Evolution of Gene Duplication in Plants

Abstract

Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.

Atypical Protein Phosphatase 2A Gene Families Do Not Expand via Paleopolyploidization

“…Detection of positive selection within the B56 domain in these subclades is more consistent with neofunctionalization, escape from adaptive conflict, or subfunctionalization models for postpolyploidy retention of paralogs, rather than strict dosage balance or paralog interference models (Conant et al, 2014;Panchy et al, 2016). Preferential expansion via paleopolyploidy also could be due to coevolution of regulator/target gene pairs following polyploidization.…”

“…This model proposes that genes encoding products that are constrained by specific actor-substrate interactions are retained preferentially to avoid haploinsufficiency. Duplicated genes that are initially retained to maintain gene dosage may be allowed to undergo subsequent divergence (for review, see Conant et al, 2014;Panchy et al, 2016). Gene duplications also provide mutational and regulatory robustness, or tolerance of innovations in protein sequences and expression patterns (Keane et al, 2014).…”

“…Despite this contrast, PP2A gene family expansion in both plants and animals is associated with ancient wholegenome duplications and triplications (paleopolyploidy events), indicating a shared genomic mechanism for PP2A isoform evolution among eukaryotes. Some gene families may expand primarily via paleopolyploidy events because gene dosage favors the maintenance of some duplicated loci (Birchler and Veitia, 2007;Freeling, 2009;Veitia et al, 2013;Panchy et al, 2016); the adaptive value of increased dosage or of maintaining proper stoichiometry between regulators and specific gene targets prevents the loss of some gene classes after polyploidization. Alternatively, the maintenance of duplicated genes may provide mutational robustness and/or allow the evolution of phenotypic plasticity (Keane et al, 2014;Fares, 2015;Li et al, 2016).…”

Synteny-based phylogenomic networks for comparative genomics

“…This question has been addressed frequently in recent years. It has been proposed that adaptation to novel or stressful environments is correlated with the retention of duplicated genes (Flagel and Wendel, 2009;Jiao et al, 2011;Kondrashov, 2012;Panchy et al, 2016). Among the many models for duplicated gene evolution (Conant and Wolfe, 2008;Innan and Kondrashov, 2010), it is suggested that genes that should be rapidly or constantly produced in response to environmental stress might be more prone to selection after duplication (Kondrashov, 2012).…”

“…Gene and genome duplication plays a fundamental role in evolution by providing the genetic material by which new traits can arise (Conant et al, 2014;Panchy et al, 2016). Thus, comparative analysis of synteny is a powerful approach to understand the evolutionary trajectory of genes and genomes and ultimately of traits and organisms (Lee et al, 2013;Jiao et al, 2014).…”