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

• 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
• ISSN: 0960-9822; 1879-0445
• DOI: 10.1016/j.cub.2011.12.027

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