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Abstract By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts. We show that many of the events show a relative rate of duplicate gene loss before the first postpolyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate postpolyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with 2 distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is, therefore, possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass reciprocal gene loss barriers.
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A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges
Abstract We describe four ancient polyploidy events where the descendant taxa retain many more duplicated gene copies than has been seen in other paleopolyploidies of similar ages. Using POInT (the Polyploidy Orthology Inference Tool), we modeled the evolution of these four events, showing that they do not represent recent independent polyploidies despite the rarity of shared gene losses. We find that these events have elevated rates of interlocus gene conversion and that these gene conversion events are spatially clustered in the genomes. Regions of gene conversion also show very low synonymous divergence between the corresponding paralogous genes. We suggest that these genomes have experienced a delay in the return to a diploid state after their polyploidies. Under this hypothesis, homoeologous exchanges between the duplicated regions created by the polyploidy persist to this day, explaining the high rates of duplicate retention. Genomes with these characteristics arguably represent a new class of paleopolyploid taxa because they possess evolutionary patterns distinct from the more common and well-known paradigm of the rapid loss of many of the duplicated pairs created by polyploidy.
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- Award ID(s):
- 2241312
- PAR ID:
- 10580993
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Genome Biology and Evolution
- Volume:
- 17
- Issue:
- 4
- ISSN:
- 1759-6653
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract We describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated and lost duplicated genes that these polyploidies produce can confound the identification of orthologous genes between genomes. POInT uses conserved synteny and phylogenetic models to infer orthologous genes between genomes with a shared polyploidy. It also gives confidence estimates for those orthology inferences. POInTbrowsegives both graphical and query-based access to these inferences from 12 different polyploidy events, allowing users to visualize genomic regions produced by polyploidies and perform batch queries for each polyploidy event, downloading genes trees and coding sequences for orthologous genes meeting user-specified criteria. POInTbrowseand the associated data are online athttps://wgd.statgen.ncsu.edu.more » « less
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