Abstract
BackgroundThe sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention.ResultsWe survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database.ConclusionsWe identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
Highlights
The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention
The landscape of gene duplication in the plant kingdom In 141 sequenced plant genomes, we identified duplicated genes using DupGen_finder and classified them into one of the five categories (Additional file 1: Figure S1 and Additional file 2), being derived from WGD, tandem duplication (TD), Proximal duplication (PD), transposed duplication (TRD), and Dispersed duplication (DSD)
The higher percentages of WGD-derived gene pairs were detected in plants experiencing more recent WGDs such as soybean (Glycine max, ~ 13 million years ago (Mya)) and flax (Linum usitatissimum, 3.7~6.8 Mya)
Summary
The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. The finding that the first fully sequenced eukaryote genome, that of the budding yeast (Saccharomyces cerevisiae) [1], had experienced whole-genome duplication (WGD, or defined as polyploidization) [2] invigorated research into this evolutionary mechanism of central importance. The ancestral vertebrate is thought to have undergone two rounds of ancient WGD (defined as 1R and 2R) at least ~ 450 million years ago (Mya) [6,7,8]—about 20–30% of human genes are thought to be paralogs produced by these two WGDs, and these “ohnologs” have a strong association with human disease [7, 9]. The most recent genome duplication currently known in vertebrates has been uncovered in the common carp (Cyprinus carpio) (4R, ~ 8.2 Mya) [14, 15].
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