No evidence for the radiation time lag model after whole genome duplications in Teleostei

AbstractThe short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the evolutionary success of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of key innovations, although the evolutionary success would not become apparent until a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed evolutionary success after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to evolutionary success in fishes.

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No evidence for the radiation time lag model after whole genome duplications in Teleostei

PLoS ONE ◽

10.1371/journal.pone.0176384 ◽

2017 ◽

Vol 12 (4) ◽

pp. e0176384 ◽

Cited By ~ 8

Author(s):

Sacha Laurent ◽

Nicolas Salamin ◽

Marc Robinson-Rechavi

Keyword(s):

Time Lag ◽

Whole Genome ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Lag Model ◽

Radiation Time

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Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

GigaScience ◽

10.1093/gigascience/giaa004 ◽

2020 ◽

Vol 9 (2) ◽

Cited By ~ 8

Author(s):

Zheng Li ◽

Michael S Barker

Keyword(s):

Gene Family ◽

False Positive Rate ◽

Nuclear Gene ◽

Plant Evolution ◽

Plant Genome ◽

Total Evidence ◽

Whole Genome ◽

Green Plants ◽

Whole Genome Duplications ◽

Genome Duplications

Abstract Background Polyploidy, or whole-genome duplications (WGDs), repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced >1,000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project. Results In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walk-through examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole-genome synteny analyses and our total evidence approach may minimize the false-positive rate throughout the dataset. Conclusions We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.

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Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

10.1101/735076 ◽

2019 ◽

Cited By ~ 2

Author(s):

Zheng Li ◽

Michael S Barker

Keyword(s):

Gene Family ◽

Nuclear Gene ◽

Plant Evolution ◽

Plant Genome ◽

Total Evidence ◽

Whole Genome ◽

Data Set ◽

Green Plants ◽

Whole Genome Duplications ◽

Genome Duplications

AbstractPolyploidy or whole genome duplications (WGDs) repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced over 1000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place ancient WGDs. Overall, 244 putative ancient WGDs were inferred across the Viridiplantae. Here, we describe these analyses and evaluate the consistency of the WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole genome synteny analyses and our total evidence approach may minimize the false positive rate throughout the data set. Given these resources will be useful for many future analyses on gene and genome evolution in green plants, we release 383,679 nuclear gene family phylogenies and 2,306 gene age distribution (Ks) plots from the 1KP capstone paper.

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Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution

Molecular Biology and Evolution ◽

10.1093/molbev/msaa302 ◽

2020 ◽

Author(s):

Akihiro Ezoe ◽

Kazumasa Shirai ◽

Kousuke Hanada

Keyword(s):

Gene Duplication ◽

Related Species ◽

Plant Evolution ◽

Whole Genome ◽

Duplicated Genes ◽

Closely Related Species ◽

Whole Genome Duplications ◽

New Genes ◽

Genome Duplications ◽

Tandem Duplications

Abstract Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.

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Linked by ancestral bonds: multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe

Molecular Biology and Evolution ◽

10.1093/molbev/msaa327 ◽

2020 ◽

Author(s):

Xinyi Guo ◽

Terezie Mandáková ◽

Karolína Trachtová ◽

Barış Özüdoğru ◽

Jianquan Liu ◽

...

Keyword(s):

Genome Evolution ◽

Reticulate Evolution ◽

Land Plant ◽

Whole Genome ◽

Plant Family ◽

Whole Genome Duplications ◽

Genome Duplications ◽

History Of ◽

Single Genus ◽

Genomic Relatedness

Abstract Pervasive hybridization and whole genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. While frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (c. 60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring post-polyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.

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Vertebrate whole genome duplications shaped the current 3D genome architecture

10.1101/2021.06.11.448047 ◽

2021 ◽

Author(s):

Caelinn James ◽

Marco Trevisan-Herraz ◽

Daniel Rico

Keyword(s):

Regulatory Networks ◽

Whole Genome ◽

3D Genome ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Topologically Associated Domains ◽

Major Transition ◽

Evolution Of Gene Regulation ◽

Evolutionary Success

Topologically associated domains (TADs) are interaction sub-networks of 3D genomes. TAD boundaries frequently coincide with genome breaks while their deletion is under negative selection, suggesting that TADs act as modules facilitating genome rearrangements and metazoan evolution. However, the role of TADs in the evolution of gene regulation and essentiality is not well understood. Here, we show that TADs play a role organising ancestral functions and evolutionary novelty. We discovered that genes co-localise by evolutionary age in the human and mouse genomes, resulting in TADs that have different proportions of younger and older genes. A major transition in the TAD age co-localisation patterns is observed between the genes born as a result of the vertebrate whole genome duplications (WGDs) or before, and those born afterwards. We also found that primate- and rodent-specific genes are more frequently essential when they are located in 'aged' TADs and connected to genes that have not duplicated since the WGD. Our data suggests that evolutionary success of recent genes may increase when located in functionally relevant TADs with established regulatory networks.

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Molecular evolution of GDP-L-galactose phosphorylase, a key regulatory gene in plant ascorbate biosynthesis

AoB Plants ◽

10.1093/aobpla/plaa055 ◽

2020 ◽

Vol 12 (6) ◽

Author(s):

Junjie Tao ◽

Zhuan Hao ◽

Chunhui Huang

Keyword(s):

Molecular Evolution ◽

Abiotic Stress Tolerance ◽

Regulatory Gene ◽

Purifying Selection ◽

Plant Evolution ◽

Rapid Expansion ◽

Whole Genome ◽

Evolutionary Patterns ◽

Whole Genome Duplications ◽

Genome Duplications

Abstract Ascorbic acid (AsA) is a widespread antioxidant in living organisms, and plays essential roles in the growth and development of animals and plants as well as in the response to abiotic stress tolerance. The GDP-L-galactose phosphorylase (GGP) is a key regulatory gene in plant AsA biosynthesis that can regulate the concentration of AsA at the transcriptional and translational levels. The function and regulation mechanisms of GGP have been well understood; however, the molecular evolutionary patterns of the gene remain unclear. In this study, a total of 149 homologous sequences of GGP were sampled from 71 plant species covering the major groups of Viridiplantae, and the phylogenetic relationships, gene duplication and molecular evolution analyses of the genes were systematically investigated. Results showed that GGP genes are present throughout the plant kingdom and five shared whole-genome duplications and several lineage-specific whole-genome duplications were found, which led to the rapid expansion of GGPs in seed plants, especially in angiosperms. The structure of GGP genes was more conserved in land plants, but varied greatly in green algae, indicating that GGP may have undergone great differentiation in the early stages of plant evolution. Most GGP proteins had a conserved motif arrangement and composition, suggesting that plant GGPs have similar catalytic functions. Molecular evolutionary analyses showed that GGP genes were predominated by purifying selection, indicating that the gene is functionally conserved due to its vital importance in AsA biosynthesis. Most of the branches under positive selection identified by the branch-site model were mainly in the chlorophytes lineage, indicating episodic diversifying selection may contribute to the evolution of GGPs, especially in the chlorophyte lineage. The conserved function of GGP and its rapid expansion in angiosperms maybe one of the reasons for the increase of AsA content in angiosperms, enabling angiosperms to adapt to changing environments.

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Land-plant Phylogenomic and Pomegranate Transcriptomic Analyses Reveal an Evolutionary Scenario of CYP75 Genes Subsequent to Whole Genome Duplications

Journal of Plant Biology ◽

10.1007/s12374-018-0319-9 ◽

2019 ◽

Vol 62 (1) ◽

pp. 48-60 ◽

Cited By ~ 5

Author(s):

Taikui Zhang ◽

Cuiyu Liu ◽

Xianbin Huang ◽

Hanyao Zhang ◽

Zhaohe Yuan

Keyword(s):

Land Plant ◽

Whole Genome ◽

Whole Genome Duplications ◽

Evolutionary Scenario ◽

Genome Duplications

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Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0353 ◽

2014 ◽

Vol 369 (1648) ◽

pp. 20130353 ◽

Cited By ~ 90

Author(s):

Kevin Vanneste ◽

Steven Maere ◽

Yves Van de Peer

Keyword(s):

Large Scale ◽

Plant Evolution ◽

Small Scale ◽

Whole Genome ◽

Polyploid Species ◽

Plant Genomes ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Duplication Events ◽

Biological Innovations

Genome sequencing has demonstrated that besides frequent small-scale duplications, large-scale duplication events such as whole genome duplications (WGDs) are found on many branches of the evolutionary tree of life. Especially in the plant lineage, there is evidence for recurrent WGDs, and the ancestor of all angiosperms was in fact most likely a polyploid species. The number of WGDs found in sequenced plant genomes allows us to investigate questions about the roles of WGDs that were hitherto impossible to address. An intriguing observation is that many plant WGDs seem associated with periods of increased environmental stress and/or fluctuations, a trend that is evident for both present-day polyploids and palaeopolyploids formed around the Cretaceous–Palaeogene (K–Pg) extinction at 66 Ma. Here, we revisit the WGDs in plants that mark the K–Pg boundary, and discuss some specific examples of biological innovations and/or diversifications that may be linked to these WGDs. We review evidence for the processes that could have contributed to increased polyploid establishment at the K–Pg boundary, and discuss the implications on subsequent plant evolution in the Cenozoic.

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