The Temporal Distribution of Gene Duplication Events in a Set of Highly Conserved Human Gene Families

AbstractBackgroundGene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.FindingsA certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we have converted the command line Ensembl Compara GeneTrees pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.ConclusionsGeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy’s user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

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Gene duplications and the origins of vertebrate development

Development ◽

10.1242/dev.1994.supplement.125 ◽

1994 ◽

Vol 1994 (Supplement) ◽

pp. 125-133 ◽

Cited By ~ 2

Author(s):

Peter W. H. Holland ◽

Jordi Garcia-Fernàndez ◽

Nic A. Williams ◽

Arend Sidow

Keyword(s):

Gene Duplication ◽

Functional Divergence ◽

Expression Patterns ◽

Homeobox Gene ◽

Gene Families ◽

Gene Clusters ◽

Second Phase ◽

Genetic Changes ◽

New Genes ◽

Duplication Events

All vertebrates possess anatomical features not seen in their closest living relatives, the protochordates (tunicates and amphioxus). Some of these features depend on developmental processes or cellular behaviours that are again unique to vertebrates. We are interested in the genetic changes that may have permitted the origin of these innovations. Gene duplication, followed by functional divergence of new genes, may be one class of mutation that permits major evolutionary change. Here we examine the hypothesis that gene duplication events occurred close to the origin and early radiation of the vertebrates. Genome size comparisons are compatible with the occurrence of duplications close to vertebrate origins; more precise insight comes from cloning and phylogenetic analysis of gene families from amphioxus, tunicates and vertebrates. Comparisons of Hox gene clusters, other homeobox gene families, Wnt genes and insulin-related genes all indicate that there was a major phase of gene duplication close to vertebrate origins, after divergence from the amphioxus lineage; we suggest there was probably a second phase of duplication close to jawed vertebrate origins. From amphioxus and vertebrate homeobox gene expression patterns, we suggest that there are multiple routes by which new genes arising from gene duplication acquire new functions and permit the evolution of developmental innovations.

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Gene and Genome Duplication in Acanthamoeba polyphaga Mimivirus

Journal of Virology ◽

10.1128/jvi.79.22.14095-14101.2005 ◽

2005 ◽

Vol 79 (22) ◽

pp. 14095-14101 ◽

Cited By ~ 56

Author(s):

Karsten Suhre

Keyword(s):

Gene Duplication ◽

Model Comparison ◽

Genome Duplication ◽

Gene Families ◽

Detection Methods ◽

Acanthamoeba Polyphaga ◽

Homology Detection ◽

Dna Viruses ◽

Duplication Events ◽

Acanthamoeba Polyphaga Mimivirus

ABSTRACT Gene duplication is key to molecular evolution in all three domains of life and may be the first step in the emergence of new gene function. It is a well-recognized feature in large DNA viruses but has not been studied extensively in the largest known virus to date, the recently discovered Acanthamoeba polyphaga Mimivirus. Here, I present a systematic analysis of gene and genome duplication events in the mimivirus genome. I found that one-third of the mimivirus genes are related to at least one other gene in the mimivirus genome, either through a large segmental genome duplication event that occurred in the more remote past or through more recent gene duplication events, which often occur in tandem. This shows that gene and genome duplication played a major role in shaping the mimivirus genome. Using multiple alignments, together with remote-homology detection methods based on Hidden Markov Model comparison, I assign putative functions to some of the paralogous gene families. I suggest that a large part of the duplicated mimivirus gene families are likely to interfere with important host cell processes, such as transcription control, protein degradation, and cell regulatory processes. My findings support the view that large DNA viruses are complex evolving organisms, possibly deeply rooted within the tree of life, and oppose the paradigm that viral evolution is dominated by lateral gene acquisition, at least in regard to large DNA viruses.

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Promoter architecture links gene duplication with transcriptional divergence

10.1101/2021.07.03.450995 ◽

2021 ◽

Author(s):

Tzachi Hagai ◽

Evgeny Fraimovitch

Keyword(s):

Gene Duplication ◽

Regulatory Element ◽

Cpg Islands ◽

Gene Families ◽

Gene Expansion ◽

Promoter Architecture ◽

Duplication Events ◽

Long Term Retention

Gene duplication is thought to be a central mechanism in evolution to gain new functions, but gene families vary greatly in their rates of gene duplication and long-term retention. Here, we discover a link between the promoter architecture of vertebrate genes and their rate of duplication: Genes that harbor CpG Islands in their promoters (CGI genes) - nearly 60% of our genes - have rarely duplicated in recent evolutionary times, and most CGI gene duplication events predate the emergence of CGI as a major regulatory element of vertebrate genes. In contrast, CGI-less genes predominate duplications that have occurred since the divergence of vertebrates. Furthermore, CGI-less paralogs are transcriptionally more divergent than CGI paralogs, even when comparing CGI and CGI-less paralogs that have duplicated at similar evolutionary times - suggesting greater capacity of CGI-less promoters to enable divergence in expression. This higher divergence between CGI-less paralogs is also reflected in lower similarity of transcription factors that bind to the promoters of CGI-less paralog pairs in comparison with CGI paralogs. Finally, CGI-less paralogs have a greater tendency to sub- and neo-functionalize, and they transcriptionally diversify faster following duplication. Our results highlight the links between promoter architecture, gene expression plasticity and their impact on gene expansion, and unravel an unappreciated role of CGI elements in shaping genome evolution.

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(TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length

BMC Genomics ◽

10.1186/1471-2164-6-83 ◽

2005 ◽

Vol 6 (1) ◽

Cited By ~ 13

Author(s):

Vineet K Sharma ◽

Samir K Brahmachari ◽

Srinivasan Ramachandran

Keyword(s):

Human Gene ◽

Gene Families ◽

Gene Length ◽

Patterns Of Distribution

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Fructosyltransferase and invertase genes evolved by gene duplication and rearrangements: rice, perennial ryegrass, and wheat gene families

Genome ◽

10.1139/g06-066 ◽

2006 ◽

Vol 49 (9) ◽

pp. 1081-1091 ◽

Cited By ~ 14

Author(s):

Michael G. Francki ◽

Esther Walker ◽

John W. Forster ◽

German Spangenberg ◽

Rudi Appels

Keyword(s):

Perennial Ryegrass ◽

Abiotic Stress Tolerance ◽

Gene Families ◽

Amino Acid Similarity ◽

Gene Variation ◽

Wheat Gene ◽

Multiple Copies ◽

Duplication Events ◽

Invertase Gene ◽

Gene Orthologs

The invertase enzyme family is responsible for carbohydrate metabolism in rice, perennial ryegrass, and wheat. Fructan molecules accumulate in cell vacuoles of perennial ryegrass and wheat and are associated with abiotic stress tolerance. High levels of amino acid similarity between the fructosyltransferases responsible for fructan accumulation indicates that they may have evolved from invertase-like ancestral genes. In this study, we have applied comparative genomics to determine the mechanisms that lead to the evolution of fructosytransferase and invertase genes in rice, perennial ryegrass, and wheat. Duplications and rearrangements have been inferred to generate variant forms of the rice invertases since divergence from a common grass progenitor. The occurrence of multiple copies of fructosyltransferase genes indicated that duplication events continued during evolution of the wheat and perennial ryegrass lineages. Further gene rearrangements were evident in perennial ryegrass genes, albeit at a reduced level compared with the rice invertases. Gene orthologs were largely static after duplication during evolution of the wheat lineage. This study details evolutionary events that contribute to fructosyltransferase and invertase gene variation in grasses.

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Promoter-mediated diversification of transcriptional bursting dynamics following gene duplication

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1800943115 ◽

2018 ◽

Vol 115 (33) ◽

pp. 8364-8369 ◽

Cited By ~ 17

Author(s):

Edward Tunnacliffe ◽

Adam M. Corrigan ◽

Jonathan R. Chubb

Keyword(s):

Gene Duplication ◽

Expression Profiles ◽

Single Cells ◽

Family Members ◽

Gene Families ◽

Developmental Expression ◽

Upstream Sequence ◽

Genomic Context ◽

Entire Family ◽

Transcriptional Bursting

During the evolution of gene families, functional diversification of proteins often follows gene duplication. However, many gene families expand while preserving protein sequence. Why do cells maintain multiple copies of the same gene? Here we have addressed this question for an actin family with 17 genes encoding an identical protein. The genes have divergent flanking regions and are scattered throughout the genome. Surprisingly, almost the entire family showed similar developmental expression profiles, with their expression also strongly coupled in single cells. Using live cell imaging, we show that differences in gene expression were apparent over shorter timescales, with family members displaying different transcriptional bursting dynamics. Strong “bursty” behaviors contrasted steady, more continuous activity, indicating different regulatory inputs to individual actin genes. To determine the sources of these different dynamic behaviors, we reciprocally exchanged the upstream regulatory regions of gene family members. This revealed that dynamic transcriptional behavior is directly instructed by upstream sequence, rather than features specific to genomic context. A residual minor contribution of genomic context modulates the gene OFF rate. Our data suggest promoter diversification following gene duplication could expand the range of stimuli that regulate the expression of essential genes. These observations contextualize the significance of transcriptional bursting.

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

Physiological Reviews ◽

10.1152/physrev.00040.2011 ◽

2012 ◽

Vol 92 (4) ◽

pp. 1543-1576 ◽

Cited By ~ 100

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.

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Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes

Genome Research ◽

10.1101/gr.160001 ◽

2001 ◽

Vol 11 (5) ◽

pp. 771-780 ◽

Cited By ~ 2

Author(s):

Austin L. Hughes ◽

Jack da Silva ◽

Robert Friedman

Keyword(s):

Phylogenetic Analysis ◽

Gene Duplication ◽

Genome Duplication ◽

Gene Families ◽

Gene Duplications ◽

Human Chromosomes ◽

Time Period ◽

Genome Duplications

The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the fourHox-bearing chromosomes (the chromosomes bearing theHox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the humanHox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hoxclusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.

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