Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication

Abstract

Genome duplication followed by massive gene loss has permanently shaped the genomes of many higher eukaryotes, particularly angiosperms. It has long been believed that a primary advantage of genome duplication is the opportunity for the evolution of genes with new functions by modification of duplicated genes. If so, then patterns of genetic diversity among strains within taxa might reveal footprints of selection that are consistent with this advantage. Contrary to classical predictions that duplicated genes may be relatively free to acquire unique functionality, we find among both Arabidopsis ecotypes and Oryza subspecies that

Biological consequences of dosage dependent gene regulatory systems

“…To some degree, this almost certainly occurs, but the evidence for purifying selection against mutation accumulation for the retained classes of genes suggests otherwise for many genes (10). Sub and neo functionalization of duplicates is apparently a slower process than once thought.…”

“…As this process continues over evolutionary time, there is a progression toward a diploid state again. However, recent evidence indicates that there is a preferential retention of transcription factors and signal transduction components as duplicates from the most recent respective events of polyploidization and diploidization in both Arabidopsis and rice (8)(9)(10)28). Indeed, there is evidence of purifying selection for the genes that are preferentially retained (10).…”

“…The availability of genomic sequences for Arabidopsis and rice has revealed that there have been repeated cycles of polyploidization and diploidization in the evolution of the angiosperms (8)(9)(10)(26)(27)(28). Allotetraploids have occurred by the hybridization of related species followed by chromosomal doubling.…”

“…However, recent evidence indicates that there is a preferential retention of transcription factors and signal transduction components as duplicates from the most recent respective events of polyploidization and diploidization in both Arabidopsis and rice (8)(9)(10)28). Indeed, there is evidence of purifying selection for the genes that are preferentially retained (10). By comparison, studies of the types of genes present in segmental duplications, which increase the copy number of only a small portion of the genome, provide a complementary picture, namely, a relative dearth of transcription factors and signal transduction components (30).…”

“…Typically, the imbalance was considered to involve gene products of housekeeping or metabolic processes. However, recent evidence from studies of gene expression in aneuploidy and ploidy series and the identification of the genes responsible for these effects (7), together with studies of the retention of regulatory genes during the process of diploidization following multiple rounds of polyploidization in the evolutionary lineage of the plant kingdom (8)(9)(10), would suggest that the balance is primarily one involving regulatory molecules. This balance would affect the expression of the target genes, which might cause the aneuploid syndromes by reductions in expression of critical products regardless of whether there is an addition or subtraction of a chromosome from the genotype (11)(12).…”