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Linda Z. Holland - One of the best experts on this subject based on the ideXlab platform.
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Evolution of basal deuterostome nervous systems
Journal of Experimental Biology, 2015Co-Authors: Linda Z. HollandAbstract:Understanding the evolution of deuterostome nervous systems has been complicated by the ambiguous phylogenetic position of the Xenocoelomorpha (Xenoturbellids, acoel flat worms, nemertodermatids), which has been placed either as basal bilaterians, basal deuterostomes or as a sister group to the hemiChordate/echinoderm clade (Ambulacraria), which is a sister group of the Chordata. None of these groups has a single longitudinal nerve cord and a brain. A further complication is that echinoderm nerve cords are not likely to be evolutionarily related to the Chordate central nervous system. For hemiChordates, opinion is divided as to whether either one or none of the two nerve cords is homologous to the Chordate nerve cord. In Chordates, opposition by two secreted signaling proteins, bone morphogenetic protein (BMP) and Nodal, regulates partitioning of the ectoderm into central and peripheral nervous systems. Similarly, in echinoderm larvae, opposition between BMP and Nodal positions the ciliary band and regulates its extent. The apparent loss of this opposition in hemiChordates is, therefore, compatible with the scenario, suggested by Dawydoff over 65 years ago, that a true centralized nervous system was lost in hemiChordates.
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Evolution of basal deuterostome nervous systems.
The Journal of experimental biology, 2015Co-Authors: Linda Z. HollandAbstract:Understanding the evolution of deuterostome nervous systems has been complicated by the by the ambiguous phylogenetic position of the Xenocoelomorpha (Xenoturbellids, acoel flat worms, nemertodermatids), which has been placed either as basal bilaterians, basal deuterostomes or as a sister group to the hemiChordate/echinoderm clade (Ambulacraria), which is a sister group of the Chordata. None of these groups has a single longitudinal nerve cord and a brain. A further complication is that echinoderm nerve cords are not likely to be evolutionarily related to the Chordate central nervous system. For hemiChordates, opinion is divided as to whether either one or none of the two nerve cords is homologous to the Chordate nerve cord. In Chordates, opposition by two secreted signaling proteins, bone morphogenetic protein (BMP) and Nodal, regulates partitioning of the ectoderm into central and peripheral nervous systems. Similarly, in echinoderm larvae, opposition between BMP and Nodal positions the ciliary band and regulates its extent. The apparent loss of this opposition in hemiChordates is, therefore, compatible with the scenario, suggested by Dawydoff over 65 years ago, that a true centralized nervous system was lost in hemiChordates.
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roles of retinoic acid and tbx1 10 in pharyngeal segmentation amphioxus and the ancestral Chordate condition
Evodevo, 2014Co-Authors: Demian Koop, Linda Z. Holland, Jie Chen, Maria Theodosiou, Joao E Carvalho, Susana Alvarez, Angel R De Lera, Michael SchubertAbstract:Background: Although Chordates descend from a segmented ancestor, the evolution of head segmentation has been very controversial for over 150 years. Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate Chordates, such as the cephaloChordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the Chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest. Results: Focusing on the role of retinoic acid (RA) in post-gastrulation pharyngeal morphogenesis, we found that during gastrulation, RA signaling in the endoderm is required for defining pharyngeal and non-pharyngeal domains and that this process involves active degradation of RA anteriorly in the embryo. Subsequent extension of the pharyngeal territory depends on the creation of a low RA environment and is coupled to body elongation. RA further functions in pharyngeal segmentation in a regulatory network involving the mutual inhibition of RA- and Tbx1/10-dependent signaling. Conclusions: These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral Chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of Chordates.
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Roles of retinoic acid and Tbx1/10 in pharyngeal segmentation: amphioxus and the ancestral Chordate condition
EvoDevo, 2014Co-Authors: Demian Koop, Linda Z. Holland, Jie Chen, Maria Theodosiou, Joao E Carvalho, Susana Alvarez, Angel R De Lera, Michael SchubertAbstract:Background: Although Chordates descend from a segmented ancestor, the evolution of head segmentation has been very controversial for over 150 years. Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate Chordates, such as the cephaloChordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the Chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest. Results: Focusing on the role of retinoic acid (RA) in post-gastrulation pharyngeal morphogenesis, we found that during gastrulation, RA signaling in the endoderm is required for defining pharyngeal and non-pharyngeal domains and that this process involves active degradation of RA anteriorly in the embryo. Subsequent extension of the pharyngeal territory depends on the creation of a low RA environment and is coupled to body elongation. RA further functions in pharyngeal segmentation in a regulatory network involving the mutual inhibition of RA-and Tbx1/10-dependent signaling. Conclusions: These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral Chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of Chordates.
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a cdna resource for the cephaloChordate amphioxus branchiostoma floridae
Development Genes and Evolution, 2008Co-Authors: Jr-kai Yu, Linda Z. Holland, Yuji Kohara, Mingchih Wang, Tadasu Shini, Noriyuki Satoh, Yutaka SatouAbstract:CephaloChordates are the basal invertebrate Chordates within the phylum Chordata. They are widely used as a model system for research in evolutionary developmental biology (EvoDevo) to understand the basic patterning mechanisms for the Chordate body plan and the origin of vertebrates. Recently, the genome of the cephaloChordate Branchiostoma floridae was sequenced, which further brings this organism to the front for comparative genomic studies. In this paper, we report the generation of large-scale 5′- and 3′-expressed sequence tags (ESTs) from B. floridae and the complementary deoxyribonucleic acid (cDNA) resource for this species. Both 5′- and 3′-ESTs were sequenced for approximately 140,000 cDNA clones derived from five developmental stages, and the cDNA clones were subsequently grouped into independent clusters using 3′-EST sequences. We identified 21,229 cDNA clusters, and each corresponds to a unique transcript species from B. floridae. We then chose 24,020 cDNA clones representing all of these 21,229 clusters to generate the “Branchiostoma floridae Gene Collection Release 1.” We also constructed a database with a searchable interface for this EST dataset and the related information on “Branchiostoma floridae Gene Collection Release 1.” This set of cDNA clones along with our cDNA database will serve as an important resource for future research in this basal Chordate. This Gene Collection and the original 140,000 individual cDNA clones are available to the research community upon request.
Kevin J Peterson - One of the best experts on this subject based on the ideXlab platform.
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testing putative hemiChordate homologues of the Chordate dorsal nervous system and endostyle expression of nk2 1 ttf 1 in the acorn worm ptychodera flava hemichordata ptychoderidae
Evolution & Development, 2002Co-Authors: Carter M Takacs, Kevin J PetersonAbstract:SUMMARY Recent phylogenetic investigations have confirmed that hemiChordates and echinoderms are sister taxa. However, hemiChordates share several cardinal characteristics with Chordates and are thus an important taxon for testing hypotheses of homology between key Chordate characters and their putative hemiChordate antecedents. The Chordate dorsal nervous system (DNS) and endostyle are intriguing characters because both hemiChordate larval and adult structures have been hypothesized as homologues. This study attempts to test these purported homologies through examination of the expression pattern of a Ptychodera flava NK2 gene, PfNK2.1, because this gene is expressed both in the DNS and endostyle/thyroid in a wide range of Chordate taxa. We found that PfNK2.1 is expressed in both neuronal and pharyngeal structures, but its expression pattern is broken up into distinct embryonic and juvenile phases. During embryogenesis, PfNK2.1 is expressed in the apical ectoderm, with transcripts later detected in presumable neuronal structures, including the apical organ and ciliated feeding band. In the developing juvenile we detected PfNK2.1 signal throughout the pharynx, including the stomochord, and later in the hindgut. We conclude that the similar utilization of NK2.1 in apical organ development and Chordate DNS is probably due to a more general role for NK2.1 in neurogenesis and that hemiChordates do not possess a homologue of the Chordate DNS. In addition, we conclude that P. flava most likely does not possess a true endostyle; rather during the evolution of the endostyle NK2.1 was recruited from its more general role in pharynx development.
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Testing putative hemiChordate homologues of the Chordate dorsal nervous system and endostyle: expression of NK2.1 (TTF‐1) in the acorn worm Ptychodera flava (Hemichordata, Ptychoderidae)
Evolution & Development, 2002Co-Authors: Carter M Takacs, Kevin J PetersonAbstract:SUMMARY Recent phylogenetic investigations have confirmed that hemiChordates and echinoderms are sister taxa. However, hemiChordates share several cardinal characteristics with Chordates and are thus an important taxon for testing hypotheses of homology between key Chordate characters and their putative hemiChordate antecedents. The Chordate dorsal nervous system (DNS) and endostyle are intriguing characters because both hemiChordate larval and adult structures have been hypothesized as homologues. This study attempts to test these purported homologies through examination of the expression pattern of a Ptychodera flava NK2 gene, PfNK2.1, because this gene is expressed both in the DNS and endostyle/thyroid in a wide range of Chordate taxa. We found that PfNK2.1 is expressed in both neuronal and pharyngeal structures, but its expression pattern is broken up into distinct embryonic and juvenile phases. During embryogenesis, PfNK2.1 is expressed in the apical ectoderm, with transcripts later detected in presumable neuronal structures, including the apical organ and ciliated feeding band. In the developing juvenile we detected PfNK2.1 signal throughout the pharynx, including the stomochord, and later in the hindgut. We conclude that the similar utilization of NK2.1 in apical organ development and Chordate DNS is probably due to a more general role for NK2.1 in neurogenesis and that hemiChordates do not possess a homologue of the Chordate DNS. In addition, we conclude that P. flava most likely does not possess a true endostyle; rather during the evolution of the endostyle NK2.1 was recruited from its more general role in pharynx development.
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A phylogenetic test of the calciChordate scenario
Lethaia, 1995Co-Authors: Kevin J PetersonAbstract:The calciChordate scenario of Jefferies and colleagues purports to explain the origin and early evolution of the phyla Echinodermata and Chordata. CalciChordate proponents have argued that echinoderms are the sister group of the Chordates and uroChordates are the sister group of the craniates. These phylogenetic hypotheses, which differ from the traditional groupings, are derived primarily from morphological interpretations of carpoids (solutes, cornutes, and mitrates), an enigmatic fossil group usually held to be primitive stem-group echinoderms. Although the scenario has received only limited support, it has yet to be falsified. The difficulty with falsifying the calciChordate scenario is proving that the morphological interpretations, for example, that carpoids possessed notochords, dorsal hollow nerve cords, and other typical Chordate or craniate characters, are incorrect. Here, rather than argue over the interpretation of fossils, the phylogenetic hypotheses embedded within the scenario are tested. It is found that the calciChordate scenario fails such a test, even if both the Recent and fossils forms are coded according to the calciChordate scenario. It is argued that: (1) the erection of scenarios must follow the construction of a cladogram; and (2) fossils are unable to dictate the relationships among phyla. □CalciChordate scenario, Carpoidea, Deuterostomia, Echinodermata, Chordata, phylogeny, cladistics.
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A phylogenetic test of the calciChordate scenario
Lethaia, 1995Co-Authors: Kevin J PetersonAbstract:The calciChordate scenario of Jefferies and colleagues purports to explain the origin and early evolution of the phyla Echinodermata and Chordata. CalciChordate proponents have argued that echinoderms are the sister group of the Chordates and uroChordates are the sister group of the craniates. These phylogenetic hypotheses, which differ from the traditional groupings, are derived primarily from morphological interpretations of carpoids (solutes, cornutes, and mitrates), an enigmatic fossil group usually held to be primitive stem-group echinoderms. Although the scenario has received only limited support, it has yet to be falsified. The difficulty with falsifying the calciChordate scenario is proving that the morphological interpretations, for example, that carpoids possessed notochords, dorsal hollow nerve cords, and other typical Chordate or craniate characters, are incorrect. Here, rather than argue over the interpretation of fossils, the phylogenetic hypotheses embedded within the scenario are tested. It is found that the calciChordate scenario fails such a test, even if both the Recent and fossils forms are coded according to the calciChordate scenario. It is argued that: (1) the erection of scenarios must follow the construction of a cladogram; and (2) fossils are unable to dictate the relationships among phyla. □CalciChordate scenario, Carpoidea, Deuterostomia, Echinodermata, Chordata, phylogeny, cladistics.
Noriyuki Satoh - One of the best experts on this subject based on the ideXlab platform.
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Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution.
Molecular biology and evolution, 2018Co-Authors: Jun G. Inoue, Noriyuki SatohAbstract:Fish-like larvae were foundational to the Chordate body plan, given the basal placement of free-living lancelets. That body plan probably made it possible for Chordate ancestors to swim by beating a tail formed of notochord and bilateral paraxial muscles. In order to investigate the molecular genetic basis of the origin and evolution of paraxial muscle, we deduced the evolutionary histories of 16 contractile protein genes from paraxial muscle, based on genomic data from all five deuterostome lineages, using a newly developed orthology identification pipeline and a species tree. As a result, we found that more than twice as many orthologs of paraxial muscle genes are present in Chordates, as in nonChordate deuterostomes (ambulacrarians). Orthologs of paraxial-type actin and troponin C genes are absent in ambulacrarians and most paraxial muscle protein isoforms diversified via gene duplications that occurred in each Chordate lineage. Analyses of genes with known expression sites indicated that some isoforms were reutilized in specific muscles of nonvertebrate Chordates via gene duplications. As orthologs of most paraxial muscle genes were present in ambulacrarians, in addition to expression patterns of related genes and functions of the two protein isoforms, regulatory mechanisms of muscle genes should also be considered in future studies of the origin of paraxial muscle.
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The New Organizers Hypothesis for Chordate Origins
Chordate Origins and Evolution, 2016Co-Authors: Noriyuki SatohAbstract:What is the most plausible explanation for mechanisms involved in the origins and evolution of Chordates? Most Chordate-specific characters are associated with the emergence of a fish-like larva that locomotes efficiently by beating its tail. Comparisons of embryogenesis in cephaloChordates and hemiChordates offer insights about Chordate origins. The new organizers hypothesis emerges from this comparison.
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Chordate evolution and the three-phylum system.
Proceedings of The Royal Society B: Biological Sciences, 2014Co-Authors: Noriyuki Satoh, Daniel S Rokhsar, Teruaki NishikawaAbstract:Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of Chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three Chordate groups themselves. Accumulating evidence shows that echinoderms and hemiChordates form a clade (the Ambulacraria), and that within the Chordata, cephaloChordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of Chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics.
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On a possible evolutionary link of the stomochord of hemiChordates to pharyngeal organs of Chordates
Genesis (New York N.Y. : 2000), 2014Co-Authors: Noriyuki Satoh, Kunifumi Tagawa, Christopher J. Lowe, Takeshi Kawashima, Hiroki Takahashi, Michio Ogasawara, Marc W. Kirschner, Kanako HisataAbstract:As a group closely related to Chordates, hemiChordate acorn worms are in a key phylogenic position for addressing hypotheses of Chordate origins. The stomochord of acorn worms is an anterior outgrowth of the pharynx endoderm into the proboscis. In 1886 Bateson proposed homology of this organ to the Chordate notochord, crowning this animal group "hemiChordates." Although this proposal has been debated for over a century, the question still remains unresolved. Here we review recent progress related to this question. First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in Chordates, does not support the stomochord/notochord homology. Third, FoxE that is expressed in the stomochord-forming region in acorn worm juveniles is expressed in the club-shaped gland and in the endostyle of amphioxus, in the endostyle of ascidians, and in the thyroid gland of vertebrates. Based on these findings, together with the anterior endodermal location of the stomochord, we propose that the stomochord has evolutionary relatedness to Chordate organs deriving from the anterior pharynx rather than to the notochord.
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On a possible evolutionary link of the stomochord of hemiChordates to pharyngeal organs of Chordates
Genesis, 2014Co-Authors: Noriyuki Satoh, Jr-kai Yu, Kunifumi Tagawa, Christopher J. Lowe, Takeshi Kawashima, Hiroki Takahashi, Michio Ogasawara, Marc W. Kirschner, Kanako Hisata, Yi-hsien SuAbstract:Summary As a group closely related to Chordates, hemiChordate acorn worms are in a key phylogenic position for addressing hypotheses of Chordate origins. The stomochord of acorn worms is an anterior outgrowth of the pharynx endoderm into the proboscis. In 1886 Bateson proposed homology of this organ to the Chordate notochord, crowning this animal group “hemiChordates.” Although this proposal has been debated for over a century, the question still remains unresolved. Here we review recent progress related to this question. First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in Chordates, does not support the stomochord/notochord homology. Third, FoxE that is expressed in the stomochord-forming region in acorn worm juveniles is expressed in the club-shaped gland and in the endostyle of amphioxus, in the endostyle of ascidians, and in the thyroid gland of vertebrates. Based on these findings, together with the anterior endodermal location of the stomochord, we propose that the stomochord has evolutionary relatedness to Chordate organs deriving from the anterior pharynx rather than to the notochord. genesis 52:925–934, 2014. © 2014 Wiley Periodicals, Inc.
Michael Schubert - One of the best experts on this subject based on the ideXlab platform.
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roles of retinoic acid and tbx1 10 in pharyngeal segmentation amphioxus and the ancestral Chordate condition
Evodevo, 2014Co-Authors: Demian Koop, Linda Z. Holland, Jie Chen, Maria Theodosiou, Joao E Carvalho, Susana Alvarez, Angel R De Lera, Michael SchubertAbstract:Background: Although Chordates descend from a segmented ancestor, the evolution of head segmentation has been very controversial for over 150 years. Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate Chordates, such as the cephaloChordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the Chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest. Results: Focusing on the role of retinoic acid (RA) in post-gastrulation pharyngeal morphogenesis, we found that during gastrulation, RA signaling in the endoderm is required for defining pharyngeal and non-pharyngeal domains and that this process involves active degradation of RA anteriorly in the embryo. Subsequent extension of the pharyngeal territory depends on the creation of a low RA environment and is coupled to body elongation. RA further functions in pharyngeal segmentation in a regulatory network involving the mutual inhibition of RA- and Tbx1/10-dependent signaling. Conclusions: These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral Chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of Chordates.
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Roles of retinoic acid and Tbx1/10 in pharyngeal segmentation: amphioxus and the ancestral Chordate condition
EvoDevo, 2014Co-Authors: Demian Koop, Linda Z. Holland, Jie Chen, Maria Theodosiou, Joao E Carvalho, Susana Alvarez, Angel R De Lera, Michael SchubertAbstract:Background: Although Chordates descend from a segmented ancestor, the evolution of head segmentation has been very controversial for over 150 years. Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate Chordates, such as the cephaloChordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the Chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest. Results: Focusing on the role of retinoic acid (RA) in post-gastrulation pharyngeal morphogenesis, we found that during gastrulation, RA signaling in the endoderm is required for defining pharyngeal and non-pharyngeal domains and that this process involves active degradation of RA anteriorly in the embryo. Subsequent extension of the pharyngeal territory depends on the creation of a low RA environment and is coupled to body elongation. RA further functions in pharyngeal segmentation in a regulatory network involving the mutual inhibition of RA-and Tbx1/10-dependent signaling. Conclusions: These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral Chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of Chordates.
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Amphioxus Postembryonic Development Reveals the Homology of Chordate Metamorphosis
Current biology : CB, 2008Co-Authors: Mathilde Paris, Michael Schubert, Hector Escriva, Frédéric Brunet, Julius Brtko, Fabrice Ciesielski, Dominique Roecklin, Valérie Vivat-hannah, Emilien L. Jamin, Jean Pierre CravediAbstract:Summary Most studies in evolution are centered on how homologous genes, structures, and/or processes appeared and diverged. Although historical homology is well defined as a concept, in practice its establishment can be problematic, especially for some morphological traits or developmental processes. Metamorphosis in Chordates is such an enigmatic character. Defined as a spectacular postembryonic larva-to-adult transition, it shows a wide morphological diversity between the different Chordate lineages, suggesting that it might have appeared several times independently. In vertebrates, metamorphosis is triggered by binding of the thyroid hormones (THs) T 4 and T 3 to thyroid-hormone receptors (TRs). Here we show that a TH derivative, triiodothyroacetic acid (TRIAC), induces metamorphosis in the cephaloChordate amphioxus. The amphioxus TR (amphiTR) mediates spontaneous and TRIAC-induced metamorphosis because it strongly binds to TRIAC, and a specific TR antagonist, NH3, inhibits both spontaneous and TRIAC-induced metamorphosis. Moreover, as in amphibians, amphiTR expression levels increase around metamorphosis and are enhanced by THs. Therefore, TH-regulated metamorphosis, mediated by TR, is an ancestral feature of all Chordates. This conservation of a regulatory network supports the homology of metamorphosis in the Chordate lineage.
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Retinoic acid signaling and the evolution of Chordates
International journal of biological sciences, 2006Co-Authors: Ferdinand Marlétaz, Linda Z. Holland, Vincent Laudet, Michael SchubertAbstract:In Chordates, which comprise uroChordates, cephaloChordates and vertebrates, the vitamin A-derived morphogen retinoic acid (RA) has a pivotal role during development. Altering levels of endogenous RA signaling during early embryology leads to severe malformations, mainly due to incorrect positional codes specifying the embryonic anteroposterior body axis. In this review, we present our current understanding of the RA signaling pathway and its roles during Chordate development. In particular, we focus on the conserved roles of RA and its downstream mediators, the Hox genes, in conveying positional patterning information to different embryonic tissues, such as the endoderm and the central nervous system. We find that some of the control mechanisms governing RA-mediated patterning are well conserved between vertebrates and invertebrate Chordates, such as the cephaloChordate amphioxus. In contrast, outside the Chordates, evidence for roles of RA signaling is scarce and the evolutionary origin of the RA pathway itself thus remains elusive. In sum, to fully understand the evolutionary history of the RA pathway, future research should focus on identification and study of components of the RA signaling cascade in non-Chordate deuterostomes (such as hemiChordates and echinoderms) and other invertebrates, such as insects, mollusks and cnidarians.
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Amphioxus and tunicates as evolutionary model systems
Trends in Ecology and Evolution, 2006Co-Authors: Michael Schubert, Hector Escriva, José Xavier-neto, Vincent LaudetAbstract:One important question in evolutionary biology concerns the origin of vertebrates from invertebrates. The current consensus is that the proximate ancestor of vertebrates was an invertebrate Chordate. Today, the invertebrate Chordates comprise cephaloChordates (amphioxus) and tunicates (each a subphylum in the phylum Chordata, which also includes the vertebrate subphylum). It was widely accepted that, within the Chordates, tunicates represent the sister group of a clade of cephaloChordates plus vertebrates. However, recent studies suggest that the evolutionary positions of tunicates and cephaloChordates should be reversed, the implications of which are considered here. We also review the two major groups of invertebrate Chordates and compare relative advantages (and disadvantages) of each as model systems for elucidating the origin of the vertebrates.
Yutaka Satou - One of the best experts on this subject based on the ideXlab platform.
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Regulatory genes in the ancestral Chordate genomes
Development Genes and Evolution, 2008Co-Authors: Yutaka Satou, Yasunori Sasakura, Shuichi Wada, Nori SatohAbstract:Changes or innovations in gene regulatory networks for the developmental program in the ancestral Chordate genome appear to be a major component in the evolutionary process in which tadpole-type larvae, a unique characteristic of Chordates, arose. These alterations may include new genetic interactions as well as the acquisition of new regulatory genes. Previous analyses of the Ciona genome revealed that many genes may have emerged after the divergence of the tunicate and vertebrate lineages. In this paper, we examined this possibility by examining a second non-vertebrate Chordate genome. We conclude from this analysis that the ancient Chordate included almost the same repertory of regulatory genes, but less redundancy than extant vertebrates, and that approximately 10% of vertebrate regulatory genes were innovated after the emergence of vertebrates. Thus, refined regulatory networks arose during vertebrate evolution mainly as preexisting regulatory genes multiplied rather than by generating new regulatory genes. The inferred regulatory gene sets of the ancestral Chordate would be an important foundation for understanding how tadpole-type larvae, a unique characteristic of Chordates, evolved.
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a cdna resource for the cephaloChordate amphioxus branchiostoma floridae
Development Genes and Evolution, 2008Co-Authors: Jr-kai Yu, Linda Z. Holland, Yuji Kohara, Mingchih Wang, Tadasu Shini, Noriyuki Satoh, Yutaka SatouAbstract:CephaloChordates are the basal invertebrate Chordates within the phylum Chordata. They are widely used as a model system for research in evolutionary developmental biology (EvoDevo) to understand the basic patterning mechanisms for the Chordate body plan and the origin of vertebrates. Recently, the genome of the cephaloChordate Branchiostoma floridae was sequenced, which further brings this organism to the front for comparative genomic studies. In this paper, we report the generation of large-scale 5′- and 3′-expressed sequence tags (ESTs) from B. floridae and the complementary deoxyribonucleic acid (cDNA) resource for this species. Both 5′- and 3′-ESTs were sequenced for approximately 140,000 cDNA clones derived from five developmental stages, and the cDNA clones were subsequently grouped into independent clusters using 3′-EST sequences. We identified 21,229 cDNA clusters, and each corresponds to a unique transcript species from B. floridae. We then chose 24,020 cDNA clones representing all of these 21,229 clusters to generate the “Branchiostoma floridae Gene Collection Release 1.” We also constructed a database with a searchable interface for this EST dataset and the related information on “Branchiostoma floridae Gene Collection Release 1.” This set of cDNA clones along with our cDNA database will serve as an important resource for future research in this basal Chordate. This Gene Collection and the original 140,000 individual cDNA clones are available to the research community upon request.
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a cdna resource for the cephaloChordate amphioxus branchiostoma floridae
Development Genes and Evolution, 2008Co-Authors: Jr-kai Yu, Linda Z. Holland, Yuji Kohara, Mingchih Wang, Tadasu Shini, Noriyuki Satoh, Yutaka SatouAbstract:CephaloChordates are the basal invertebrate Chordates within the phylum Chordata. They are widely used as a model system for research in evolutionary developmental biology (EvoDevo) to understand the basic patterning mechanisms for the Chordate body plan and the origin of vertebrates. Recently, the genome of the cephaloChordate Branchiostoma floridae was sequenced, which further brings this organism to the front for comparative genomic studies. In this paper, we report the generation of large-scale 5′- and 3′-expressed sequence tags (ESTs) from B. floridae and the complementary deoxyribonucleic acid (cDNA) resource for this species. Both 5′- and 3′-ESTs were sequenced for approximately 140,000 cDNA clones derived from five developmental stages, and the cDNA clones were subsequently grouped into independent clusters using 3′-EST sequences. We identified 21,229 cDNA clusters, and each corresponds to a unique transcript species from B. floridae. We then chose 24,020 cDNA clones representing all of these 21,229 clusters to generate the “Branchiostoma floridae Gene Collection Release 1.” We also constructed a database with a searchable interface for this EST dataset and the related information on “Branchiostoma floridae Gene Collection Release 1.” This set of cDNA clones along with our cDNA database will serve as an important resource for future research in this basal Chordate. This Gene Collection and the original 140,000 individual cDNA clones are available to the research community upon request.
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a genomewide survey of developmentally relevant genes in ciona intestinalis v genes for receptor tyrosine kinase pathway and notch signaling pathway
Development Genes and Evolution, 2003Co-Authors: Yutaka Satou, Yasunori Sasakura, Lixy Yamada, Kaoru S Imai, Nori Satoh, Bernard M DegnanAbstract:In the present survey, we identified most of the genes involved in the receptor tyrosine kinase (RTK), mitogen activated protein kinase (MAPK) and Notch signaling pathways in the draft genome sequence of Ciona intestinalis, a basal Chordate. Compared to vertebrates, most of the genes found in the Ciona genome had fewer paralogues, although several genes including ephrin, Eph and fringe appeared to have multiplied or duplicated independently in the ascidian genome. In contrast, some genes including kit/flt, PDGF and Trk receptor tyrosine kinases were not found in the present survey, suggesting that these genes are innovations in the vertebrate lineage or lost in the ascidian lineage. The gene set identified in the present analysis provides an insight into genes for the RTK, MAPK and Notch signaling pathways in the ancient Chordate genome and thereby how Chordates evolved these signaling pathway.
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the draft genome of ciona intestinalis insights into Chordate and vertebrate origins
Science, 2002Co-Authors: Paramvir Dehal, Brad Davidson, Anna Di Gregorio, Maarten Sollewijn D Gelpke, Jarrod Chapman, Robert K. Campbell, Bernhard M Degnan, Yutaka Satou, Anthony W De Tomaso, David GoodsteinAbstract:The first Chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral Chordates. To illuminate the origins of Chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains similar to16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
