Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

Abstract

Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5-12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars. genome evolution | paleopolyploidy | synteny

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

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The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

“…The rest of the syntenic gene pairs that showed non-dominance were classified as neutral genes. To test whether the occurrences of BjuA dominant gene pairs and the occurrences of BjuB dominant gene pairs are equal, we performed double-side binomial tests on dominant gene pairs for all samples 64 (Supplementary Table 27a,b). Additional details are available in the Supplementary Note.…”

Improved maize reference genome with single-molecule technologies

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