Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

Li, Zhen; Defoort, Jonas; Tasdighian, Setareh; Maere, Steven; Peer, Yves Van de; Smet, Riet De

doi:10.1105/tpc.15.00877

Cited by 196 publications

(312 citation statements)

References 131 publications

(191 reference statements)

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“…The retention of duplicated PP2A genes and the detection of positive selection within the conserved core domain of B56 isoforms are consistent with the proposal that retention of gene duplicates provides mutational and phenotypic robustness (Keane et al, 2014;Li et al, 2016), allowing the evolution of advantageous adaptations. Within the vertebrate B9a/b/« clade, we detected positive selection only on B9a, suggesting that B9b and B9« may be functionally overlapping.…”

Section: B56 Isoform Specializationsupporting

confidence: 84%

“…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). Our selection analysis of the B56 family reveals the prevalence of positive selection among both mammalian and flowering plant isoforms and suggests relatively recent diversification in the evolution of PP2A-B56 isoforms in plants.…”

mentioning

confidence: 84%

“…This lack of expansion indicates that different subclades within a single gene family can be subject to very different evolutionary pressures. Previous work has shown that genes involved in very specific physiological processes revert to single copy rapidly after paleopolyploidy events (Li et al, 2016). Because FASS/TON2 and M. truncatula PP2AB91 are members of old clades that are represented by a single isoform in most plant species, the lack of expansion alone can explain the strong phenotypes observed in loss-of-function mutants, which are unlike the mild phenotypes observed in other PP2A subunit mutants.…”

Section: Nonexpanding Clades Are Linked To Specialized Functionsmentioning

confidence: 99%

“…A recent report found that flowering plant gene families revert quickly to single-copy postpaleopolyploidy, are maintained for tens of millions of years but ultimately revert to single copy, or are maintained indefinitely in multicopy form (Li et al, 2016). These expansion patterns may be constrained by gene function, with the indefinitely maintained multicopy families often playing roles in signal transduction, transport, and cell wall functions; expansion in these families thus may provide a selective advantage for phenotypic plasticity and tolerance of environmental stress (Keane et al, 2014;Li et al, 2016).…”

Section: Retention Of Duplicated Pp2a Subunit Genesmentioning

confidence: 99%

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

Booker

DeLong

2016

Plant Physiol.

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Protein phosphatase 2A (PP2A) presents unique opportunities for analyzing molecular mechanisms of functional divergence between gene family members. The canonical PP2A holoenzyme regulates multiple eukaryotic signaling pathways by dephosphorylating target proteins and contains a catalytic (C) subunit, a structural/scaffolding (A) subunit, and a regulatory (B) subunit. Genes encoding PP2A subunits have expanded into multigene families in both flowering plants and mammals, and the extent to which different isoform functions may overlap is not clearly understood. To gain insight into the diversification of PP2A subunits, we used phylogenetic analyses to reconstruct the evolutionary histories of PP2A gene families in Arabidopsis (Arabidopsis thaliana). Genes encoding PP2A subunits in mammals represent ancient lineages that expanded early in vertebrate evolution, while flowering plant PP2A subunit lineages evolved much more recently. Despite this temporal difference, our data indicate that the expansion of PP2A subunit gene families in both flowering plants and animals was driven by whole-genome duplications followed by nonrandom gene loss. Selection analysis suggests that the expansion of one B subunit gene family (B56/PPP2R5) was driven by functional diversification rather than by the maintenance of gene dosage. We also observed reduced expansion rates in three distinct B subunit subclades. One of these subclades plays a highly conserved role in cell division, while the distribution of a second subclade suggests a specialized function in supporting beneficial microbial associations. Thus, while whole-genome duplications have driven the expansion and diversification of most PP2A gene families, members of functionally specialized subclades quickly revert to singleton status after duplication events.

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Section: B56 Isoform Specializationsupporting

confidence: 84%

mentioning

confidence: 84%

Section: Nonexpanding Clades Are Linked To Specialized Functionsmentioning

confidence: 99%

Section: Retention Of Duplicated Pp2a Subunit Genesmentioning

confidence: 99%

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

Booker

DeLong

2016

Plant Physiol.

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“…Stems and leaves are both photosynthetic tissues, especially leaves. Functional enrichment analyses have revealed a class of single copy genes involved in organellerelated functions and photosynthetic processes (De Smet et al, 2013;Li et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Genes Encoding Flower- and Root-Specific Functions are More Resistant to Fractionation than Globally Expressed Genes in Brassica rapa

Kolkailah¹

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Like many angiosperms, Brassica rapa underwent several rounds of whole genome duplication during its evolutionary history. Brassica rapa is particularly valuable for studying genome evolution because it also experienced whole genome triplication shortly after it diverged from the common ancestor it shares with Arabidopsis thaliana about 17-20 million years ago. While many B. rapa genes appear resistant to paralog retention, close to 50% of B. rapa genes have retained multiple, paralogous loci for millions of years and appear to be multi-copy tolerant. Based on previous studies, gene function may contribute to the selective pressure driving certain genes back to singleton status. It is suspected that other factors, such as gene expression patterns, also play a role in determining the fate of genes following whole genome triplication. Published RNA-seq data was used to determine if gene expression patterns influence the retention of extra gene copies. It is hypothesized that retention of genes in duplicate and triplicate is more likely if those genes are expressed in a tissue-specific manner, as opposed to being expressed globally across all tissues. This study shows that genes expressed specifically in flowers and roots in B. rapa are more resistant to fractionation than globally expressed genes following whole genome triplication. In particular, there appears to have been selection on genes expressed specifically in flower tissues to retain higher copy numbers and for all three copies to exhibit the same flower-specific expression pattern. Future research to determine if these observations in Brassica rapa are consistent with other angiosperms that have undergone recent whole genome duplication would confirm that retention of flower-specific-expressed genes is a general feature in plant genome evolution and not specific to B. rapa.

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Comparative and evolutionary analyses of the divergence of plant oligosaccharyltransferase STT3 isoforms

et al. 2020

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STT3 is a catalytic subunit of hetero‐oligomeric oligosaccharyltransferase (OST), which is important for asparagine‐linked glycosylation. In mammals and plants, OSTs with different STT3 isoforms exhibit distinct levels of enzymatic efficiency or different responses to stressors. Although two different STT3 isoforms have been identified in both plants and animals, it remains unclear whether these isoforms result from gene duplication in an ancestral eukaryote. Furthermore, the molecular mechanisms underlying the functional divergences between the two STT3 isoforms in plant have not been well elucidated. Here, we conducted phylogenetic analysis of the major evolutionary node species and suggested that gene duplications of STT3 may have occurred independently in animals and plants. Across land plants, the exon–intron structure differed between the two STT3 isoforms, but was highly conserved for each isoform. Most angiosperm STT3a genes had 23 exons with intron phase 0, while STT3b genes had 6 exons with intron phase 2. Characteristic motifs (motif 18 and 19) of STT3s were mapped to different structure domains in the plant STT3 proteins. These two motifs overlap with regions of high nonsynonymous‐to‐synonymous substitution rates, suggesting the regions may be related to functional difference between STT3a and STT3b. In addition, promoter elements and gene expression profiles were different between the two isoforms, indicating expression pattern divergence of the two genes. Collectively, the identified differences may result in the functional divergence of plant STT3s.

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Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

Cited by 196 publications

References 131 publications

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

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

Genes Encoding Flower- and Root-Specific Functions are More Resistant to Fractionation than Globally Expressed Genes in Brassica rapa

Comparative and evolutionary analyses of the divergence of plant oligosaccharyltransferase STT3 isoforms

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