The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
John H Postlethwait - One of the best experts on this subject based on the ideXlab platform.
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evolutionary divergence of the vertebrate tnfaip8 gene family applying the spotted gar orthology bridge to understand ohnolog loss in Teleosts
PLOS ONE, 2017Co-Authors: Con Sullivan, Christopher R Lage, Jeffrey A Yoder, John H PostlethwaitAbstract:: Comparative functional genomic studies require the proper identification of gene orthologs to properly exploit animal biomedical research models. To identify gene orthologs, comprehensive, conserved gene synteny analyses are necessary to unwind gene histories that are convoluted by two rounds of early vertebrate genome duplication, and in the case of the Teleosts, a third round, the Teleost genome duplication (TGD). Recently, the genome of the spotted gar, a holostean outgroup to the Teleosts that did not undergo this third genome duplication, was sequenced and applied as an orthology bridge to facilitate the identification of Teleost orthologs to human genes and to enhance the power of Teleosts as biomedical models. In this study, we apply the spotted gar orthology bridge to help describe the gene history of the vertebrate TNFAIP8 family. Members of the TNFAIP8 gene family have been linked to regulation of immune function and homeostasis and the development of multiple cancer types. Through a conserved gene synteny analysis, we identified zebrafish orthologs to human TNFAIP8L1 and TNFAIP8L3 genes and two co-orthologs to human TNFAIP8L2, but failed to identify an ortholog to human TNFAIP8. Through the application of the orthology bridge, we determined that Teleost orthologs to human TNFAIP8 genes were likely lost in a genome inversion event after their divergence from their common ancestor with spotted gar. These findings demonstrate the value of this enhanced approach to gene history analysis and support the development of Teleost models to study complex questions related to an array of biomedical issues, including immunity and cancer.
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bac recombineering of the agouti loci from spotted gar and zebrafish reveals the evolutionary ancestry of dorsal ventral pigment asymmetry in fish
Journal of Experimental Zoology, 2017Co-Authors: Manuel Megias, John H Postlethwait, Ingo Braasch, Jose Miguel Cerdareverter, Josep RotllantAbstract:Dorsoventral pigment patterning, characterized by a light ventrum and a dark dorsum, is one of the most widespread chromatic adaptations in vertebrate body coloration. In mammals, this countershading depends on differential expression of agouti-signaling protein (ASIP), which drives a switch of synthesis of one type of melanin to another within melanocytes. Teleost fish share countershading, but the pattern results from a differential distribution of multiple types of chromatophores, with black–brown melanophores most abundant in the dorsal body and reflective iridophores most abundant in the ventral body. We previously showed that Asip1 (a fish ortholog of mammalian ASIP) plays a role in patterning melanophores. This observation leads to the surprising hypothesis that agouti may control an evolutionarily conserved pigment pattern by regulating different mechanisms in mammals and fish. To test this hypothesis, we compared two ray-finned fishes: the Teleost zebrafish and the nonTeleost spotted gar (Lepisosteus oculatus). By examining the endogenous pattern of asip1 expression in gar, we demonstrate a dorsoventral-graded distribution of asip1 expression that is highest ventrally, similar to Teleosts. Additionally, in the first reported experiments to generate zebrafish transgenic lines carrying a bacterial artificial chromosome (BAC) from spotted gar, we show that both transgenic zebrafish lines embryos replicate the endogenous asip1 expression pattern in adult zebrafish, showing that BAC transgenes from both species contain all of the regulatory elements required for regular asip1 expression within adult ray-finned fishes. These experiments provide evidence that the mechanism leading to an environmentally important pigment pattern was likely in place before the origin of Teleosts.
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a rad tag genetic map for the platyfish xiphophorus maculatus reveals mechanisms of karyotype evolution among Teleost fish
Genetics, 2014Co-Authors: Angel Amores, Julian M Catchen, Indrajit Nanda, Wesley C Warren, Ronald B Walter, Manfred Schartl, John H PostlethwaitAbstract:Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, Teleost fish genomes are stable (24-25 in 58% of Teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform Teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of Teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the Teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in Teleost chromosomes over hundreds of millions of years.
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Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal Teleosts, and tetrapods.
Comparative Biochemistry and Physiology - Part C: Toxicology and Pharmacology, 2014Co-Authors: Ingo Braasch, Yann Guiguen, Ryan Loker, John H Letaw, Allyse Ferrara, Julien Bobe, John H PostlethwaitAbstract:Teleost fish are important models for human biology, health, and disease. Because genome duplication in a Teleost ancestor (TGD) impacts the evolution of Teleost genome structure and gene repertoires, we must discriminate gene functions that are shared and ancestral from those that are lineage-specific in Teleosts or tetrapods to accurately apply inferences from Teleost disease models to human health. Generalizations must account both for the TGD and for divergent evolution between Teleosts and tetrapods after the likely two rounds of genome duplication shared by all vertebrates. Progress in sequencing techniques provides new opportunities to generate genomic and transcriptomic information from a broad range of phylogenetically informative taxa that facilitate detailed understanding of gene family and gene function evolution. We illustrate here the use of new sequence resources from spotted gar (Lepisosteus oculatus), a rayfin fish that diverged from Teleosts before the TGD, as well as RNA-Seq data from gar and multiple Teleost lineages to reconstruct the evolution of the Paired-related homeobox (Prrx) transcription factor gene family, which is involved in the development of mesoderm and neural crest-derived mesenchyme. We show that for Prrx genes, the spotted gar genome and gene expression patterns mimic mammals better than Teleosts do. Analyses force the seemingly paradoxical conclusion that regulatory mechanisms for the limb expression domains of Prrx genes existed before the evolution of paired appendages. Detailed evolutionary analyses like those reported here are required to identify fish species most similar to the human genome to optimally connect fish models to human gene functions in health and disease.
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polyploidy in fish and the Teleost genome duplication
2012Co-Authors: Ingo Braasch, John H PostlethwaitAbstract:Multiple rounds of whole-genome duplications (WGDs) punctuated the evolution of rayfin fish, a species-rich group comprising about half of all vertebrates. Rayfin fish, along with lobefin vertebrates including humans, derive from early vertebrate ancestors that evolved through two rounds of polyploidization (the first and second rounds of vertebrate genome duplication, VGD1 and VGD2) at the dawn of the vertebrate lineage. Furthermore, Teleost fish underwent an additional round of polyploidization in their stem lineage, the Teleost genome duplication (TGD). Additional WGD events occurred independently in numerous species and higher level taxa of Teleosts and other rayfin fish, for example in salmonids, carp, and sturgeon, so that some fish lineages experienced at least four rounds of WGD since the origin of vertebrates. This chapter provides an overview of these polyploidization events in the fish lineage and focuses on the impact these genome duplications (GD) had on genome evolution in selected fish taxa. We then review evidence for the TGD and discuss its consequences for the evolution of gene content, order, and functions in the Teleost lineage. We argue that, although evidence remains sparse, the TGD may have had a profound influence on the evolutionary success and the biodiversity of Teleosts. Importantly, an in-depth understanding of the causes and consequences of the TGD and other Teleost GD events will help to inform us about the evolution of our own paleopolyploid genome.
Ingo Braasch - One of the best experts on this subject based on the ideXlab platform.
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evolution of gene expression after whole genome duplication new insights from the spotted gar genome
Journal of Experimental Zoology, 2017Co-Authors: Jérémy Pasquier, Ingo Braasch, Peter Batzel, Cedric Cabau, Thaovi Nguyen, Elodie Jouanno, Christophe Klopp, Jerome Montfort, Camille Berthelot, Laurent JournotAbstract:Whole-genome duplications (WGDs) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however, remains incomplete. Teleost fish experienced a common WGD (Teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest-related lineage of Teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and Teleostean fish species, including spotted gar, zebrafish, and medaka (the PhyloFish project), offers a unique opportunity to study the evolution of gene expression following TGD in Teleosts. We show that most TGD duplicates gained their current status (loss of one duplicate gene or retention of both duplicates) relatively rapidly after TGD (i.e., prior to the divergence of medaka and zebrafish lineages). The loss of one duplicate is the most common fate after TGD with a probability of approximately 80%. In addition, the fate of duplicate genes after TGD, including subfunctionalization, neofunctionalization, or retention of two "similar" copies occurred not only before but also after the divergence of species tested, in consistency with a role of the TGD in speciation and/or evolution of gene function. Finally, we report novel cases of TGD ohnolog subfunctionalization and neofunctionalization that further illustrate the importance of these processes.
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bac recombineering of the agouti loci from spotted gar and zebrafish reveals the evolutionary ancestry of dorsal ventral pigment asymmetry in fish
Journal of Experimental Zoology, 2017Co-Authors: Manuel Megias, John H Postlethwait, Ingo Braasch, Jose Miguel Cerdareverter, Josep RotllantAbstract:Dorsoventral pigment patterning, characterized by a light ventrum and a dark dorsum, is one of the most widespread chromatic adaptations in vertebrate body coloration. In mammals, this countershading depends on differential expression of agouti-signaling protein (ASIP), which drives a switch of synthesis of one type of melanin to another within melanocytes. Teleost fish share countershading, but the pattern results from a differential distribution of multiple types of chromatophores, with black–brown melanophores most abundant in the dorsal body and reflective iridophores most abundant in the ventral body. We previously showed that Asip1 (a fish ortholog of mammalian ASIP) plays a role in patterning melanophores. This observation leads to the surprising hypothesis that agouti may control an evolutionarily conserved pigment pattern by regulating different mechanisms in mammals and fish. To test this hypothesis, we compared two ray-finned fishes: the Teleost zebrafish and the nonTeleost spotted gar (Lepisosteus oculatus). By examining the endogenous pattern of asip1 expression in gar, we demonstrate a dorsoventral-graded distribution of asip1 expression that is highest ventrally, similar to Teleosts. Additionally, in the first reported experiments to generate zebrafish transgenic lines carrying a bacterial artificial chromosome (BAC) from spotted gar, we show that both transgenic zebrafish lines embryos replicate the endogenous asip1 expression pattern in adult zebrafish, showing that BAC transgenes from both species contain all of the regulatory elements required for regular asip1 expression within adult ray-finned fishes. These experiments provide evidence that the mechanism leading to an environmentally important pigment pattern was likely in place before the origin of Teleosts.
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Evolution of gene expression after whole-genome duplication: new insights from the spotted gar genome
2017Co-Authors: Jérémy Pasquier, Ingo Braasch, Peter Batzel, Cedric Cabau, Elodie Jouanno, Christophe Klopp, Jerome Montfort, Camille Berthelot, Thuy Thao Vi Nguyen, Laurent JournotAbstract:Whole genome duplications (WGD) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however remains incomplete. Teleost fish experienced a common WGD (Teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest lineage of Teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and Teleostean fish species, including spotted gar, zebrafish and medaka (the PhyloFish project), offered a unique opportunity to study the evolution of gene expression following TGD in Teleosts. We show that most TGD duplicates gained their current status (loss of one duplicate gene or retention of both duplicates) relatively rapidly after TGD (i.e. prior to the divergence of medaka and zebrafish lineages). The loss of one duplicate is the most common fate after TGD with a probability of approximately 80%. In addition, the fate of duplicate genes after TGD, including subfunctionalization, neofunctionalization, or retention of two ‘similar’ copies occurred not only before, but also after the radiation of species tested, in consistency with a role of the TGD in speciation and/or evolution of gene function. Finally, we report novel cases of TGD ohnolog subfunctionalization and neofunctionalization that further illustrate the importance of these processes.
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gene evolution and gene expression after whole genome duplication in fish the phylofish database
BMC Genomics, 2016Co-Authors: Jérémy Pasquier, Ingo Braasch, Cedric Cabau, Thaovi Nguyen, Elodie Jouanno, Dany Severac, Laurent Journot, Pierre Pontarotti, Christophe KloppAbstract:With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a Teleost-specific WGD event (TGD) that occurred at the root of the Teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of Teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from Teleosts before TGD) and 21 Teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.
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The spotted gar genome illuminates vertebrate evolution and facilitates human-Teleost comparisons
Nature Genetics, 2016Co-Authors: Ingo Braasch, Angel Amores, Andrew R. Gehrke, Jeramiah J. Smith, Kazuhiko Kawasaki, Tereza Manousaki, Jérémy Pasquier, Thomas Desvignes, Peter Batzel, Julian CatchenAbstract:To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from Teleosts before Teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges Teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-Teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated Teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
Angel Amores - One of the best experts on this subject based on the ideXlab platform.
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The spotted gar genome illuminates vertebrate evolution and facilitates human-Teleost comparisons
Nature Genetics, 2016Co-Authors: Ingo Braasch, Angel Amores, Andrew R. Gehrke, Jeramiah J. Smith, Kazuhiko Kawasaki, Tereza Manousaki, Jérémy Pasquier, Thomas Desvignes, Peter Batzel, Julian CatchenAbstract:To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from Teleosts before Teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges Teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-Teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated Teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
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a rad tag genetic map for the platyfish xiphophorus maculatus reveals mechanisms of karyotype evolution among Teleost fish
Genetics, 2014Co-Authors: Angel Amores, Julian M Catchen, Indrajit Nanda, Wesley C Warren, Ronald B Walter, Manfred Schartl, John H PostlethwaitAbstract:Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, Teleost fish genomes are stable (24-25 in 58% of Teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform Teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of Teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the Teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in Teleost chromosomes over hundreds of millions of years.
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genome evolution and meiotic maps by massively parallel dna sequencing spotted gar an outgroup for the Teleost genome duplication
Genetics, 2011Co-Authors: Angel Amores, Allyse Ferrara, Julian M Catchen, Quenton Fontenot, John H PostlethwaitAbstract:Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the Teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F1 offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from Teleosts before the TGD and its genome is organized more similarly to that of humans than Teleosts. Thus, spotted gar provides a critical link between medical models in Teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F1 dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing.
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Zebrafish hox Clusters and Vertebrate Genome Evolution
Science (New York N.Y.), 1998Co-Authors: Angel Amores, Allan Force, Chris T Amemiya, Yi-lin Yan, Lucille Joly, Andreas Fritz, James A. Langeland, Victoria E. Prince, Yanling WangAbstract:HOX genes specify cell fate in the anterior-posterior axis of animal embryos. Invertebrate chordates have one HOX cluster, but mammals have four, suggesting that cluster duplication facilitated the evolution of vertebrate body plans. This report shows that zebrafish have seven hox clusters. Phylogenetic analysis and genetic mapping suggest a chromosome doubling event, probably by whole genome duplication, after the divergence of ray-finned and lobe-finned fishes but before the Teleost radiation. Thus, Teleosts, the most species-rich group of vertebrates, appear to have more copies of these developmental regulatory genes than do mammals, despite less complexity in the anterior-posterior axis.
Jérémy Pasquier - One of the best experts on this subject based on the ideXlab platform.
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evolution of gene expression after whole genome duplication new insights from the spotted gar genome
Journal of Experimental Zoology, 2017Co-Authors: Jérémy Pasquier, Ingo Braasch, Peter Batzel, Cedric Cabau, Thaovi Nguyen, Elodie Jouanno, Christophe Klopp, Jerome Montfort, Camille Berthelot, Laurent JournotAbstract:Whole-genome duplications (WGDs) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however, remains incomplete. Teleost fish experienced a common WGD (Teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest-related lineage of Teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and Teleostean fish species, including spotted gar, zebrafish, and medaka (the PhyloFish project), offers a unique opportunity to study the evolution of gene expression following TGD in Teleosts. We show that most TGD duplicates gained their current status (loss of one duplicate gene or retention of both duplicates) relatively rapidly after TGD (i.e., prior to the divergence of medaka and zebrafish lineages). The loss of one duplicate is the most common fate after TGD with a probability of approximately 80%. In addition, the fate of duplicate genes after TGD, including subfunctionalization, neofunctionalization, or retention of two "similar" copies occurred not only before but also after the divergence of species tested, in consistency with a role of the TGD in speciation and/or evolution of gene function. Finally, we report novel cases of TGD ohnolog subfunctionalization and neofunctionalization that further illustrate the importance of these processes.
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Evolution of gene expression after whole-genome duplication: new insights from the spotted gar genome
2017Co-Authors: Jérémy Pasquier, Ingo Braasch, Peter Batzel, Cedric Cabau, Elodie Jouanno, Christophe Klopp, Jerome Montfort, Camille Berthelot, Thuy Thao Vi Nguyen, Laurent JournotAbstract:Whole genome duplications (WGD) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however remains incomplete. Teleost fish experienced a common WGD (Teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest lineage of Teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and Teleostean fish species, including spotted gar, zebrafish and medaka (the PhyloFish project), offered a unique opportunity to study the evolution of gene expression following TGD in Teleosts. We show that most TGD duplicates gained their current status (loss of one duplicate gene or retention of both duplicates) relatively rapidly after TGD (i.e. prior to the divergence of medaka and zebrafish lineages). The loss of one duplicate is the most common fate after TGD with a probability of approximately 80%. In addition, the fate of duplicate genes after TGD, including subfunctionalization, neofunctionalization, or retention of two ‘similar’ copies occurred not only before, but also after the radiation of species tested, in consistency with a role of the TGD in speciation and/or evolution of gene function. Finally, we report novel cases of TGD ohnolog subfunctionalization and neofunctionalization that further illustrate the importance of these processes.
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gene evolution and gene expression after whole genome duplication in fish the phylofish database
BMC Genomics, 2016Co-Authors: Jérémy Pasquier, Ingo Braasch, Cedric Cabau, Thaovi Nguyen, Elodie Jouanno, Dany Severac, Laurent Journot, Pierre Pontarotti, Christophe KloppAbstract:With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a Teleost-specific WGD event (TGD) that occurred at the root of the Teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of Teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from Teleosts before TGD) and 21 Teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.
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The spotted gar genome illuminates vertebrate evolution and facilitates human-Teleost comparisons
Nature Genetics, 2016Co-Authors: Ingo Braasch, Angel Amores, Andrew R. Gehrke, Jeramiah J. Smith, Kazuhiko Kawasaki, Tereza Manousaki, Jérémy Pasquier, Thomas Desvignes, Peter Batzel, Julian CatchenAbstract:To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from Teleosts before Teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges Teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-Teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated Teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
James B Claiborne - One of the best experts on this subject based on the ideXlab platform.
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immunological detection of na h exchangers in the gills of a hagfish myxine glutinosa an elasmobranch raja erinacea and a Teleost fundulus heteroclitus
Comparative Biochemistry and Physiology A-molecular & Integrative Physiology, 2002Co-Authors: Keith P Choe, Alison I Morrisonshetlar, Brian P Wall, James B ClaiborneAbstract:Abstract Na+/H+ exchangers (NHE) are a family of ion exchangers with diverse functions that are well defined in mammals. NHE-1 is expressed in the plasma membrane of most mammalian cells where it regulates intracellular pH, and usually in the basolateral membrane of epithelial cells. It has also been detected in Teleost gills where it may participate in systemic pH regulation. NHE-3 is usually expressed in the apical membrane of mammalian epithelial cells where it helps reabsorb Na+ and HCO3−; it has also been detected in Teleost gills. We used Western blotting and heterologous antibodies to screen for expression of NHE-1 and NHE-3 in gills of an agnathan (Myxine glutinosa) and an elasmobranch (Raja erinacea), and NHE-3 in gills of a Teleost (Fundulus heteroclitus). Positive NHE-1 bands were detected in gills from the agnathan and elasmobranch. Using the NHE-3 antibody, bands were detected in the gills of the elasmobranch and Teleost. These data are some of the first direct evidence of NHEs in the gills of an agnathan and elasmobranch, and confirm the presence of NHEs in the gills of Teleosts.
