scholarly journals Ankfn1 vestibular defects in zebrafish require mutations in both ancestral and derived paralogs.

2021 ◽  
Author(s):  
Kevin D. Ross ◽  
Jie Ren ◽  
Ruilin Zhang ◽  
Neil C. Chi ◽  
Bruce A. Hamilton
Keyword(s):  
Single Copy ◽  
Comparative Genetics ◽  
Mouse Homolog ◽  
Animal Evolution ◽  
Sensorimotor Deficits ◽  
Drosophila Homolog ◽  
Duplication Events ◽  
Swim Bladder Inflation ◽  
Partial Redundancy ◽  
Early Lethality

How and to what degree gene duplication events create regulatory innovation, redundancy, or neofunctionalization remain important questions in animal evolution and comparative genetics. Ankfn1 genes are single copy in most invertebrates, partially duplicated in jawed vertebrates, and only the derived copy retained in most mammals. Null mutations in the single mouse homolog have vestibular and neurological abnormalities. Null mutation of the single Drosophila homolog is typically lethal with severe sensorimotor deficits in rare survivors. The functions and potential redundancy of paralogs in species with two copies is not known. Here we define a vestibular role for Ankfn1 homologs in zebrafish based on simultaneous disruption of each locus. Zebrafish with both paralogs disrupted showed vestibular defects and early lethality from swim bladder inflation failure. One intact copy at either locus was sufficient to prevent major phenotypes. Our results show that vertebrate Ankfn1 genes are required for vestibular-related functions, with at least partial redundancy between ancestral and derived paralogs.

scholarly journals Ankfn1-mutant vestibular defects require loss of both ancestral and derived paralogs for penetrance in zebrafish

2021 ◽  
Author(s):  
Kevin D Ross ◽  
Jie Ren ◽  
Ruilin Zhang ◽  
Neil C Chi ◽  
Bruce A Hamilton
Keyword(s):  
Single Copy ◽  
Comparative Genetics ◽  
Mouse Homolog ◽  
Animal Evolution ◽  
Sensorimotor Deficits ◽  
Drosophila Homolog ◽  
Duplication Events ◽  
Swim Bladder Inflation ◽  
Partial Redundancy ◽  
Early Lethality

Abstract How and to what degree gene duplication events create regulatory innovation, redundancy, or neofunctionalization remain important questions in animal evolution and comparative genetics. Ankfn1 genes are single copy in most invertebrates, partially duplicated in jawed vertebrates, and only the derived copy retained in most mammals. Null mutations in the single mouse homolog have vestibular and neurological abnormalities. Null mutation of the single Drosophila homolog is typically lethal with severe sensorimotor deficits in rare survivors. The functions and potential redundancy of paralogs in species with two copies is not known. Here we define a vestibular role for Ankfn1 homologs in zebrafish based on simultaneous disruption of each locus. Zebrafish with both paralogs disrupted showed vestibular defects and early lethality from swim bladder inflation failure. One intact copy at either locus was sufficient to prevent major phenotypes. Our results show that vertebrate Ankfn1 genes are required for vestibular-related functions, with at least partial redundancy between ancestral and derived paralogs.

Evolution of the vertebrate globin gene family

Hemoglobin ◽  
2018 ◽  
pp. 94-123
Author(s):  
Jay F. Storz
Keyword(s):  
Whole Genome Duplication ◽  
Evolutionary History ◽  
Functional Divergence ◽  
Globin Gene ◽  
Globin Genes ◽  
Tandem Gene Duplication ◽  
Animal Evolution ◽  
Phylogenetic Reconstructions ◽  
Duplication Events ◽  
History Of

Chapter 5 provides an overview of the evolutionary history of the globin gene superfamily and places the evolution of vertebrate-specific globins in phylogenetic context. The duplication and functional divergence of globin genes has promoted key physiological innovations in respiratory gas transport and other physiological functions during animal evolution. A combination of both tandem gene duplication and whole-genome duplication contributed to the diversification of vertebrate globins. Phylogenetic reconstructions arrange vertebrate globins into those that derive from vertebrate-specific duplications (cytoglobin, globin E, globin Y, and the independently derived myoglobin-like and hemoglobin-like genes of jawed vertebrates and jawless fishes [lampreys and hagfish]) and those that derive from far more ancient duplication events that predate the divergence between deuterostomes and protostomes (androglobin, globin X, and neuroglobin). Tracing the evolutionary history of deuterostome globins reveals evidence for the repeated culling of ancestral diversity, followed by lineage-specific diversification of surviving gene lineages via repeated rounds of duplication and divergence.

scholarly journals Concurrent duplication of the Cid and Cenp-C genes in the Drosophila subgenus with signatures of subfunctionalization and male germline-biased expression

2017 ◽  
Author(s):  
José R. Teixeira ◽  
Guilherme B. Dias ◽  
Marta Svartman ◽  
Alfredo Ruiz ◽  
Gustavo C. S. Kuhn
Keyword(s):  
Chromosome Segregation ◽  
Functional Unit ◽  
Single Copy ◽  
Cellular Functions ◽  
Specific Context ◽  
Male Germline ◽  
Duplication Events ◽  
Independent Duplication ◽  
And Function ◽  
Species Being

AbstractDespite their essential role in the process of chromosome segregation in eukaryotes, kinetochore proteins are highly diverse across species, being lost, duplicated, created, or diversified during evolution. Based on comparative genomics, the duplication of the inner kinetochore proteins CenH3 and Cenp-C, which are interdependent in their roles of stablishing centromere identity and function, can be said to be rare in animals. Surprisingly, the Drosophila CenH3 homolog Cid underwent four independent duplication events during evolution. Particularly interesting are the highly diverged and subfunctionalized Cid1 and Cid5 paralogs of the Drosophila subgenus, which show that over one thousand Drosophila species may encode two Cid genes, making those with a single copy a minority. Given that CenH3 and Cenp-C likely co-evolve as a functional unit, we investigated the molecular evolution of Cenp-C in species of Drosophila. We report yet another Cid duplication within the Drosophila subgenus and show that not only Cid, but also Cenp-C is duplicated in the entire subgenus. The Cenp-C paralogs, which we named Cenp-C1 and Cenp-C2, are highly divergent. The retention of key motifs involved in centromere localization and function by both Cenp-C1 and Cenp-C2 makes neofunctionalization unlikely. In contrast, the alternate conservation of some functional motifs between the proteins is indicative of subfunctionalization. Interestingly, both Cid5 and Cenp-C2 are male germline-biased and evolved adaptively. Our findings point towards a specific inner kinetochore composition in a specific context (i.e., spermatogenesis), which could prove valuable for the understanding of how the extensive kinetochore diversity is related to essential cellular functions.

scholarly journals The eukaryotic MEP-pathway genes are evolutionarily conserved and originated from Chlaymidia and cyanobacteria

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Liping Zeng ◽  
Katayoon Dehesh
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Mep Pathway ◽  
Syntenic Block ◽  
Bioinformatics Analyses ◽  
Expression Levels ◽  
Methylerythritol Phosphate ◽  
Duplication Events ◽  
History Of ◽  
The Individual

Abstract Background Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes. Results Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development. Conclusion Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.

scholarly journals Two ancient genome duplication events shape diversity in Hibiscus L. (Malvaceae)

2020 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Genome Doubling ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested a series of scenarios describing different polyploidization events.Results: Using target sequence capture, we generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. Species of Hibiscus shared one genome duplication with H. syriacus and one whole genome duplication occurred along the branch leading to H. syriacus.Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

2021 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Target Sequence ◽  
Whole Genome ◽  
Genome Doubling ◽  
Sequence Capture ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals The MEP-pathway genes are polyphyletic origin and evolutionary conserved

2020 ◽  
Author(s):  
Liping Zeng ◽  
Katayoon Dehesh
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Mep Pathway ◽  
Syntenic Block ◽  
Bioinformatics Analyses ◽  
Expression Levels ◽  
Duplication Events ◽  
History Of ◽  
The Individual ◽  
Comprehensive Study

Abstract BackgroundIsoprenoids are amongst the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol dicyclophosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.ResultsHere, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development. ConclusionCollectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.

scholarly journals A chelicerate Wnt gene expression atlas: novel insights into the complexity of arthropod Wnt-patterning

EvoDevo ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ralf Janssen ◽  
Matthias Pechmann ◽  
Natascha Turetzek
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Large Family ◽  
Animal Evolution ◽  
Gene Expression Atlas ◽  
Outgroup Species ◽  
Expression Atlas ◽  
Duplication Events ◽  
Complete Set ◽  
High Degree

AbstractThe Wnt genes represent a large family of secreted glycoprotein ligands that date back to early animal evolution. Multiple duplication events generated a set of 13 Wnt families of which 12 are preserved in protostomes. Embryonic Wnt expression patterns (Wnt-patterning) are complex, representing the plentitude of functions these genes play during development. Here, we comprehensively investigated the embryonic expression patterns of Wnt genes from three species of spiders covering both main groups of true spiders, Haplogynae and Entelegynae, a mygalomorph species (tarantula), as well as a distantly related chelicerate outgroup species, the harvestman Phalangium opilio. All spiders possess the same ten classes of Wnt genes, but retained partially different sets of duplicated Wnt genes after whole genome duplication, some of which representing impressive examples of sub- and neo-functionalization. The harvestman, however, possesses a more complete set of 11 Wnt genes but with no duplicates. Our comprehensive data-analysis suggests a high degree of complexity and evolutionary flexibility of Wnt-patterning likely providing a firm network of mutational protection. We discuss the new data on Wnt gene expression in terms of their potential function in segmentation, posterior elongation, and appendage development and critically review previous research on these topics. We conclude that earlier research may have suffered from the absence of comprehensive gene expression data leading to partial misconceptions about the roles of Wnt genes in development and evolution.

scholarly journals Essential Requirement of CCAAT/Enhancer Binding Proteins in Embryogenesis

2004 ◽  
Vol 24 (22) ◽  
pp. 9744-9751 ◽  
Author(s):  
Valérie Bégay ◽  
Jeske Smink ◽  
Achim Leutz
Keyword(s):  
Transcription Factors ◽  
Binding Proteins ◽  
Single Copy ◽  
Gene Replacement ◽  
Essential Requirement ◽  
Enhancer Binding Proteins ◽  
Complete Development ◽  
Chorionic Plate ◽  
Partial Redundancy

ABSTRACT The CCAAT/enhancer binding proteins C/EBPα and C/EBPβ are related transcription factors that are important for the function of various organs in the postnatal mouse. Gene replacement and tissue culture experiments have suggested partial redundancy of both transcription factors. Here we show that mouse embryos deficient of both C/EBPα and C/EBPβ (C/EBPαβ−/−) die between embryonic day 10 (E10) and E11 and display defective placentas. In situ hybridization revealed that C/EBPα and C/EBPβ are coexpressed in the chorionic plate at E9.5 and later in the trophoblasts of the labyrinthine layer. In C/EBPαβ−/− placentas, allantoic blood vessels invaded the chorion; however, vessel expansion and development of the labyrinthine layer was impaired. Furthermore, a single copy of either C/EBPα in the absence of C/EBPβ or C/EBPβ in the absence of C/EBPα is sufficient to complete development, suggesting complementation of these C/EBPs during embryogenesis. A single copy of C/EBPα in the absence of C/EBPβ, however, fails to rescue survival after birth, suggesting haploinsufficiency of C/EBPα in newborns. Our data thus reveal novel essential, redundant, and dosage dependent functions of C/EBPs.

scholarly journals Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases

2009 ◽  
Vol 83 (15) ◽  
pp. 7547-7559 ◽  
Author(s):  
Jörg Zielonka ◽  
Ignacio G. Bravo ◽  
Daniela Marino ◽  
Elea Conrad ◽  
Mario Perković ◽  
...  
Keyword(s):  
Equine Infectious Anemia Virus ◽  
Single Copy ◽  
Adeno Associated Virus ◽  
Cytidine Deaminases ◽  
Evolutionary Advantage ◽  
Duplication Events ◽  
Equine Infectious Anemia ◽  
Antiviral Activities ◽  
Natural Target ◽  
Anemia Virus

ABSTRACT The mammalian APOBEC3 (A3) proteins comprise a multigene family of cytidine deaminases that act as potent inhibitors of retroviruses and retrotransposons. The A3 locus on the chromosome 28 of the horse genome contains multiple A3 genes: two copies of A3Z1, five copies of A3Z2, and a single copy of A3Z3, indicating a complex evolution of multiple gene duplications. We have cloned and analyzed for expression the different equine A3 genes and examined as well the subcellular distribution of the corresponding proteins. Additionally, we have tested the functional antiretroviral activity of the equine and of several of the human and nonprimate A3 proteins against the Equine infectious anemia virus (EIAV), the Simian immunodeficiency virus (SIV), and the Adeno-associated virus type 2 (AAV-2). Hematopoietic cells of horses express at least five different A3s: A3Z1b, A3Z2a-Z2b, A3Z2c-Z2d, A3Z2e, and A3Z3, whereas circulating macrophages, the natural target of EIAV, express only part of the A3 repertoire. The five A3Z2 tandem copies arose after three consecutive, recent duplication events in the horse lineage, after the split between Equidae and Carnivora. The duplicated genes show different antiviral activities against different viruses: equine A3Z3 and A3Z2c-Z2d are potent inhibitors of EIAV while equine A3Z1b, A3Z2a-Z2b, A3Z2e showed only weak anti-EIAV activity. Equine A3Z1b and A3Z3 restricted AAV and all equine A3s, except A3Z1b, inhibited SIV. We hypothesize that the horse A3 genes are undergoing a process of subfunctionalization in their respective viral specificities, which might provide the evolutionary advantage for keeping five copies of the original gene.

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