Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants

2009 ◽  
Vol 16 (8) ◽  
pp. 1071-1083 ◽  
Author(s):  
J.G. Burleigh ◽  
M.S. Bansal ◽  
A. Wehe ◽  
O. Eulenstein
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Duplication Events

scholarly journals Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

2019 ◽  
Author(s):  
Grant T Godden ◽  
Taliesin J Kinser ◽  
Pamela S Soltis ◽  
Douglas E Soltis
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Plant Traits ◽  
Divergence Time ◽  
Evolutionary Process ◽  
Driver Gene ◽  
Important Species ◽  
Plant Groups ◽  
Duplication Events ◽  
Gene Duplicates

Abstract Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7–18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the non-uniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.

scholarly journals Duplication accelerates the evolution of structural complexity in protein quaternary structure

2020 ◽  
Author(s):  
Alexander S. Leonard ◽  
Sebastian E. Ahnert
Keyword(s):  
Gene Duplication ◽  
Lattice Model ◽  
Self Assembly ◽  
Large Scale ◽  
Quaternary Structure ◽  
Protein Complexes ◽  
Structural Complexity ◽  
Data Bank ◽  
Coarse Grained ◽  
Duplication Events

AbstractGene duplication, from single genes to whole genomes, has been observed in organisms across all taxa. Despite its prevalence, the evolutionary benefits of this mechanism are the subject of ongoing debate. Gene duplication can significantly alter the self-assembly of protein quaternary structures, impacting the dosage or interaction proclivity. Here we use a lattice model of self-assembly as a coarse-grained representation of protein complex assembly, and show that it can be used to examine potential evolutionary advantages of duplication. Duplication provides a unique mechanism for increasing the evolvability of protein complexes by enabling the transformation of symmetric homomeric interactions into heteromeric ones. This transformation is extensively observed in in silico evolutionary simulations of the lattice model, with duplication events significantly accelerating the rate at which structural complexity increases. These coarse-grained simulation results are corroborated with a large-scale analysis of complexes from the Protein Data Bank.

Evolution of Placental Function in Mammals: The Molecular Basis of Gas and Nutrient Transfer, Hormone Secretion, and Immune Responses

2012 ◽  
Vol 92 (4) ◽  
pp. 1543-1576 ◽  
Author(s):  
Anthony M. Carter
Keyword(s):  
Gene Duplication ◽  
Convergent Evolution ◽  
Globin Gene ◽  
Hormone Secretion ◽  
Human Leukocyte ◽  
Amino Acid Transporters ◽  
Placental Lactogens ◽  
Wide Range ◽  
Duplication Events ◽  
Range Of Functions

Placenta has a wide range of functions. Some are supported by novel genes that have evolved following gene duplication events while others require acquisition of gene expression by the trophoblast. Although not expressed in the placenta, high-affinity fetal hemoglobins play a key role in placental gas exchange. They evolved following duplications within the beta-globin gene family with convergent evolution occurring in ruminants and primates. In primates there was also an interesting rearrangement of a cassette of genes in relation to an upstream locus control region. Substrate transfer from mother to fetus is maintained by expression of classic sugar and amino acid transporters at the trophoblast microvillous and basal membranes. In contrast, placental peptide hormones have arisen largely by gene duplication, yielding for example chorionic gonadotropins from the luteinizing hormone gene and placental lactogens from the growth hormone and prolactin genes. There has been a remarkable degree of convergent evolution with placental lactogens emerging separately in the ruminant, rodent, and primate lineages and chorionic gonadotropins evolving separately in equids and higher primates. Finally, coevolution in the primate lineage of killer immunoglobulin-like receptors and human leukocyte antigens can be linked to the deep invasion of the uterus by trophoblast that is a characteristic feature of human placentation.

Two gene duplication events in the human and primate dopamine D5 receptor gene family

Gene ◽  
1995 ◽  
Vol 154 (2) ◽  
pp. 153-158 ◽  
Author(s):  
Adriano Marchese ◽  
Timothy V. Beischlag ◽  
Tuan Nguyen ◽  
Hyman B. Niznik ◽  
Richard L. Weinshank ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Receptor Gene ◽  
Duplication Events ◽  
Dopamine D5 Receptor ◽  
Receptor Gene Family

Ancestral genome duplication in rice

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 610-614 ◽  
Author(s):  
Romain Guyot ◽  
Beat Keller
Keyword(s):  
Large Scale ◽  
Genome Duplication ◽  
Rice Genome ◽  
Block Size ◽  
Pairwise Comparisons ◽  
Comparative Genome Analysis ◽  
Important Species ◽  
Duplication Events ◽  
First Time ◽  
Grass Genomes

The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >1 Mb appears to be the rule and not the exception. Comparative mapping has shown high genetic colinearity among chromosomes of cereals, promoting rice as a model for studying grass genomes. Further comparative genome analysis should allow the study of the conservation and evolution of these duplication events in other important cereals such as rye, barley, and wheat.Key words: rice, genome duplication, genome evolution.

scholarly journals In with the Old, in with the New: The Promiscuity of the Duplication Process Engenders Diverse Pathways for Novel Gene Creation

2012 ◽  
Vol 2012 ◽  
pp. 1-24 ◽  
Author(s):  
Vaishali Katju
Keyword(s):  
Gene Duplication ◽  
Population Size ◽  
Population Genetic ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Dna And Rna ◽  
Duplication Events ◽  
History Of ◽  
Theoretical Population ◽  
Novel Exon

The gene duplication process has exhibited far greater promiscuity in the creation of paralogs with novel exon-intron structures than anticipated even by Ohno. In this paper I explore the history of the field, from the neo-Darwinian synthesis through Ohno’s formulation of the canonical model for the evolution of gene duplicates and culminating in the present genomic era. I delineate the major tenets of Ohno’s model and discuss its failure to encapsulate the full complexity of the duplication process as revealed in the era of genomics. I discuss the diverse classes of paralogs originating from both DNA- and RNA-mediated duplication events and their evolutionary potential for assuming radically altered functions, as well as the degree to which they can function unconstrained from the pressure of gene conversion. Lastly, I explore theoretical population-genetic considerations of how the effective population size (Ne) of a species may influence the probability of emergence of genes with radically altered functions.

scholarly journals STRIDE: Species Tree Root Inference from Gene Duplication Events

2017 ◽  
Vol 34 (12) ◽  
pp. 3267-3278 ◽  
Author(s):  
David M Emms ◽  
Steven Kelly
Keyword(s):  
Gene Duplication ◽  
Species Tree ◽  
Duplication Events

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

scholarly journals Patterns of gene evolution following duplications and speciations in vertebrates

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8813 ◽  
Author(s):  
Kyle T. David ◽  
Jamie R. Oaks ◽  
Kenneth M. Halanych
Keyword(s):  
Gene Duplication ◽  
Gene Evolution ◽  
Strong Support ◽  
Duplication Event ◽  
Gene Trees ◽  
Loss Of Function ◽  
Eukaryotic Genes ◽  
Gene Copies ◽  
Duplication Events ◽  
And Function

Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

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