I’ve spent the last week in Rovinj, Croatia at the International Conference on Polyploidy, Hybridization, and Biodiversity. I’ve been thinking (and writing) a great deal about polyploidy recently, and this meeting was certainly the impetus for much, much more of that.
Having a history of multiple genomes is becoming a more and more prevalent cog in the evolution of most taxa. Once considered only marginally important evolutionarily and confined taxonomically, both contemporary and ancient polyploidization events are now detectable and important across a large number of fungi, animals, and plants.
Because polyploidy is such a widespread phenomenon, the diversity of study systems and questions was fantastic at this meeting (more fantastic that the food, wine, and location? Not sure about that).
Here are my big three takeaways:
The evolutionary ebb and flow of polyploidization
Genome duplications are now standard processes in botany and well-recognized for their evolutionary influence across multiple groups. In contrast, polyploidy in animals is, well, a little more fringe. Mike Barker (University of Arizona) applied recent bioinformatic advances for detecting ancient polyploidization events to 150 published insect transcriptomes/genomes. Gene age distributions provided strong evidence for over 30 (!) instances of whole genome duplications across insects, suggesting that repeat rounds of genome duplications may be more prevalent across animal taxa that first believed.
Yves Van de Peer (Ghent University) told an engaging story that related the unusual temporal clustering of plant polyploid events to the K/Pg mass extinction. He reviewed multiple lines of research that suggest a co-diversification of polyploids lineages following the K/Pg boundary, and he discussed the ecological principles that may have allowed for the neutral and adaptive radiation of these new polyploids.
New methodologies for multiple genomes
There were multiple talks that presented new ways to utilize the continued influx of genomic data from polyploid groups.
Eric Schranz (Wageningen University) asked the audience to consider conserved genomic context (synteny) when analyzing gene families in polyploids where whole genomes are available. To approach the computational challenges associated with synteny analyses in polyploids, he introduced Synteny-Networks (Syn-Nets) that perform network analyses used to visualize syntenic connections between polyploid genomes. He presented work on the MADS-box gene family of plants that used Syn-Nets to make novel inferences for the development of regulatory genes.
Clayton Visger (Soltis lab, University of Florida) presented a new approach to quantifying gene expression differences in autopolyploids. To avoid the limitations in only measuring relative expression among subgenomes or taxa, Visger spiked RNA standards into the transcripts from the autotetraploid Tolmiea menziesii and a related diploid T. menziesii in order to normalize expression count data. This allowed for the quantification of relative divergence per-transcriptome, per-cell, and per-biomass.
Duplicated genes within polyploid species provide a real challenge for establishing orthology. That’s why Armel Salmon (University of Rennes) introduced the Pyro- and Illu-haplotyper bioinformatics pipelines that detect duplicated homoeologs by aligning polyploid reads to parental haplotypes (and a bunch of other stuff). Get a flavor for this approach in this recent publication.
Speaking of homoeologs/homeologs, what does that term actually mean? It turns out that depends on who you talk to according to Natasha Glover (University of Lausanne). She provided one of the most talked about presentations, defining and discussing the history and function of homoelogs (knowing that this is the correct spelling singlehandedly rocked my world). You can read the paper here.
More genomes, more ecology?
There is certainly a lot of interesting stuff going on inside the cells of polyploid organisms, but having more genomes can drastically alter phenotypes and ecological relationships too. I really admire the work done by Andrew Leitch and colleagues (Queen Mary University) that makes connections between genome size, ploidy, biomass, and nutrient availability in plant communities. The long-term plots at Park Grass provided a fascinating result: when nitrogen and phosphorus are more abundant, polyploid species are selected for and produce greater proportions of biomass. This result isn’t just unique to Park Grass though, as fellow ICPHB participant Petr Šmarda (Masaryk University) has published similar findings from plots at the Rengen Grassland Experiment. Want even more ecology? Here you go: these results are greatly affected by the introduction of herbivores (rabbits specifically) because they preferentially eat species with larger genomes!
Maurine Neiman and students (University of Iowa) brought a healthy dose of snail polyploidy to the meeting by introducing several projects centered on New Zealand snails (Potomopyrgus antipodarum) that naturally occur in mixed sexual/asexual populations of varying ploidy levels. This study system is now producing results that link phosphorus availability to increased ploidy, identify positive selection on candidate genes related to parasite resistance (Laura Bankers), and characterize a recent burst of transposable element abundance across ploidy levels of asexual snails (Kyle McElroy).
Overall, it was a collegial and synergetic meeting in a beautiful setting. So spike your transcriptomes, assemble your homoeologs, and measure your C-values: the next iteration of the International Conference on Polyploidy, Hybridization, and Biodiversity will be in 2019 at an undisclosed, but likely incredible, location in Ghent, Belgium.