scholarly journals Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

2013 ◽  
Vol 161 (4) ◽  
pp. 1844-1861 ◽  
Author(s):  
Wen-kai Jiang ◽  
Yun-long Liu ◽  
En-hua Xia ◽  
Li-zhi Gao
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Flowering Plants ◽  
Whole Genome ◽  
Duplicated Genes

scholarly journals Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome

2013 ◽  
Vol 2013 ◽  
pp. 1-4
Author(s):  
Yanmei Yang ◽  
Jinpeng Wang ◽  
Jianyong Di
Keyword(s):  
Statistical Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplication Event ◽  
Plant Evolution ◽  
Soybean Genome ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Genome Duplication Event ◽  
Scientific Value

Soybean (Glycine max) is one of the most important crop plants for providing protein and oil. It is important to investigate soybean genome for its economic and scientific value. Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource for genetic innovation. Improved sequence alignment criteria and statistical analysis are used to identify and characterize duplicated genes produced by polyploidization in soybean. Based on the collinearity method, duplicated genes by whole genome duplication account for 70.3% in soybean. From the statistical analysis of the molecular distances between duplicated genes, our study indicates that the whole genome duplication event occurred more than once in the genome evolution of soybean, which is often distributed near the ends of chromosomes.

scholarly journals Species-rich and polyploid-poor: Insights into the evolutionary role of whole-genome duplication from the Cape flora biodiversity hotspot

2016 ◽  
Vol 103 (7) ◽  
pp. 1336-1347 ◽  
Author(s):  
Kenneth C. Oberlander ◽  
Léanne L. Dreyer ◽  
Peter Goldblatt ◽  
Jan Suda ◽  
H. Peter Linder
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Biodiversity Hotspot ◽  
Whole Genome ◽  
Evolutionary Role

scholarly journals An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ya Wang ◽  
Fei Chen ◽  
Yuanchun Ma ◽  
Taikui Zhang ◽  
Pengchuan Sun ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Tea Plant ◽  
Plant Evolution ◽  
Plant Genome ◽  
Whole Genome ◽  
Biosynthesis Pathway ◽  
Duplicated Genes ◽  
Tandem Gene Duplication ◽  
Tea Plants

AbstractTea, coffee, and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value. The genomes of four tea plant varieties have recently been sequenced, but there is some debate regarding the characterization of a whole-genome duplication (WGD) event in tea plants. Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered. Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication (WGT) event. This WGD was shared by the Polemonioids-Primuloids-Core Ericales (PPC) sections, encompassing at least 17 families in the order Ericales. In addition, our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway, four pairs of duplicated genes in the theanine biosynthesis pathway, and one pair of genes in the caffeine biosynthesis pathway, which were expanded and retained following this WGD. Nearly all these gene pairs were expressed in tea plants, implying the contribution of the WGD. This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes, the WGD may have been another main factor driving the evolution of tea flavor.

scholarly journals Distinguish between Duplication of Essential Genes and Duplication of Dispensable Genes

2020 ◽  
Author(s):  
Xun Gu
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Essential Gene ◽  
Distinct Pattern ◽  
Essential Genes ◽  
Whole Genome ◽  
Computational Pipeline ◽  
Genetic Robustness ◽  
Genetic Buffering

AbstractWhen a dispensable gene is duplicated (ancestral dispensability), genetic buffering and duplicate compensation together maintain the gene dispensability, whereas duplicate compensation is the only mechanism when an essential gene is duplicated (ancestral essentiality). To explore the distinct pattern of genetic robustness between these evolutionary scenarios, we formulated a probabilistic model with some biologically reasonable assumptions for analyzing a set of duplicate pairs with three possible states: double-dispensable (DD), semi-dispensable (one dispensable one essential, DE) or double-essential (EE). A computational pipeline is then developed to predict the distribution of three states (DD, DE and EE) conditional of ancestral dispensability or essentiality, respectively. This model was applied to yeast duplicate pairs from a whole-genome duplication, revealing that the process of essentiality of those duplicated from essential genes could be significantly higher than that of those duplicated from dispensable genes. We thus proposed a hypothesis that the process of sub-functionalization may be faster than neo-functionalization. Our analysis may provide some new insights about the role of duplicate compensation on genetic robustness.

scholarly journals Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

Science ◽  
2020 ◽  
Vol 368 (6498) ◽  
pp. eaaz5667 ◽  
Author(s):  
Elena Kuzmin ◽  
Benjamin VanderSluis ◽  
Alex N. Nguyen Ba ◽  
Wen Wang ◽  
Elizabeth N. Koch ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Interaction ◽  
Interaction Analysis ◽  
Quantitative Measure ◽  
Duplicate Gene ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Genome Duplication Event ◽  
Genetic Interaction Analysis

Whole-genome duplication has played a central role in the genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated, and factors that influence the retention of persisting duplicates remain poorly understood. We describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping of digenic interactions for a deletion mutant of each paralog, and of trigenic interactions for the double mutant, provides insight into their roles and a quantitative measure of their functional redundancy. Trigenic interaction analysis distinguishes two classes of paralogs: a more functionally divergent subset and another that retained more functional overlap. Gene feature analysis and modeling suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and structural entanglement factors.

scholarly journals Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Le Zhang ◽  
Jingtian Zhao ◽  
Hao Bi ◽  
Xiangyu Yang ◽  
Zhiyang Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Populus Euphratica ◽  
Epigenetic Modifications ◽  
Chromatin Organization ◽  
Whole Genome ◽  
Duplicated Genes

AbstractThe nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

scholarly journals Using digital organisms to investigate the effect of whole genome duplication in (artificial) evolution

2019 ◽  
Author(s):  
Yao Yao ◽  
Lorenzo Carretero-Paulet ◽  
Yves Van de Peer
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Computational Simulation ◽  
Model Organisms ◽  
Whole Genome ◽  
Mutational Robustness ◽  
Digital Organisms ◽  
Extinction Events ◽  
The Impact

AbstractThe potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary ‘dead end’, there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual artificial genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that increased complexity, modularity, and redundancy of duplicated GRNs might provide DOs with increased adaptive potential under extinction events, while ensuring mutational robustness of the whole GRN. Our results confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome the traditional limitations of evolution experiments with model organisms, and provide some additional insights into how genome duplication might help organisms to compete for novel niches and survive ecological turmoil.

scholarly journals Origin of horsetails and the role of whole-genome duplication in plant macroevolution

2019 ◽  
Vol 286 (1914) ◽  
pp. 20191662 ◽  
Author(s):  
James W. Clark ◽  
Mark N. Puttick ◽  
Philip C. J. Donoghue
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Morphological Evolution ◽  
Land Plant ◽  
Plant Evolution ◽  
Whole Genome ◽  
Geological Time ◽  
Term Survival

Whole-genome duplication (WGD) has occurred commonly in land plant evolution and it is often invoked as a causal agent in diversification, phenotypic and developmental innovation, as well as conferring extinction resistance. The ancient and iconic lineage of Equisetum is no exception, where WGD has been inferred to have occurred prior to the Cretaceous–Palaeogene (K–Pg) boundary, coincident with WGD events in angiosperms. In the absence of high species diversity, WGD in Equisetum is interpreted to have facilitated the long-term survival of the lineage. However, this characterization remains uncertain as these analyses of the Equisetum WGD event have not accounted for fossil diversity. Here, we analyse additional available transcriptomes and summarize the fossil record. Our results confirm support for at least one WGD event shared among the majority of extant Equisetum species. Furthermore, we use improved dating methods to constrain the age of gene duplication in geological time and identify two successive Equisetum WGD events. The two WGD events occurred during the Carboniferous and Triassic, respectively, rather than in association with the K–Pg boundary. WGD events are believed to drive high rates of trait evolution and innovations, but analysed trends of morphological evolution across the historical diversity of Equisetum provide little evidence for further macroevolutionary consequences following WGD. WGD events cannot have conferred extinction resistance to the Equisetum lineage through the K–Pg boundary since the ploidy events occurred hundreds of millions of years before this mass extinction and we find evidence of extinction among fossil polyploid Equisetum lineages. Our findings precipitate the need for a review of the proposed roles of WGDs in biological innovation and extinction survival in angiosperm and non-angiosperm lineages alike.

scholarly journals Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication

2016 ◽  
Author(s):  
Zhicheng Zhang ◽  
Heleen Coenen ◽  
Philip Ruelens ◽  
Rashmi R. Hazarika ◽  
Tareq Al Hindi ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Interaction Network ◽  
Reproductive Development ◽  
Network Evolution ◽  
Flowering Plants ◽  
Whole Genome ◽  
Core Eudicots ◽  
The Impact

AbstractThe evolution of plants is characterized by several rounds of ancient whole genome duplication, sometimes closely associated with the origin of large groups of species. A good example is the γ triplication at the origin of core eudicots. Core eudicots comprise about 75% of flowering plants and are characterized by the canalization of reproductive development. To better understand the impact of this genomic event, we studied the protein interaction network of MADS-domain transcription factors, which are key regulators of reproductive development. We accurately inferred, resurrected and tested the interactions of ancestral proteins before and after the triplication and directly compared these ancestral networks to the networks of Arabidopsis and tomato. We find that the γ triplication generated a dramatically innovated network that strongly rewired through the addition of many new interactions. Many of these interactions were established between paralogous proteins and a new interaction partner, establishing new redundancy. Simulations show that both node and edge addition through the triplication were important to maintain modularity in the network. In addition to generating insights into the impact of whole genome duplication and elementary processes involved in network evolution, our data provide a resource for comparative developmental biology in flowering plants.

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