RT Journal Article
SR Electronic
T1 Gene fractionation and function in the ancient subgenomes of maize
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 095547
DO 10.1101/095547
A1 Simon Renny-Byfield
A1 Eli Rodgers-Melnick
A1 Jeffrey Ross-Ibarra
YR 2016
UL http://biorxiv.org/content/early/2016/12/19/095547.abstract
AB The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts. Furthermore, paralogous genes in the least-fractionated subgenome account for a greater degree of phenotypic diversity than those resident on the more-fractionated subgenome. We also show that the two subgenomes of maize are distinct in epigenetic characteristics. Intriguingly, analysis of singleton genes reveals that these differences persist even after fractionation is complete.