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

GigaScience ◽  
2020 ◽  
Vol 9 (2) ◽  
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.

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

2019 ◽  
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.

scholarly journals One thousand plant transcriptomes and the phylogenomics of green plants

Nature ◽  
2019 ◽  
Vol 574 (7780) ◽  
pp. 679-685 ◽  
Author(s):  
Keyword(s):  
Genome Evolution ◽  
Nuclear Gene ◽  
Gene Families ◽  
Plant Genome ◽  
Gene Trees ◽  
Green Plants ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Multiple Species ◽  
The One

Abstract Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

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

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.

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

2017 ◽  
Author(s):  
Sacha Laurent ◽  
Nicolas Salamin ◽  
Marc Robinson-Rechavi
Keyword(s):  
Time Lag ◽  
Land Plant ◽  
Plant Evolution ◽  
Whole Genome ◽  
Long Term Effects ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Lag Model ◽  
Evolutionary Success ◽  
Radiation Time

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.

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

AoB Plants ◽  
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.

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

2014 ◽  
Vol 369 (1648) ◽  
pp. 20130353 ◽  
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.

scholarly journals Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies in Paramecium species

2017 ◽  
Vol 28 (8) ◽  
pp. 1101-1110 ◽  
Author(s):  
Lydia J. Bright ◽  
Jean-Francois Gout ◽  
Michael Lynch
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Rab Gtpase ◽  
Rab Proteins ◽  
Whole Genome ◽  
Amino Acid Residues ◽  
Functional Diversification ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
New Gene

New gene functions arise within existing gene families as a result of gene duplication and subsequent diversification. To gain insight into the steps that led to the functional diversification of paralogues, we tracked duplicate retention patterns, expression-level divergence, and subcellular markers of functional diversification in the Rab GTPase gene family in three Paramecium aurelia species. After whole-genome duplication, Rab GTPase duplicates are more highly retained than other genes in the genome but appear to be diverging more rapidly in expression levels, consistent with early steps in functional diversification. However, by localizing specific Rab proteins in Paramecium cells, we found that paralogues from the two most recent whole-genome duplications had virtually identical localization patterns, and that less closely related paralogues showed evidence of both conservation and diversification. The functionally conserved paralogues appear to target to compartments associated with both endocytic and phagocytic recycling functions, confirming evolutionary and functional links between the two pathways in a divergent eukaryotic lineage. Because the functionally diversifying paralogues are still closely related to and derived from a clade of functionally conserved Rab11 genes, we were able to pinpoint three specific amino acid residues that may be driving the change in the localization and thus the function in these proteins.

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