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 OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates

2019 ◽  
Author(s):  
Param Priya Singh ◽  
Hervé Isambert
Keyword(s):  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Diseases ◽  
Genomic Analysis ◽  
Biased Sampling ◽  
Whole Genome ◽  
Genome Duplications ◽  
Evolutionary Genomic ◽  
The Impact

Abstract All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.

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 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 Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shijing Feng ◽  
Zhenshan Liu ◽  
Jian Cheng ◽  
Zihe Li ◽  
Lu Tian ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Repetitive Sequences ◽  
Close Relative ◽  
Specific Gene ◽  
Gene Gain ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
A Genome ◽  
The Impact

AbstractZanthoxylum bungeanum is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites, which create a characteristic aroma and tingling sensation in the mouth. Owing to the high proportion of repetitive sequences, high heterozygosity, and increased chromosome number of Z. bungeanum, the assembly of its chromosomal pseudomolecules is extremely challenging. Here, we present a genome sequence for Z. bungeanum, with a dramatically expanded size of 4.23 Gb, assembled into 68 chromosomes. This genome is approximately tenfold larger than that of its close relative Citrus sinensis. After the divergence of Zanthoxylum and Citrus, the lineage-specific whole-genome duplication event η-WGD approximately 26.8 million years ago (MYA) and the recent transposable element (TE) burst ~6.41 MYA account for the substantial genome expansion in Z. bungeanum. The independent Zanthoxylum-specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture. Integrative genomic and transcriptomic analyses suggested that prominent species-specific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools, terpenoids, and anthocyanins, which contribute to the special flavor and appearance of Z. bungeanum. In summary, the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate Zanthoxylum improvement.

scholarly journals Impact of genome duplication on secondary metabolite composition in non-cultivated species: a systematic meta-analysis

2020 ◽  
Vol 126 (3) ◽  
pp. 363-376
Author(s):  
Michelle L Gaynor ◽  
Simone Lim-Hing ◽  
Chase M Mason
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Meta Analysis ◽  
Plant Secondary Metabolites ◽  
Cultivated Plants ◽  
Whole Genome ◽  
Species Complexes ◽  
Related Plant ◽  
Cultivated Species ◽  
The Impact

Abstract Background and Aims Whole-genome duplication is known to influence ecological interactions and plant physiology; however, despite abundant case studies, much is still unknown about the typical impact of genome duplication on plant secondary metabolites (PSMs). In this study, we assessed the impact of polyploidy events on PSM characteristics in non-cultivated plants. Methods We conducted a systematic review and meta-analysis to compare composition and concentration of PSMs among closely related plant species or species complexes differing in ploidy level. Key Results We assessed 53 studies that focus on PSMs among multiple cytotypes, of which only 14 studies compared concentration quantitatively among cytotypes. We found that whole-genome duplication can have a significant effect on PSM concentration; however, these effects are highly inconsistent. Conclusion Overall, there was no consistent effect of whole-genome duplication on PSM concentrations or profiles.

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 OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates

2019 ◽  
Author(s):  
Param Priya Singh ◽  
Hervé Isambert
Keyword(s):  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Diseases ◽  
Genomic Analysis ◽  
Biased Sampling ◽  
Whole Genome ◽  
Protein Coding ◽  
Genome Duplications ◽  
The Impact

ABSTRACTAll vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, developmental patterns and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We have previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database, which also includes non-protein coding RNA genes. We find that teleost fish have retained most 2R-WGD ohnologs common to amniotes, which have also retained significantly more ohnologs from 3R-WGD, whereas a higher rate of 2R-WGD ohnolog loss is observed in sauropsids compared to mammals and fish. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.

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