Rapid, Repeated, and Clustered Loss of Duplicate Genes in Allopolyploid Plant Populations of Independent Origin

The predictability of evolution is debatable, with recent evidence suggesting that outcomes may be constrained by gene interaction networks [1]. Whole-genome duplication (WGD; polyploidization—ubiquitous in plant evolution [2]) provides the opportunity to evaluate the predictability of genome reduct...

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Bibliographic Details
Published in:Current biology 2012-02, Vol.22 (3), p.248-252
Main Authors: Buggs, Richard J.A., Chamala, Srikar, Wu, Wei, Tate, Jennifer A., Schnable, Patrick S., Soltis, Douglas E., Soltis, Pamela S., Barbazuk, W. Brad
Format: Article
Language:English
Subjects:
allopolyploidy
Asteraceae
Diploids
diploidy
duplicate genes
Evolution
Evolution, Molecular
Evolutionary genetics
Gene Deletion
Gene dosage
Gene Duplication
gene interaction
Genome, Plant
Genomes
Helianthus
Helianthus annuus
hybridization
loci
parents
Polyploidy
Tragopogon - genetics
Tragopogon miscellus
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Summary:The predictability of evolution is debatable, with recent evidence suggesting that outcomes may be constrained by gene interaction networks [1]. Whole-genome duplication (WGD; polyploidization—ubiquitous in plant evolution [2]) provides the opportunity to evaluate the predictability of genome reduction, a pervasive feature of evolution [3, 4]. Repeated patterns of genome reduction appear to have occurred via duplicated gene (homeolog) loss in divergent species following ancient WGD [5–9], with evidence for preferential retention of duplicates in certain gene classes [8–10]. The speed at which these patterns arise is unknown. We examined presence/absence of 70 homeologous loci in 59 Tragopogon miscellus plants from five natural populations of independent origin; this allotetraploid arose ∼80 years ago via hybridization between diploid parents and WGD [11]. Genes were repeatedly retained or lost in clusters, and the gene ontology categories of the missing genes correspond to those lost after ancient WGD in the same family (Asteraceae; sunflower family) [6] and with gene dosage sensitivity [8]. These results provide evidence that the outcomes of WGD are predictable, even in 40 generations, perhaps due to the connectivity of gene products [8, 10, 12]. The high frequency of single-allele losses detected and low frequency of changes fixed within populations provide evidence for ongoing evolution. ► Duplicate genes are rapidly lost in young allotetraploid T. miscellus populations ► Clusters of genes tend to be lost together repeatedly in independent populations ► Patterns of loss are similar to those in ancient polyploids of the same plant family ► The connectivity of gene products in networks may determine which genes are lost
ISSN:0960-9822
1879-0445
DOI:10.1016/j.cub.2011.12.027