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 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 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.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

scholarly journals Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gareth B. Gillard ◽  
Lars Grønvold ◽  
Line L. Røsæg ◽  
Matilde Mengkrog Holen ◽  
Øystein Monsen ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Whole Genome Duplication ◽  
Genome Stability ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Whole Genome ◽  
Specific Expression ◽  
Tissue Specific ◽  
Genome Doubling ◽  
Expression Evolution

Abstract Background Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago. Results We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. Conclusions Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

scholarly journals Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amit Rai ◽  
Hideki Hirakawa ◽  
Ryo Nakabayashi ◽  
Shinji Kikuchi ◽  
Koki Hayashi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Experimental Validation ◽  
Genome Duplication ◽  
Indole Alkaloids ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Plant Genomes ◽  
Genome Triplication ◽  
Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

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