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Trends in Genetics : TIG Jan 2022Gene duplication is a prevalent phenomenon across the tree of life. The processes that lead to the retention of duplicated genes are not well understood. Functional... (Review)
Review
Gene duplication is a prevalent phenomenon across the tree of life. The processes that lead to the retention of duplicated genes are not well understood. Functional genomics approaches in model organisms, such as yeast, provide useful tools to test the mechanisms underlying retention with functional redundancy and divergence of duplicated genes, including fates associated with neofunctionalization, subfunctionalization, back-up compensation, and dosage amplification. Duplicated genes may also be retained as a consequence of structural and functional entanglement. Advances in human gene editing have enabled the interrogation of duplicated genes in the human genome, providing new tools to evaluate the relative contributions of each of these factors to duplicate gene retention and the evolution of genome structure.
Topics: Evolution, Molecular; Gene Duplication; Genes, Duplicate; Humans; Saccharomyces cerevisiae
PubMed: 34294428
DOI: 10.1016/j.tig.2021.06.016 -
MBio Feb 2023Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly... (Review)
Review
Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.
Topics: Humans; Evolution, Molecular; Poxviridae; Host Specificity; Gene Duplication
PubMed: 36515529
DOI: 10.1128/mbio.01526-22 -
ELife Nov 2023A genetic duplication event during evolution allowed male wood tiger moths to have either yellow or white patterns on their wings.
A genetic duplication event during evolution allowed male wood tiger moths to have either yellow or white patterns on their wings.
Topics: Male; Animals; Gene Duplication; Lepidoptera
PubMed: 37917141
DOI: 10.7554/eLife.92763 -
Genes Aug 2021Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently... (Review)
Review
Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently observed in human malignancies and many of the products of these events are pathogenic, representing significant drivers of tumourigenesis and cancer evolution. In certain subsets of cancers duplicated and fused genes appear to be essential for initiation of tumour formation, and some even have the capability of transforming normal cells, highlighting the importance of understanding the events that result in their formation. The mechanisms that drive gene duplication and fusion are unregulated in cancer and they facilitate rapid evolution by selective forces akin to Darwinian survival of the fittest on a cellular level. In this review, we examine current knowledge of the landscape and prevalence of gene duplication and gene fusion in human cancers.
Topics: Carcinogenesis; Evolution, Molecular; Gene Duplication; Gene Fusion; Humans; Neoplasms
PubMed: 34573358
DOI: 10.3390/genes12091376 -
Plant Physiology Aug 2016Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These... (Review)
Review
Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.
Topics: Evolution, Molecular; Gene Duplication; Genome, Plant; Phylogeny; Plants
PubMed: 27288366
DOI: 10.1104/pp.16.00523 -
Current Opinion in Genetics &... Oct 2022Oligomeric proteins are central to cellular life and the duplication and divergence of their genes is a key driver of evolutionary innovations. The duplication of a gene... (Review)
Review
Oligomeric proteins are central to cellular life and the duplication and divergence of their genes is a key driver of evolutionary innovations. The duplication of a gene coding for an oligomeric protein has numerous possible outcomes, which motivates questions on the relationship between structural and functional divergence. How do protein oligomeric states diversify after gene duplication? In the simple case of duplication of a homo-oligomeric protein gene, what properties can influence the fate of descendant paralogs toward forming independent homomers or maintaining their interaction as a complex? Furthermore, how are functional innovations associated with the diversification of oligomeric states? Here, we review recent literature and present specific examples in an attempt to illustrate and answer these questions.
Topics: Biological Evolution; Evolution, Molecular; Gene Duplication
PubMed: 36007298
DOI: 10.1016/j.gde.2022.101966 -
Bioinformatics (Oxford, England) Jul 2021It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell....
MOTIVATION
It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree.
RESULTS
We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.
AVAILABILITY AND IMPLEMENTATION
EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.
Topics: Algorithms; Evolution, Molecular; Gene Duplication; Gene Transfer, Horizontal; Genome; Phylogeny; Symbiosis
PubMed: 34252921
DOI: 10.1093/bioinformatics/btab328 -
Viruses May 2022Human metapneumovirus (HMPV) is an important respiratory pathogen and is divided in two main groups (A and B). HMPV strains with partial duplications (111-nt and 180-nt...
Human metapneumovirus (HMPV) is an important respiratory pathogen and is divided in two main groups (A and B). HMPV strains with partial duplications (111-nt and 180-nt duplication) of the G gene have been reported in recent years. Since the initial reports, viruses with these characteristics have been reported in several countries. We analyzed all complete HMPV G gene ectodomain sequences available at GenBank to determine if viruses with 111-nt or 180-nt duplication have become the leading HMPV strains worldwide, and to describe their temporal and geographic distribution. We identified 1462 sequences that fulfilled study criteria (764 HMPV A and 698 HMPV B) reported from 37 countries. The most frequent HMPV A genotype was A2b2 ( = 366), and the most frequent B genotype was B2 ( = 374). A total of 84 sequences contained the 111-nt duplication, and 90 sequences contained the 180-nt duplication. Since 2016, viruses with a partial duplication comprise the most frequent HMPV A sequences globally and have displaced other HMPV A viruses in Asia, Europe, and South America; no sequences of viruses with partial duplication have been reported in North America or Africa so far. Continued surveillance of HMPV is required to identify the emergence and spread of epidemiologically relevant variants.
Topics: Gene Duplication; Genotype; Humans; Metapneumovirus; Paramyxoviridae Infections; Phylogeny
PubMed: 35632799
DOI: 10.3390/v14051058 -
Sexual Development : Genetics,... 2021Sex determination and differentiation varies widely across vertebrates, but is most dramatically diverse in fishes. Among fishes sex reversal and sex change are observed... (Review)
Review
Sex determination and differentiation varies widely across vertebrates, but is most dramatically diverse in fishes. Among fishes sex reversal and sex change are observed in 41 teleost families spanning 7 orders. These sex-changing fish perhaps highlight better than any other system that sex determination is not the narrow and fixed construct we once thought, but a plastic trait that is better viewed as a reaction norm. However, while this stunning transformation is increasingly understood, a fundamental question arises, which is why some fish species have retained this inherent plasticity in sexual fate, while others have not? Here, we explore our current understanding of sex change in fish, some of the factors that permit and constrain sex reversal, and posit that gene duplication and neofunctionalization contribute to the sexual lability observed in fish.
Topics: Animals; Fishes; Gene Duplication; Phenotype; Sex Determination Analysis; Vertebrates
PubMed: 34167118
DOI: 10.1159/000515425 -
Genome Biology Feb 2019The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and... (Comparative Study)
Comparative Study
BACKGROUND
The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention.
RESULTS
We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database.
CONCLUSIONS
We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
Topics: Biological Evolution; Databases as Topic; Gene Conversion; Gene Duplication; Gene Expression; Genome, Plant; Multigene Family; Plants; Polyploidy; Selection, Genetic; Software
PubMed: 30791939
DOI: 10.1186/s13059-019-1650-2