Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

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Abstract
Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homeologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity to be easily identifiable. Using sorghum exons as the query sequence, we studied the fate of both orthologous genes in maize following the maize tetraploidy. We show that genes are predominantly lost, not relocated, and that single-gene loss by deletion is the rule. Based on comparisons with orthologous sorghum and rice genes, we also infer that the sequences present before the deletion events were flanked by short direct repeats, a signature of intra-chromosomal recombination. Evidence of this deletion mechanism is found 2.3 times more frequently on one of the maize homeologs, consistent with earlier observations of biased fractionation. The over-fractionated homeolog is also a greater than 3-fold better target for transposon removal, but does not have an observably higher synonymous base substitution rate, nor could we find differentially placed methylation domains. We conclude that fractionation is indeed biased in maize and that intra-chromosomal or possibly a similar illegitimate recombination is the primary mechanism by which fractionation occurs. The mechanism of intra-chromosomal recombination explains the observed bias in both gene and transposon loss in the maize lineage. The existence of fractionation bias demonstrates that the frequency of deletion is modulated. Among the evolutionary benefits of this deletion/fractionation mechanism is bulk DNA removal and the generation of novel combinations of regulatory sequences and coding regions. All genomes can accumulate dispensable DNA in the form of duplications of individual genes or even partial or whole genome duplications. Genomes also can accumulate selfish DNA elements. Duplication events specifically are often followed by extensive gene loss. The maize genome is particularly extreme, having become tetraploid 10 million years ago and played host to massive transposon amplifications. We compared the genome of sorghum (which is homologous to the pre-tetraploid maize genome) with the two identifiable parental genomes retained in maize. The two maize genomes differ greatly: one of the parental genomes has lost 2.3 times more genes than the other, and the selfish DNA regions between genes were even more frequently lost, suggesting maize can distinguish between the parental genomes present in the original tetraploid. We show that genes are actually lost, not simply relocated. Deletions were rarely longer than a single gene, and occurred between repeated DNA sequences, suggesting mis-recombination as a mechanism of gene removal. We hypothesize an epigenetic mechanism of genome distinction to account for the selective loss. To the extent that the rate of base substitutions tracks time, we neither support nor refute claims of maize allotetraploidy. Finally, we explain why it makes sense that purifying selection in mammals does not operate at all like the gene and genome deletion program we describe here.