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Jr-kai Yu - One of the best experts on this subject based on the ideXlab platform.
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an updated staging system for Cephalochordate development one table suits them all
bioRxiv, 2020Co-Authors: João E. Carvalho, Jr-kai Yu, François Lahaye, Hector Escriva, Luok Wen Yong, Jenifer C Croce, Michael SchubertAbstract:Abstract Background The chordates are divided into three subphyla: Vertebrata, Tunicata and Cephalochordata. Phylogenetically, the Cephalochordata, more commonly known as lancelets or amphioxus, constitute the sister group of Vertebrata plus Tunicata. Due to their phylogenetic position and their conserved morphology and genome architecture, lancelets are important models for understanding the evolutionary history of chordates. Lancelets are small, marine filter-feeders, and the few dozen species that have so far been described have been grouped into three genera: Branchiostoma, Epigonichthys and Asymmetron. Given their relevance for addressing questions about the evolutionary diversification of chordates, lancelets have been the subjects of study by generations of scientists, with the first descriptions of adult anatomy and developmental morphology dating back to the 19th century. Today, several different lancelet species are used as laboratory models, predominantly for developmental, molecular and genomic studies. It is thus very surprising that there is currently no universal staging system and no unambiguous nomenclature for developing lancelets. Results We illustrated the development of the European amphioxus (Branchiostoma lanceolatum) using confocal microscopy and compiled a streamlined developmental staging system, from fertilization through larval life, with an unambiguous stage nomenclature. By tracing growth curves of the European amphioxus reared at different temperatures, we were able to show that our staging system permits the easy conversion of any developmental time into a defined stage name. Furthermore, comparisons of embryos and larvae from the European amphioxus (B. lanceolatum), the Florida amphioxus (B. floridae), the Chinese amphioxus (B. belcheri), the Japanese amphioxus (B. japonicum) and the Bahamas lancelet (Asymmetron lucayanum) demonstrated that our staging system can readily be applied to other lancelet species. Conclusions Here, we propose an updated staging and nomenclature system for lancelets. Although the detailed staging description was carried out on developing B. lanceolatum, comparisons with other lancelet species strongly suggest that both staging and nomenclature are applicable to all extant lancelets. We thus believe that this description of embryonic and larval development can be of great use for the scientific community and hope that it will become the new standard for defining and naming developing lancelets.
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Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle
Genome Biology and Evolution, 2016Co-Authors: Iryna Kozmikova, Jr-kai Yu, Nicholas H. Putnam, Carlos W. Nossa, Zbynek Kozmik, Linda Z. HollandAbstract:Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant Cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120–160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the Cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between Cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in Cephalochordates.
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tracing the evolutionary origin of vertebrate skeletal tissues insights from Cephalochordate amphioxus
Current Opinion in Genetics & Development, 2016Co-Authors: Luok Wen Yong, Jr-kai YuAbstract:Vertebrate mineralized skeletal tissues are widely considered as an evolutionary novelty. Despite the importance of these tissues to the adaptation and radiation of vertebrate animals, the evolutionary origin of vertebrate skeletal tissues remains largely unclear. Cephalochordates (Amphioxus) occupy a key phylogenetic position and can serve as a valuable model for studying the evolution of vertebrate skeletal tissues. Here we summarize recent advances in amphioxus developmental biology and comparative genomics that can help to elucidate the evolutionary origins of the vertebrate skeletal tissues and their underlying developmental gene regulatory networks (GRN). By making comparisons to the developmental studies in vertebrate models and recent discoveries in paleontology and genomics, it becomes evident that the collagen matrix-based connective tissues secreted by the somite-derived cells in amphioxus likely represent the rudimentary skeletal tissues in chordates. We propose that upon the foundation of this collagenous precursor, novel tissue mineralization genes that arose from gene duplications were incorporated into an ancestral mesodermal GRN that makes connective and supporting tissues, leading to the emergence of highly-mineralized skeletal tissues in early vertebrates.
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discovery of germline related genes in Cephalochordate amphioxus a genome wide survey using genome annotation and transcriptome data
Marine Genomics, 2015Co-Authors: Kunlung Li, Jr-kai YuAbstract:Abstract The generation of germline cells is a critical process in the reproduction of multicellular organisms. Studies in animal models have identified a common repertoire of genes that play essential roles in primordial germ cell (PGC) formation. However, comparative studies also indicate that the timing and regulation of this core genetic program vary considerably in different animals, raising the intriguing questions regarding the evolution of PGC developmental mechanisms in metazoans. Cephalochordates (commonly called amphioxus or lancelets) represent one of the invertebrate chordate groups and can provide important information about the evolution of developmental mechanisms in the chordate lineage. In this study, we used genome and transcriptome data to identify germline-related genes in two distantly related Cephalochordate species, Branchiostoma floridae and Asymmetron lucayanum. Branchiostoma and Asymmetron diverged more than 120 MYA, and the most conspicuous difference between them is their gonadal morphology. We used important germline developmental genes in several model animals to search the amphioxus genome and transcriptome dataset for conserved homologs. We also annotated the assembled transcriptome data using Gene Ontology (GO) terms to facilitate the discovery of putative genes associated with germ cell development and reproductive functions in amphioxus. We further confirmed the expression of 14 genes in developing oocytes or mature eggs using whole mount in situ hybridization, suggesting their potential functions in amphioxus germ cell development. The results of this global survey provide a useful resource for testing potential functions of candidate germline-related genes in Cephalochordates and for investigating differences in gonad developmental mechanisms between Branchiostoma and Asymmetron species.
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The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution.
Genome Biology and Evolution, 2014Co-Authors: Jr-kai Yu, Nicholas H. Putnam, Linda Z. HollandAbstract:Cephalochordates, the sister group of tunicates plus vertebrates, have been called “living fossils” due to their resemblance to fossil chordates from Cambrian strata. The genome of the Cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a Cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both Cephalochordates and 10 vertebrates using an echinoderm, a hemichordate, and a mollusk as outgroups showed that Cephalochordates are evolving more slowly than the slowest evolving vertebrate known (the elephant shark), with A. lucayanum evolving even more slowly than B. floridae. Against this background of slow evolution, some genes, notably several involved in innate immunity, stand out as evolving relatively quickly. This may be due to the lack of an adaptive immune system and the relatively high levels of bacteria in the inshore waters Cephalochordates inhabit. Molecular dating analysis including several time constraints revealed a divergence time of ~120 Ma for A. lucayanum and B. floridae. The divisions between Cephalochordates and vertebrates, and that between chordates and the hemichordate plus echinoderm clade likely occurred before the Cambrian.
Shicui Zhang - One of the best experts on this subject based on the ideXlab platform.
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Characterization, organization and expression of AmphiLysC, an acidic c-type lysozyme gene in amphioxus Branchiostoma belcheri tsingtauense
Gene, 2005Co-Authors: Shicui Zhang, Hongyan Li, Anlong XuAbstract:Abstract The study on lysozymes remains open in amphioxus, a Cephalochordate. Here we show the existence of c-type lysozyme gene (AmphiLysC) in amphioxus, first such data in the basal chordates including urochordate and Cephalochordate. This is in contrast to the absence of c-type lysozyme genes in urochordate. It is found that there exist two copies of c-type lysozyme genes in amphioxus genome, and their gene organization is similar to vertebrate c-type lysozyme genes with respect to the number and the size of both exons and introns. AmphiLysC possesses main features characteristic of the digestive c-type lysozyme such as lower number of basic amino acids (low pI values) and pH-optimum in acidic range. Moreover, AmphiLysC is predominantly expressed in the gut. These indicate that AmphiLysC is possibly a digestive c-type enzyme. However, the ubiquitous expression of AmphiLysC in non-digestive tissues such as ovaries, testes, notochord, gill and muscle suggests that it may also play a non-digestive role like antibacterial activity. It is highly likely that AmphiLysC is an enzyme with a combined function of digestion and bacteriolysis.
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two classic cadherin related molecules with no cadherin extracellular repeats in the Cephalochordate amphioxus distinct adhesive specificities and possible involvement in the development of multicell layered structures
Journal of Cell Science, 2004Co-Authors: Yasuko Akiyamaoda, Shicui ZhangAbstract:We previously reported the existence of Bb-cadherin, a molecule related to classic cadherin, in the Cephalochordate amphioxus ( Branchiostoma belcheri ) . The structure of Bb-cadherin is unique in that it lacks the cadherin extracellular repeats, although its cytoplasmic domain shows close similarities to those of typical classic cadherins. The extracellular region of Bb-cadherin consists of laminin globular domains and a cysteine-rich EGF-like domain that are similar to domains in nonchordate classic cadherins. In this study, we identified a second amphioxus cadherin. It was designated Bb2-cadherin (Bb2C) while the previously reported cadherin has been renamed Bb1-cadherin (Bb1C). Bb2C is very similar to Bb1C in its overall structure and amino acid sequence. Genomic BLAST searches and phylogenetic analyses suggested that these two amphioxus genes have been generated through a gene duplication that occurred after separation of the Cephalochordates from the other animals. They also bear distinct adhesive specificities. Immunohistochemical analyses showed that Bb1C and Bb2C, together with β-catenin, appear to function as adherens junction constituents in the epithelia of different germ layers of the amphioxus embryo. Differential expression of the two cadherins was also observed in the developing, multicell-layered notochord. These observations suggest that, despite their unique structures, the functions and developmental roles of Bb1C and Bb2C are comparable to those of the classic cadherins characterized to date in other animal groups, such as the vertebrate E- and N-cadherins and the Drosophila D E- and D N-cadherins. The possible involvement of Bb1C and Bb2C in the development of multicell-layered structures characteristic of the Cephalochordate body plan is presented.
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Two classic cadherin-related molecules with no cadherin extracellular repeats in the Cephalochordate amphioxus: distinct adhesive specificities and possible involvement in the development of multicell-layered structures.
Journal of cell science, 2004Co-Authors: Yasuko Akiyama-oda, Shicui ZhangAbstract:We previously reported the existence of Bb-cadherin, a molecule related to classic cadherin, in the Cephalochordate amphioxus (Branchiostoma belcheri). The structure of Bb-cadherin is unique in that it lacks the cadherin extracellular repeats, although its cytoplasmic domain shows close similarities to those of typical classic cadherins. The extracellular region of Bb-cadherin consists of laminin globular domains and a cysteine-rich EGF-like domain that are similar to domains in nonchordate classic cadherins. In this study, we identified a second amphioxus cadherin. It was designated Bb2-cadherin (Bb2C) while the previously reported cadherin has been renamed Bb1-cadherin (Bb1C). Bb2C is very similar to Bb1C in its overall structure and amino acid sequence. Genomic BLAST searches and phylogenetic analyses suggested that these two amphioxus genes have been generated through a gene duplication that occurred after separation of the Cephalochordates from the other animals. They also bear distinct adhesive specificities. Immunohistochemical analyses showed that Bb1C and Bb2C, together with beta-catenin, appear to function as adherens junction constituents in the epithelia of different germ layers of the amphioxus embryo. Differential expression of the two cadherins was also observed in the developing, multicell-layered notochord. These observations suggest that, despite their unique structures, the functions and developmental roles of Bb1C and Bb2C are comparable to those of the classic cadherins characterized to date in other animal groups, such as the vertebrate E- and N-cadherins and the Drosophila DE- and DN-cadherins. The possible involvement of Bb1C and Bb2C in the development of multicell-layered structures characteristic of the Cephalochordate body plan is presented.
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The karyotype of amphioxus Branchiostoma belcheri tsingtauense (Cephalochordata)
Journal of the Marine Biological Association of the United Kingdom, 2003Co-Authors: Changliu Wang, Shicui Zhang, Yongzhong ZhangAbstract:The chromosome number and karyotype of amphioxus Branchiostoma belcheri tsingtauense were studied using embryonic cells. The diploid chromosome number (2n) of B. belcheri tsingtauense is 36, and its karyotype 2n=36, 2st + 34t, FN=36. This is the first report on the karyotype of the Cephalochordate. Evidence suggesting the possible presence of a pair of sex-chromosomes in the amphioxus has been provided.
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Histochemical localization of constitutive nitric oxide synthases in amphioxus Branchiostoma belcheri tsingtauense
Journal of the Marine Biological Association of the United Kingdom, 2002Co-Authors: Shicui Zhang, Li Li, Hongyan LiAbstract:The present study demonstrated histochemically that the enzyme activity was present in the cerebral vesicle, epidermis, muscles, endostyle and anus of amphioxus Branchiostoma belcheri tsingtaunese . This is the first noted report on localization of constitutive nitric oxide synthases in a celphalochordate.
Noriyuki Satoh - One of the best experts on this subject based on the ideXlab platform.
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The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition
Zoological Letters, 2017Co-Authors: Jun Inoue, Yuuri Yasuoka, Hiroki Takahashi, Noriyuki SatohAbstract:Background The T-box family transcription-factor gene, Brachyury , has two expression domains with discrete functions during animal embryogenesis. The primary domain, associated with the blastopore, is shared by most metazoans, while the secondary domain, involved in the notochord, is specific to chordates. In most animals , Brachyury is present in a single copy, but in Cephalochordates, the most basal of the chordates, the gene is present in two copies, suggesting allotment of the two domains to each of the duplicates. Results In order to clarify whether Brachyury duplication occurred in the common ancestor of chordates after which one of duplicates was lost in the urochordate and vertebrate lineages, we estimated phylogenetic relationships of Brachyury genes and examined the synteny of a Brachyury -containing genomic region of deuterostomes with decoded genomes . The monophyletic origin of tandemly arranged Brachyury genes of Cephalochordates indicates that the tandem duplication occurred in the Cephalochordate lineage, but not in the chordate ancestor. Conclusions Our results thus suggest that, in the common ancestor of chordates, a single copy of Brachyury acquired two expression domains and that the duplication was not involved in the acquisition of the notochord. However, in relation to regulatory mechanisms, both possibilities—namely a single copy with two domains and two copies with different domains—should be considered in future studies of Brachyury .
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The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition
Zoological letters, 2017Co-Authors: Jun G. Inoue, Hiroki Takahashi, Yuuri Yasuoka, Noriyuki SatohAbstract:The T-box family transcription-factor gene, Brachyury, has two expression domains with discrete functions during animal embryogenesis. The primary domain, associated with the blastopore, is shared by most metazoans, while the secondary domain, involved in the notochord, is specific to chordates. In most animals, Brachyury is present in a single copy, but in Cephalochordates, the most basal of the chordates, the gene is present in two copies, suggesting allotment of the two domains to each of the duplicates. In order to clarify whether Brachyury duplication occurred in the common ancestor of chordates after which one of duplicates was lost in the urochordate and vertebrate lineages, we estimated phylogenetic relationships of Brachyury genes and examined the synteny of a Brachyury-containing genomic region of deuterostomes with decoded genomes. The monophyletic origin of tandemly arranged Brachyury genes of Cephalochordates indicates that the tandem duplication occurred in the Cephalochordate lineage, but not in the chordate ancestor. Our results thus suggest that, in the common ancestor of chordates, a single copy of Brachyury acquired two expression domains and that the duplication was not involved in the acquisition of the notochord. However, in relation to regulatory mechanisms, both possibilities—namely a single copy with two domains and two copies with different domains—should be considered in future studies of Brachyury.
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Chordate Evolution: An Extension of the New Organizers Hypothesis
Chordate Origins and Evolution, 2016Co-Authors: Noriyuki SatohAbstract:After their appearance, chordates evolved into three independent lineages: Cephalochordates, urochordates, and vertebrates. Cephalochordates probably have retained their original form for more than 500 million years. On the other hand, urochordates and vertebrates developed unique morphologies to adapt as advanced filter feeders with tunics and specialized predators with heads and jaws, respectively. The fossil record suggests that vertebrate evolution was protracted.
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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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eLS - Analysis of the Amphioxus Genome
Encyclopedia of Life Sciences, 2009Co-Authors: Noriyuki SatohAbstract:Amphioxus or Cephalochordates are small fish-like marine invertebrates. The sequenced genome of Branchiostoma floridae is approximately 520 Mb in size and estimated to contain approximately 21 900 protein-coding loci. Comparison of the amphioxus genome with genomes of other animals made a great impact on the resolution of the long-standing question of the origin of vertebrates. First, chordates are monophyletic group, in which Cephalochordates represent the most basal extant chordate lineage, with urochordates sister to vertebrates. Second, there is highly conserved synteny between the Cephalochordate and vertebrate genomes. This allows reconstruction of 17 ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes. Third, the two rounds of genome-wide duplications occurred in the vertebrate lineage after their divergence from Cephalochordates and urochordates. Fourth, whereas most duplicate genes have been lost, a disproportionate number of genes are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology. Key concepts The phylum Chordata consists of the subphyla Cephalochordata (amphioxus), Urochordata (ascidians) and Vertebrata, and these three groups are characterized by possession of a notochord, a hollow dorsal neural tube, a perforated pharyngeal region and a post-anal tail. Chordates are monophyletic group in which Cephalochordates represent the most basal extant lineage, suggesting a free-living ancestor of chordates. Seventeen ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes are revealed by highly conserved synteny between the two genomes. The two rounds of genome-wide gene duplications occurred in the vertebrate lineage after their divergence from Cephalochordates and urochordates. A disproportionate number of genes which were produced by the genome-wide duplication are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology. Keywords: amphioxus genome; evolution of chordates; origin of vertebrates; ancestral chordate linkage groups; two rounds of genome-wide gene duplications
Linda Z. Holland - One of the best experts on this subject based on the ideXlab platform.
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Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle
Genome Biology and Evolution, 2016Co-Authors: Iryna Kozmikova, Jr-kai Yu, Nicholas H. Putnam, Carlos W. Nossa, Zbynek Kozmik, Linda Z. HollandAbstract:Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant Cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120–160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the Cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between Cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in Cephalochordates.
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The evolution of genes encoding for green fluorescent proteins: insights from Cephalochordates (amphioxus)
Scientific Reports, 2016Co-Authors: Nicholas D. Holland, Linda Z. Holland, Dimitri D. DeheynAbstract:Green Fluorescent Protein (GFP) was originally found in cnidarians, and later in copepods and Cephalochordates (amphioxus) (Branchiostoma spp). Here, we looked for GFP-encoding genes in Asymmetron, an early-diverged Cephalochordate lineage, and found two such genes closely related to some of the Branchiostoma GFPs. Dim fluorescence was found throughout the body in adults of Asymmetron lucayanum, and, as in Branchiostoma floridae, was especially intense in the ripe ovaries. Spectra of the fluorescence were similar between Asymmetron and Branchiostoma. Lineage-specific expansion of GFP-encoding genes in the genus Branchiostoma was observed, largely driven by tandem duplications. Despite such expansion, purifying selection has strongly shaped the evolution of GFP-encoding genes in Cephalochordates, with apparent relaxation for highly duplicated clades. All Cephalochordate GFP-encoding genes are quite different from those of copepods and cnidarians. Thus, the ancestral Cephalochordates probably had GFP, but since GFP appears to be lacking in more early-diverged deuterostomes (echinoderms, hemichordates), it is uncertain whether the ancestral Cephalochordates (i.e. the common ancestor of Asymmetron and Branchiostoma) acquired GFP by horizontal gene transfer (HGT) from copepods or cnidarians or inherited it from the common ancestor of copepods and deuterostomes, i.e. the ancestral bilaterians.
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The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution.
Genome Biology and Evolution, 2014Co-Authors: Jr-kai Yu, Nicholas H. Putnam, Linda Z. HollandAbstract:Cephalochordates, the sister group of tunicates plus vertebrates, have been called “living fossils” due to their resemblance to fossil chordates from Cambrian strata. The genome of the Cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a Cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both Cephalochordates and 10 vertebrates using an echinoderm, a hemichordate, and a mollusk as outgroups showed that Cephalochordates are evolving more slowly than the slowest evolving vertebrate known (the elephant shark), with A. lucayanum evolving even more slowly than B. floridae. Against this background of slow evolution, some genes, notably several involved in innate immunity, stand out as evolving relatively quickly. This may be due to the lack of an adaptive immune system and the relatively high levels of bacteria in the inshore waters Cephalochordates inhabit. Molecular dating analysis including several time constraints revealed a divergence time of ~120 Ma for A. lucayanum and B. floridae. The divisions between Cephalochordates and vertebrates, and that between chordates and the hemichordate plus echinoderm clade likely occurred before the Cambrian.
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Early development of Cephalochordates (amphioxus).
Wiley Interdisciplinary Reviews-Developmental Biology, 2011Co-Authors: Linda Z. Holland, Takayuki OnaiAbstract:The Phylum Chordata includes three groups—Vertebrata, Tunicata, and Cephalochordata. In Cephalochordates, commonly called amphioxus or lancelets, which are basal in the Chordata, the eggs are small and relatively non-yolky. As in vertebrates, cleavage is indeterminate with cell fates determined gradually as development proceeds. The oocytes are attached to the ovarian follicle at the animal pole, where the oocyte nucleus is located. The cytoplasm at the opposite side of the egg, the vegetal pole, contains the future germ plasm or pole plasm, which includes determinants of the germline. After fertilization, additional asymmetries are established by movements of the egg and sperm nuclei, resulting in a concentration of mitochondria at one side of the animal hemisphere. This may be related to establishment of the dorsal/ventral axis. Patterning along the embryonic axes is mediated by secreted signaling proteins. Dorsal identity is specified by Nodal/Vg1 signaling, while during the gastrula stage, opposition between Nodal/Vg1 and BMP signaling establishes dorsal/anterior (i.e., head) and ventral/posterior (i.e., trunk/tail) identities, respectively. Wnt/β-catenin signaling specifies posterior identity while retinoic acid signaling specifies positions along the anterior/posterior axis. These signals are further modulated by a number of secreted antagonists. This fundamental patterning mechanism is conserved, with some modifications, in vertebrates. WIREs Dev Biol 2012, 1:167–183. doi: 10.1002/wdev.11 For further resources related to this article, please visit the WIREs website.
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a cdna resource for the Cephalochordate amphioxus branchiostoma floridae
Development Genes and Evolution, 2008Co-Authors: Jr-kai Yu, Noriyuki Satoh, Linda Z. Holland, Yuji Kohara, Mingchih Wang, Tadasu Shini, 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.
Hector Escriva - One of the best experts on this subject based on the ideXlab platform.
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an updated staging system for Cephalochordate development one table suits them all
bioRxiv, 2020Co-Authors: João E. Carvalho, Jr-kai Yu, François Lahaye, Hector Escriva, Luok Wen Yong, Jenifer C Croce, Michael SchubertAbstract:Abstract Background The chordates are divided into three subphyla: Vertebrata, Tunicata and Cephalochordata. Phylogenetically, the Cephalochordata, more commonly known as lancelets or amphioxus, constitute the sister group of Vertebrata plus Tunicata. Due to their phylogenetic position and their conserved morphology and genome architecture, lancelets are important models for understanding the evolutionary history of chordates. Lancelets are small, marine filter-feeders, and the few dozen species that have so far been described have been grouped into three genera: Branchiostoma, Epigonichthys and Asymmetron. Given their relevance for addressing questions about the evolutionary diversification of chordates, lancelets have been the subjects of study by generations of scientists, with the first descriptions of adult anatomy and developmental morphology dating back to the 19th century. Today, several different lancelet species are used as laboratory models, predominantly for developmental, molecular and genomic studies. It is thus very surprising that there is currently no universal staging system and no unambiguous nomenclature for developing lancelets. Results We illustrated the development of the European amphioxus (Branchiostoma lanceolatum) using confocal microscopy and compiled a streamlined developmental staging system, from fertilization through larval life, with an unambiguous stage nomenclature. By tracing growth curves of the European amphioxus reared at different temperatures, we were able to show that our staging system permits the easy conversion of any developmental time into a defined stage name. Furthermore, comparisons of embryos and larvae from the European amphioxus (B. lanceolatum), the Florida amphioxus (B. floridae), the Chinese amphioxus (B. belcheri), the Japanese amphioxus (B. japonicum) and the Bahamas lancelet (Asymmetron lucayanum) demonstrated that our staging system can readily be applied to other lancelet species. Conclusions Here, we propose an updated staging and nomenclature system for lancelets. Although the detailed staging description was carried out on developing B. lanceolatum, comparisons with other lancelet species strongly suggest that both staging and nomenclature are applicable to all extant lancelets. We thus believe that this description of embryonic and larval development can be of great use for the scientific community and hope that it will become the new standard for defining and naming developing lancelets.
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developmental cell cell communication pathways in the Cephalochordate amphioxus actors and functions
The International Journal of Developmental Biology, 2017Co-Authors: Stephanie Bertrand, Ildiko M L Somorjai, Yann Le Pétillon, Hector EscrivaAbstract:The laboratory of H.E. was supported by the CNRS and the ANR16-CE12-0008-01 and S.B. by the Institut Universitaire de France. The laboratory of I.M.L.S. is currently supported by Wellcome Trust ISSF grant 204821/Z/16/Z
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Developmental cell-cell communication pathways in the Cephalochordate amphioxus: actors and functions
International Journal of Developmental Biology, 2017Co-Authors: Stephanie Bertrand, Ildiko M L Somorjai, Yann Le Pétillon, Hector EscrivaAbstract:During embryonic development, cells of metazoan embryos need to communicate in order to construct the correct bodyplan. To do so, they use several signals that usually act through interactions between ligands and receptors. Interestingly, only a few pathways are known to be fundamental during animal development, and they are usually found in all the major metazoan clades, raising the following question: how have evolution of the actors and of the functions of these pathways participated in the appearance of the current diversity of animal morphologies? The chordate lineage comprises vertebrates, their sister group the urochordates, and the Cephalochordates (i.e. amphioxus). Urochordates are quite derived relative to the chordate ancestor, whereas Cephalochordates and vertebrates share many morphological traits. Thus, comparing embryonic development between vertebrates and Cephalochordates should give us some insight into the ancestral characters present in chordates and into the morphological evolution in this clade. However, while much is known about the function of different signalling pathways in vertebrates, data are still scarce in the literature for Cephalochordates. In this review, we summarize the current state of the field concerning the expression of actors and the function of the major cell-cell communication pathways, including Hedgehog (Hh), Notch, Nuclear Receptor (NR), Receptor Tyrosine Kinase (RTK), Transforming Growth Factor-β (TGF-β) and Wingless/Int (Wnt), in amphioxus.
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expression of fox genes in the Cephalochordate branchiostoma lanceolatum
Frontiers in Ecology and Evolution, 2015Co-Authors: Daniel Aldea, Anthony Leon, Stephanie Bertrand, Hector EscrivaAbstract:Forkhead box (Fox) genes code for transcription factors that play important roles in different biological processes. They are found in a wide variety of organisms and appeared in unicellular eukaryotes. In metazoans, the gene family includes many members that can be subdivided into 24 classes. Cephalochordates are key organisms to understand the functional evolution of gene families in the chordate lineage due to their phylogenetic position as an early divergent chordate, their simple anatomy and genome structure. In the genome of the Cephalochordate amphioxus Branchiostoma floridae, 32 Fox genes were identified, with at least one member for each of the classes that were present in the ancestor of bilaterians. In this work we describe the expression pattern of 13 of these genes during the embryonic development of the Mediterranean amphioxus, Branchiostoma lanceolatum. We found that FoxK and FoxM genes present an ubiquitous expression while all the others show specific expression patterns restricted to diverse embryonic territories. Many of these expression patterns are conserved with vertebrates, suggesting that the main functions of Fox genes in chordates were present in their common ancestor.
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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.