HOTSPOT

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The most dramatic of mutations: whole genome duplication Whole genome duplication is an important force in evolution, and while it can help to enhance the adaptability of a lineage, there are serious biological challenges in dealing with twice as many chromosomes. We spoke to Dr Levi Yant about his work investigating how different organisms adapt to having a doubled genome complement An organism with more than two complete sets of chromosomes is known as a polyploid, and while this occurs throughout the eukaryotic kingdom, it is particularly prevalent in plants. Currently based at the John Innes centre in Norwich, UK, Dr Levi Yant is the Principal Investigator of an ERC-funded project investigating the impact of whole genome duplication (WGD), the process that gives rise to polyploidy. “There are serious implications around dealing with twice as many chromosomes, as it means there are twice as many opportunities for novel associations in the nucleus,” he outlines. The focus of the ERC project is on understanding how different organisms can adapt to having a doubled genome complement, despite attendant challenges. “Understanding how a lineage with a doubled genome can deal with some of the associated challenges is a broadly interesting topic, because this impacts adaptability of a species across kingdoms, from crop domestication to polyploid cancer lineages in humans,” says Dr Yant.

interest in the project is meiotic crossovers, which are important for stabilising the segregation of chromosomes. “One crossover between homologous chromosomes is necessary to stabilise meiosis, while there’s also the benefit that this cross-over reassorts genetic material,” he explains. “So, half a chromosome from the mother is switched to be associated with half a chromosome from the father.” Arabidopsis arenosa, a major model of adaptation to genome duplication. Photo credit: Filip Kolář

Repeatability of Evolution

Meiotic crossovers This research builds on the observation that meiosis, a type of cell division, is not a straightforward process in some of these young, genome-doubled lineages. This is largely because there are simply too many opportunities for association between similar chromosomes. “Instead of having just one possible partner - a homologue - suddenly there are three other possible partners, because of the doubling of the genome,” outlines Dr Yant. A major area of

environment. “There’s a lot of risk initially, as when the genome has these interactions, too many crossovers and entanglements can lead to chromosome breakage,” explains Dr Yant. “However, if you’re able to tweak meiosis early on, you then suddenly have twice as many chromosomes to play with, and that almost certainly increases the adaptability of the lineage. This has been shown rigorously for example in yeast, where groups have been able to take haploid, diploid and tetraploid genomes, and show that more chromosome copies can enhance evolutionary potential in experimental evolution studies in vitro.”

A greater number of meioitic cross-overs means that there is a greater diversity of genetic combinations in the population, which is a positive point in evolutionary terms. Genome doubling can be thought of as a high-risk, high-gain strategy, in terms of a population’s ability to adapt to the

The main focus of attention in the ERC project is on looking at the repeatability of the striking adaptations which have been found in independent lineages. A key part of this work centres around a large-scale comparative genomics and population genomics study on different, independently-derived polyploid plant and amphibian species. “We’re looking to understand the evolutionary changes in each of these species, and how repeatable these changes are,” outlines Dr Yant. By resequencing many individual diploids, and closely related tetraploids, Dr Yant and his colleagues have been able to observe the footprints of selection on the genome following genome duplication. “We’ve resequenced hundreds of genomes in the last three years, using large scale population genomic studies that now are beginning to present clear candidate genetic changes that allowed the stabilisation of meiosis in these

Meiosis-specific proteins ZYP1 (red) and ASY1 (green) juxtaposed between the chromatin loops (blue) during meiosis in Arabidopsis arenosa. Homologous chromosomes have paired and recombined, which is essential for normal levels of genetic crossovers as well as promoting correct segregation of chromosomes during sexual reproduction. We discovered ZYP1 and ASY1 evolving rapidly in response to genome duplication (polyploidy). Credit: James Higgins

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