Adaptive evolution driving the young duplications in six Rosaceae species

Abstract

Background: In plant genomes, high proportions of duplicate copies reveals that gene duplications play an important role in the evolutionary processes of plant species. A series of gene families under positive selection after recent duplication events in plant genomes indicated the evolution of duplicates driven by adaptive evolution. However, the genome-wide evolutionary features of young duplicate genes among closely related species are rarely reported.

Results: In this study, we conducted a systematic survey of young duplicate genes at genome-wide levels among six Rosaceae species, whose whole-genome sequencing data were successively released in recent years. A total of 35,936 gene families were detected among the six species, in which 60.25% were generated by young duplications. The 21,650 young duplicate gene families could be divided into two expansion types based on their duplication patterns, species-specific and lineage-specific expansions. Our results showed the species-specific expansions advantaging over the lineage-specific expansions. In the two types of expansions, high-frequency duplicate domains exhibited functional preference in response to environmental stresses.

Conclusions: The functional preference of the young duplicate genes in both the expansion types showed that they were inclined to respond to abiotic or biotic stimuli. Moreover, young duplicate genes under positive selection in both species-specific and lineage-specific expansions suggested that they were generated to adapt to the environmental factors in Rosaceae species.

Keywords: Adaptive evolution; Environmental stresses; Lineage-specific expansion; Rosaceae species; Species-specific expansion; Young duplication.

Fig. 1

Top 20 protein domains of the young duplicate genes in species-specific expansions. The x-axis means the numbers of different domains. The y-axis means the domains taking the top 20 places of domain numbers. a: F. vesca, b: M. x domestica, c: P. communis, d: P. persica, e: R. chinensis and f: R. occidentalis

Fig. 2

Top 20 protein domains of the young duplicate genes in lineage-specific expansions. The x-axis means the numbers of different domains. The y-axis means the domains taking the top 20 places of domain numbers. a: F. vesca, b: M. x domestica, c: P. communis, d: P. persica, e: R. chinensis and f: R. occidentalis

Fig. 3

The Ks values of paralogs of young duplicate gene families in the two types of expansions. The x-axis means the range of Ks values from 0 to 1, and the range was divided into ten parts in unit of 0.1. The y-axis represents the occurrence of Ks value in each unit. a: F. vesca, b: M. x domestica, c: P. communis, d: P. persica, e: R. chinensis and f: R. occidentalis

Fig. 4

The Ka/Ks ratios of young duplicate genes in the two types of expansions. The box plots are exhibiting the distributions of Ka/Ks values among paralogs and orthologs in the two expansion types. The small square and the line in the box represent average and median values of the Ka/Ks values, respectively. a: F. vesca, b: M. x domestica, c: P. communis, d: P. persica, e: R. chinensis and f: R. occidentalis