Duplicate Retention After Small‐ and Large‐Scale Duplications

Maere, Steven; Peer, Yves Van de

doi:10.1002/9780470619902.ch3

Cited by 24 publications

(25 citation statements)

References 175 publications

(218 reference statements)

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“…therein). A likely explanation for this phenomenon is offered by the dosage balance hypothesis, which postulates that the stoichiometric quantities of proteins functioning within protein complexes and regulatory/ signaling cascades must be preserved to ensure proper function (Papp et al, 2003;Birchler et al, 2005;Veitia et al, 2008;Maere and Van de Peer, 2010). This requirement is violated by small-scale gene duplications but fulfilled by whole-genome duplications, where all components of such complexes and/or cascades are simultaneously duplicated.…”

Section: Discussionmentioning

confidence: 99%

“…Genome duplications have had a profound impact on the expansion of certain gene families in plants, in particular regulatory gene families (Maere et al, 2005;Freeling, 2009;Maere and Van de Peer, 2010). We investigated their impact on the TPP gene family by searching for collinearity of genomic segments containing TPP genes, using the PLAZA v1.0 platform (Proost et al, 2009).…”

Section: Collinearity Analysis Shows That the Tpp Gene Family In Eudimentioning

confidence: 99%

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Expansive Evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE Gene Family in Arabidopsis

et al. 2012

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Trehalose is a nonreducing sugar used as a reserve carbohydrate and stress protectant in a variety of organisms. While higher plants typically do not accumulate high levels of trehalose, they encode large families of putative trehalose biosynthesis genes. Trehalose biosynthesis in plants involves a two-step reaction in which trehalose-6-phosphate (T6P) is synthesized from UDPglucose and glucose-6-phosphate (catalyzed by T6P synthase [TPS]), and subsequently dephosphorylated to produce the disaccharide trehalose (catalyzed by T6P phosphatase [TPP]). In Arabidopsis (Arabidopsis thaliana), 11 genes encode proteins with both TPS-and TPP-like domains but only one of these (AtTPS1) appears to be an active (TPS) enzyme. In addition, plants contain a large family of smaller proteins with a conserved TPP domain. Here, we present an in-depth analysis of the 10 TPP genes and gene products in Arabidopsis (TPPA-TPPJ). Collinearity analysis revealed that all of these genes originate from wholegenome duplication events. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that all encode active TPP enzymes with an essential role for some conserved residues in the catalytic domain. These results suggest that the TPP genes function in the regulation of T6P levels, with T6P emerging as a novel key regulator of growth and development in higher plants. Extensive gene expression analyses using a complete set of promoter-b-glucuronidase/green fluorescent protein reporter lines further uncovered cell-and tissue-specific expression patterns, conferring spatiotemporal control of trehalose metabolism. Consistently, phenotypic characterization of knockdown and overexpression lines of a single TPP, AtTPPG, points to unique properties of individual TPPs in Arabidopsis, and underlines the intimate connection between trehalose metabolism and abscisic acid signaling.The presence of trehalose in a wide variety of organisms and the existence of different biosynthesis pathways suggest a pivotal and ancient role for trehalose metabolism in nature. The most widely distributed metabolic pathway consists of two consecutive enzymatic reactions, with trehalose-6-phosphate (T6P) synthase (TPS) catalyzing the transfer of a glucosyl moiety from UDP-Glc to Glc-6-phosphate to produce T6P and UDP, and T6P phosphatase (TPP) catalyzing dephosphorylation of T6P to trehalose (Cabib and Leloir, 1958; Avonce et al., 2006). Apart from operating as a (reserve) carbon source and structural component in bacteria, fungi, and invertebrates, trehalose also functions as a major stress protectant of proteins and membranes during adverse conditions such as dehydration, high salinity, hypoxia, and nutrient starvation (Elbein et al., 2003). Trehalose accumulation is also observed in a few lower vascular resurrection plants (e.g. Selaginella lepidophylla). Until about a decade ago, higher vascular plants were believed to have lost the ability to produce trehalose, but with the emergence of more sensitive assays, genome sequencing, and the use of yeast (Saccharo...

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Section: Discussionmentioning

confidence: 99%

Section: Collinearity Analysis Shows That the Tpp Gene Family In Eudimentioning

confidence: 99%

Expansive Evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE Gene Family in Arabidopsis

et al. 2012

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“…However, many of these findings are associated with studies of duplicates derived from whole-genome duplication (WGD) events, which occurred several times during the past 200 million years of angiosperm evolution (Paterson, et al 2004; Lockton and Gaut 2005; Cui, et al 2006; Van de Peer, et al 2009; Jiao, et al 2011; Rensing 2014; Panchy, et al 2016). Yet substantial evidence shows that, in both plants and animals, duplicates deriving from WGD and small-scale duplication (SSD) events differ in quantifiable ways, such as evolutionary rate, essentiality, and function (Hakes, et al 2007; Carretero-Paulet and Fares 2012; Rensing 2014; Maere and Van de Peer, 2010). Therefore, an open question is how SSD-derived genes in angiosperms evolve and are retained over long evolutionary timescales.…”

Section: Introductionmentioning

confidence: 99%

Rapid functional divergence of grass duplicate genes

Jiang

Assis

2018

Preprint

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1 Gene duplication has played an important role in the evolution and domestication of flowering plants. 2 Yet little is known about how plant duplicate genes evolve and are retained over long timescales, 3 particularly those arising from small--scale duplication (SSD) rather than whole--genome duplication 4 (WGD) events. Here we address this question in the Poaceae (grass) family by analyzing gene 5 expression data from nine tissues of Brachypodium distachyon, Oryza sativa japonica (rice), and 6 Sorghum bicolor (sorghum). Consistent with theoretical predictions, expression profiles of most grass 7 genes are conserved after SSD, suggesting that functional conservation is the primary outcome of SSD 8 in grasses. However, we also uncover support for widespread functional divergence, much of which 9 occurs asymmetrically via the process of neofunctionalization. Moreover, neofunctionalization 10 preferentially targets younger (child) duplicate gene copies, is associated with RNA--mediated 11 duplication, and occurs quickly after duplication. Further analysis reveals that functional divergence of 12 SSD--derived genes is positively correlated with both sequence divergence and tissue specificity in all 13 three grass species, and particularly with anther expression in B. distachyon. Therefore, as found in 14 many animal species, SSD--derived grass genes often undergo rapid functional divergence that may be 15 driven by natural selection on male--specific phenotypes. 16 17 12 60 MYA (Bowers, et al. 2005; Bennetzen 2007; Paterson, et al. 2009; International Brachypodium 13 Initiative 2010). Grasses represent an interesting evolutionary system because they are agriculturally 14 important (Davidson, et al. 2012) and, thus, have undergone domestication events in their recent 15 evolutionary histories. Further, these three grass species are ideal for comparison due to the availability 16 of RNA--seq data from the same nine tissues (leaf, anther, endosperm, early inflorescence, emerging 17 inflorescence, pistil, embryo, seed 5 days after pollination, and seed 10 days after pollination) that were 18 obtained in a single lab under similar experimental conditions (Davidson, et al. 2012). Hence, we have a 19 powerful toolkit with which to assess expression divergence after SSD in grasses. 20 21 RESULTS 22 Retention mechanisms of SSD--derived duplicates in grasses Assis R, Bachtrog D. 2015. Rapid divergence and diversification of mammalian duplicate gene functions. 5 metabolic network gives rise to relative and absolute dosage constraints. The Plant Cell 23:1719--6 1728. 7 Bennetzen JL, Ma J, Devos KM. 2005. Mechanisms of recent genome size variation in flowering plants.

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“…Why do some duplicates persist while others are lost? Models for duplicate gene retention in general have been reviewed elsewhere (Innan and Kondrashov, 2010;Maere and Van de Peer, 2010); here, we will focus on examples of duplicate retention in plants (Fig. 3, B -G).…”

Section: Mechanisms For Retention Of Duplicate Genes Genetic Drift Anmentioning

confidence: 99%

Evolution of Gene Duplication in Plants

2016

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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.

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Duplicate Retention After Small‐ and Large‐Scale Duplications

Cited by 24 publications

References 175 publications

Expansive Evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE Gene Family in Arabidopsis

Expansive Evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE Gene Family in Arabidopsis

Rapid functional divergence of grass duplicate genes

Evolution of Gene Duplication in Plants

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