international meetings such as Plant Animal Genome.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Within the project, we utilized many state of the art techniques and analyses such as Optical mapping of Solanum etuberosum for reconstructing and analyzing chromosomal evolution in tomato and potato.

As highlighted above, one high-impact paper has already been published, another will soon be submitted and a third manuscript is in preparation.

The results of the project are important for several reasons. In the Petunia work, we were able to show to for the first time in plants how genes may independently fractionate in different lineages (in this case tomato vs petunia) after a shared and common whole genome triplication. This result is similar to those found in yeast, but, until now not described in plants. These findings can help explain how genetic variation might be partioned and evolve in different plant lineages.

The work on chromosomal evolution in potato and tomato by comparison to our new S. etuberosum genome is important for several reasons. First off, we now have established that most chromosomal changes have occurred in the tomato lineage and not the potato lineage (in other words, the potato genome structure is more conserved). We also identified many new and novel rearrangements in tomato. These results will have implications for breeding and identifying homologous genes between lineages.

nplants201674-f3.jpg