Abstract
Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This has been explained as a consequence of protein–protein interactions, just as for other highly retained classes of genes. We show that the quantity of conserved noncoding sequences (CNSs) associated with genes predicts the likelihood of their retention as duplicate pairs following whole genome duplication. As many CNSs likely represent binding sites for transcriptional regulators, we propose that the likelihood of gene retention following tetraploidy may also be influenced by dose–sensitive protein–DNA interactions between the regulatory regions of CNS-rich genes – nicknamed bigfoot genes – and the proteins that bind to them. Using grass genomes, we show that differential loss of CNSs from one member of a pair following the pre-grass tetraploidy reduces its chance of retention in the subsequent maize lineage tetraploidy.
Highlights
It was almost half a century ago that Ohno (1970) first proposed a role for whole genome duplications in the evolution of vertebrates just as Lewis (1951) did for duplications of individual genes two decades before Ohno
Arabidopsis thaliana – a species selected for its small genome – contains readily detectable evidence of two rounds of whole genome duplication within its order and a more ancient hexaploidy, all estimated to have occurred within the last 120 million years (Bowers et al, 2003; Maere et al, 2005; Paterson et al, 2010)
Sorghum–rice conserved noncoding sequences (CNSs) obtained in automated fashion and sorted to their nearest gene An automated pipeline compared the genomes of Japonica rice and sorghum for orthologous genes (Woodhouse et al, 2010)
Summary
It was almost half a century ago that Ohno (1970) first proposed a role for whole genome duplications in the evolution of vertebrates just as Lewis (1951) did for duplications of individual genes two decades before Ohno. Duplicated regions are initially identical or near-identical, gene loss data from all studied tetraploidies show clear bias between duplicate chromosomal segments with one region sustaining the majority of gene copy deletion (Thomas et al, 2006; Sankoff et al, 2010; Woodhouse et al, 2010). This bias remains consistent across each pair of paleochromosomes in maize and is paralleled by differences in expression levels of duplicate genes located on homeologous paleochromosomes (Schnable et al, 2011)
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