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Last update: May 2021

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Evolution of duplicated genes in Apple

Malus domestica has a recent and well preserved WGD. This massive event makes the apple tree an organism of choice to study duplicate genes.

Polyploidy has long been known as a driver of genetic innovation in eukaryotic organisms, both plant and animal. A high-quality genome has recently been obtained for the domesticated apple (Malus domestica). This new version confirms a recent event of Whole Genome Duplication (WGD) (50 million years ago). This WGD is well preserved as can be seen in figure 1 and leads to a shift from nine ancestral chromosomes to 17 in the Maleae family.


Figure 1: Synthesis and distribution of genomic and epigenomic characteristics of the apple genome.
The rings indicate (from outside to inside, as shown in the box) the chromosomes (Chr), the heatmaps representing gene density (green), TE density (blue) and DNA methylation levels (orange). A map linking homologous regions of the apple genome is shown inside the figure. The colored lines connect the collinearity blocks that represent the syntenic regions that have been identified by SynMap.
From Daccord, N., Celton, JM., Linsmith, G. et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49, 1099–1106 (2017).

This duplication does not exist in other rosaceae, making the apple tree a model of choice for the study of genes after WGD. The fates of duplicated genes are multiple and different mechanisms may come into play. They are presented in figure 2. Duplicate genes will in most cases be lost by pseudogenization after the accumulation of deleterious mutations allowed by a lifting of the evolutionary constraint (A). They can be conserved either by selection of existing functions (B to E) or by the appearance of new functions (F and G). The selection of functions is allowed by different processes. The gene dosage effect (B) will appear when the doubling of the amount of gene product will give an advantage to the organism. The sub-functionalization (C) is a mechanism where the accumulation of mutations leads to the subdivision of the function of the ancestral gene among the duplicated genes. Dose balance (D) is a process where the conservation of both genes maintains stoichiometric equilibrium. Finally, there is also paralogue interference (E), where the conservation of both genes avoids interference between the products of each paralogue. The appearance of new functions can be made by two mechanisms. Neo-functionalization, a mechanism where a mutation can give rise to a new function for the copy of the gene. If this function has an evolutionary advantage, it will be subject to distinct selective constraints leading to its fixation in the population. Another mechanism is adaptive conflict avoidance (ACE) (G), where the conservation of both genes allows the independent optimization of conflicting ancestral functions. The fate of the genes depends in part on the mode of duplication.



Figure 2: Potential future of duplicate genes.
From Evolution of Gene Duplication in Plants Nicholas Panchy, Melissa Lehti-Shiu, Shin-Han Shiu Plant Physiology Aug 2016, 171 (4) 2294-2316; DOI: 10.1104/pp.16.00523