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Klaus Weber - One of the best experts on this subject based on the ideXlab platform.
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developmentally controlled expression patterns of intermediate filament proteins in the cephalochordate branchiostoma
Mechanisms of Development, 2001Co-Authors: Anton Karabinos, Georgia Panopoulou, Hans Lehrach, Dirk Wenzel, Jian Wang, Klaus WeberAbstract:Abstract Expression of cytoplasmic intermediate filament (IF) proteins starts in the gastrula with three keratins (k1, Y1, D1) and protein X1. The number of IF proteins expressed increases at the neurula and early larval stages to seven and 11, respectively, and reaches 13 in the adult. Using antibodies specific for a single IF protein the expression patterns of nine of the 13 IF proteins were analyzed at different developmental stages. Keratin k1 of the larval epidermis is replaced in the juvenile by keratin E1. Protein C1 of the larval epidermis persists only weakly and only in the most ventral part of the adult. While down-regulated in the adult epidermis k1 and C1 are major proteins in the atrial epithelium which forms in the later larva. B1 is currently the only IF protein expressed in mesodermally derived tissues such as the muscle tails and some coelomic epithelia. Two-dimensional gels confirm that keratins are the major IF proteins in the nerve cord. Immunogold electronmicroscopy shows that proteins X1 and C2 are present in epidermis and nerve cord in keratin IF.
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Homologues of vertebrate type I, II and III intermediate filament (IF) proteins in an invertebrate; the IF multigene family of the cephalochordate Branchiostoma.
FEBS Letters, 1998Co-Authors: Anton Karabinos, Dieter Riemer, Andreas Erber, Klaus WeberAbstract:We searched for functional homologues of the four subfamilies of vertebrate cytoplasmic intermediate filament (IF) proteins in the cephalochordate Branchiostoma. The epidermis contains in addition to IF proteins C2 and D1 two novel IF proteins E1 and E2. Both sequence comparisons as well as the obligatory heteropolymer formation by the recombinant proteins identify E1 as a type I keratin and E2 and D1 as type II keratins. In contrast the non-epidermal B1 forms as type III homologue homopolymeric IF. We propose that type I–III diversification of IF proteins is a property of the chordate branch of metazoa and discuss a possible origin of type IV neurofilaments.
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common and variant properties of intermediate filament proteins from lower chordates and vertebrates two proteins from the tunicate styela and the identification of a type iii homologue
Journal of Cell Science, 1998Co-Authors: Dieter Riemer, Klaus WeberAbstract:The chordates combine the vertebrates and the invertebrate phyla of the cephalo- and urochordates (tunicates). Two cytoplasmic intermediate filament (IF) proteins of the urochordate Styela plicata are characterized by cDNA cloning, gene organization, tissue specific expression patterns in the adult animal and the self assembly properties of the recombinant proteins. In line with metazoan phylogeny St-A and St-B have the short length version of the coil 1b domain found in all vertebrate and cephalochordate IF proteins while protostomic IF proteins have the longer length version with an extra 42 residues. St-A is the first IF protein from a lower chordate which can be unambiguously related to a particular vertebrate IF subfamily. St-A shares 46% sequence identity with desmin, displays the N-terminal motif necessary for filament assembly of type III proteins and forms normal homopolymeric 10 nm filaments in vitro. St-A but not St-B is present in smooth muscle cells of the body wall musculature. St-A and St-B are found as separate networks in some interior epithelia. St-B shares 30 to 35% identity with keratin 8, St-A and desmin and does not form IF under in vitro assembly conditions. Its relation to a particular vertebrate IF type or to the eight currently known IF proteins from the cephalochordate Branchiostoma remains unresolved. The striking relation between St-A and desmin predicts that the common progenitor of the urochordate (tunicate) and the cephalochordate/vertebrate lineages already possessed a type III homologue. Unlike in vertebrates intron patterns cannot be used to classify the tunicate IF genes. Although St-A is a type III homologue its gene shows an intron position which in vertebrates is restricted to keratin type II genes.
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analysis of the cdna and gene encoding a cytoplasmic intermediate filament if protein from the cephalochordate branchiostoma lanceolatum implications for the evolution of the if protein family
European Journal of Cell Biology, 1992Co-Authors: Dieter Riemer, H Dodemont, Klaus WeberAbstract:: We report the molecular cloning of a full-length cDNA encoding a non-neuronal cytoplasmic intermediate filament (IF) protein of the cephalochordate Branchiostoma lanceolatum. Sequence and structural characteristics of IF-1 reveal a close relation to vertebrate IF proteins: they all lack the extended coil 1b version and the lamin tail homology found in protostomic IF proteins. This implies that divergence of type I to IV IF genes from a common ancestor either coincided with the origin of chordates or occurred at an earlier stage in the evolution of deuterostomes. The structural organization of the cephalochordate gene shows a closer relation to vertebrate type III genes than to type I or II genes. The single gene (approximately 19 kb) is composed of 7 exons and 6 introns which are all located within the sequence encoding the rod domain. The positions and phases of the introns show perfect homology to vertebrate type III genes. In line with the absence of protein sequence similarity of the tail domain, the Branchiostoma gene does not possess the introns interrupting this region in type III genes of vertebrates.
Anton Karabinos - One of the best experts on this subject based on the ideXlab platform.
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the cephalochordate branchiostoma genome contains 26 intermediate filament if genes implications for evolution of chordate if proteins
European Journal of Cell Biology, 2013Co-Authors: Anton KarabinosAbstract:Abstract We analyzed the draft genome of the cephalochordate Branchiostoma floridae ( B. floridae ) for genes encoding intermediate filament (IF) proteins. From 26 identified IF genes 13 were not reported before. Four of the new IF genes belong to the previously established Branchiostoma IF group A, four to the Branchiostoma IF group B, one is homologous to the type II keratin E2 while the remaining four new IF sequences N1 to N4 could not be readily classified in any of the previously established Branchiostoma IF groups. All eleven identified A and B2-type IF genes are located on the same genomic scaffold and arose due to multiple cephalochordate-specific duplications. Another IF gene cluster, identified in the B. floridae genome, contains three keratins (E1, Y1, D1), two keratin-like IF genes (C2, X1), one new IF gene (N1) and one IF unrelated gene, but does not show any similarities to the well defined vertebrate type I or type II keratin gene clusters. In addition, some type III sequence features were documented in the new IF protein N2, which, however, seems to share a common ancestry with the Branchiostoma keratins D1 and two keratin-related genes C. Thus, a few type I and type II keratin genes existed in a common ancestor of cephalochordates and vertebrates, which after separation of these two lineages gave rise to the known complexities of the vertebrate cytoplasmic type I–IV IF proteins, as well as to the multiple keratin and related IF genes in cephalochordates, due to multiple gene duplications, deletions and sequence divergences.
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developmentally controlled expression patterns of intermediate filament proteins in the cephalochordate branchiostoma
Mechanisms of Development, 2001Co-Authors: Anton Karabinos, Georgia Panopoulou, Hans Lehrach, Dirk Wenzel, Jian Wang, Klaus WeberAbstract:Abstract Expression of cytoplasmic intermediate filament (IF) proteins starts in the gastrula with three keratins (k1, Y1, D1) and protein X1. The number of IF proteins expressed increases at the neurula and early larval stages to seven and 11, respectively, and reaches 13 in the adult. Using antibodies specific for a single IF protein the expression patterns of nine of the 13 IF proteins were analyzed at different developmental stages. Keratin k1 of the larval epidermis is replaced in the juvenile by keratin E1. Protein C1 of the larval epidermis persists only weakly and only in the most ventral part of the adult. While down-regulated in the adult epidermis k1 and C1 are major proteins in the atrial epithelium which forms in the later larva. B1 is currently the only IF protein expressed in mesodermally derived tissues such as the muscle tails and some coelomic epithelia. Two-dimensional gels confirm that keratins are the major IF proteins in the nerve cord. Immunogold electronmicroscopy shows that proteins X1 and C2 are present in epidermis and nerve cord in keratin IF.
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molecular evolution of calmodulin and calmodulin like genes in the cephalochordate branchiostoma
Journal of Molecular Evolution, 2000Co-Authors: Anton Karabinos, Debashish BhattacharyaAbstract:Calmodulin is a calcium-binding EF-hand protein that is an activator of many enzymes as well as ion pumps and channels. Due to its multiple targets and its central role in the cell, understanding the evolutionary history of calmodulin genes should provide insights into the origin of genetic complexity in eukaryotes. We have previously isolated and characterized a calmodulin gene from the early-diverging chordate Branchiostoma lanceolatum (CaM1). In this paper, we report the existence of a second calmodulin gene (CaM2) as well as two CaM-like genomic fragments (CaML-2, CaML-3) in B. lanceolatum and a CaM2 and three CaM-like genes (CaML-1, CaML-2, CaML-3) in B. floridae. The CaM-like genes were isolated using low-stringency PCR. Surprisingly, the nucleotide sequences of the B. lanceolatum CaM1 and CaM2 cDNAs differ by 19.3%. Moreover, the CaM2 protein differs at two positions from the amino acid sequence of CaM1; the latter is identical to calmodulins in Drosophila melanogaster, the mollusc Aplysia californica, and the tunicate Halocynthia roretzi. The two B. lanceolatum CaM-like genes are more closely related to the CaM2 than to the CaM1 gene. This relationship is supported by the phylogenetic analyses and the identical exon/intron organization of these three genes, a relationship unique among animal CaM sequences. These data demonstrate the existence of a CaM multigene family in the cephalochordate Branchiostoma, which may have evolved independently from the multigene family in vertebrates.
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Homologues of vertebrate type I, II and III intermediate filament (IF) proteins in an invertebrate; the IF multigene family of the cephalochordate Branchiostoma.
FEBS Letters, 1998Co-Authors: Anton Karabinos, Dieter Riemer, Andreas Erber, Klaus WeberAbstract:We searched for functional homologues of the four subfamilies of vertebrate cytoplasmic intermediate filament (IF) proteins in the cephalochordate Branchiostoma. The epidermis contains in addition to IF proteins C2 and D1 two novel IF proteins E1 and E2. Both sequence comparisons as well as the obligatory heteropolymer formation by the recombinant proteins identify E1 as a type I keratin and E2 and D1 as type II keratins. In contrast the non-epidermal B1 forms as type III homologue homopolymeric IF. We propose that type I–III diversification of IF proteins is a property of the chordate branch of metazoa and discuss a possible origin of type IV neurofilaments.
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the single calmodulin gene of the cephalochordate branchiostoma
Gene, 1997Co-Authors: Anton Karabinos, Dieter RiemerAbstract:The cDNA and gene for calmodulin (CaM) from the cephalochordate Branchiostoma were isolated and characterized. The nucleotide sequence of the Branchiostoma CaM cDNA is about 80% identical to the CaM of Drosophila and Aplysia. However, all nucleotide substitutions are silent, therefore the amino acid sequences of all these CaMs are identical. Branchiostoma and Aplysia CaM genes have the same exon/intron organization. PCR, Northern and genomic Southern analyses showed that Branchiostoma CaM is encoded by a single copy gene, while fish are known to have at least four CaM genes. These results fit the hypothesis that major gene duplication events occurred close to the origin of vertebrates, i.e., after the divergence of the cephalochordate lineage.
Dieter Riemer - One of the best experts on this subject based on the ideXlab platform.
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Homologues of vertebrate type I, II and III intermediate filament (IF) proteins in an invertebrate; the IF multigene family of the cephalochordate Branchiostoma.
FEBS Letters, 1998Co-Authors: Anton Karabinos, Dieter Riemer, Andreas Erber, Klaus WeberAbstract:We searched for functional homologues of the four subfamilies of vertebrate cytoplasmic intermediate filament (IF) proteins in the cephalochordate Branchiostoma. The epidermis contains in addition to IF proteins C2 and D1 two novel IF proteins E1 and E2. Both sequence comparisons as well as the obligatory heteropolymer formation by the recombinant proteins identify E1 as a type I keratin and E2 and D1 as type II keratins. In contrast the non-epidermal B1 forms as type III homologue homopolymeric IF. We propose that type I–III diversification of IF proteins is a property of the chordate branch of metazoa and discuss a possible origin of type IV neurofilaments.
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common and variant properties of intermediate filament proteins from lower chordates and vertebrates two proteins from the tunicate styela and the identification of a type iii homologue
Journal of Cell Science, 1998Co-Authors: Dieter Riemer, Klaus WeberAbstract:The chordates combine the vertebrates and the invertebrate phyla of the cephalo- and urochordates (tunicates). Two cytoplasmic intermediate filament (IF) proteins of the urochordate Styela plicata are characterized by cDNA cloning, gene organization, tissue specific expression patterns in the adult animal and the self assembly properties of the recombinant proteins. In line with metazoan phylogeny St-A and St-B have the short length version of the coil 1b domain found in all vertebrate and cephalochordate IF proteins while protostomic IF proteins have the longer length version with an extra 42 residues. St-A is the first IF protein from a lower chordate which can be unambiguously related to a particular vertebrate IF subfamily. St-A shares 46% sequence identity with desmin, displays the N-terminal motif necessary for filament assembly of type III proteins and forms normal homopolymeric 10 nm filaments in vitro. St-A but not St-B is present in smooth muscle cells of the body wall musculature. St-A and St-B are found as separate networks in some interior epithelia. St-B shares 30 to 35% identity with keratin 8, St-A and desmin and does not form IF under in vitro assembly conditions. Its relation to a particular vertebrate IF type or to the eight currently known IF proteins from the cephalochordate Branchiostoma remains unresolved. The striking relation between St-A and desmin predicts that the common progenitor of the urochordate (tunicate) and the cephalochordate/vertebrate lineages already possessed a type III homologue. Unlike in vertebrates intron patterns cannot be used to classify the tunicate IF genes. Although St-A is a type III homologue its gene shows an intron position which in vertebrates is restricted to keratin type II genes.
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the single calmodulin gene of the cephalochordate branchiostoma
Gene, 1997Co-Authors: Anton Karabinos, Dieter RiemerAbstract:The cDNA and gene for calmodulin (CaM) from the cephalochordate Branchiostoma were isolated and characterized. The nucleotide sequence of the Branchiostoma CaM cDNA is about 80% identical to the CaM of Drosophila and Aplysia. However, all nucleotide substitutions are silent, therefore the amino acid sequences of all these CaMs are identical. Branchiostoma and Aplysia CaM genes have the same exon/intron organization. PCR, Northern and genomic Southern analyses showed that Branchiostoma CaM is encoded by a single copy gene, while fish are known to have at least four CaM genes. These results fit the hypothesis that major gene duplication events occurred close to the origin of vertebrates, i.e., after the divergence of the cephalochordate lineage.
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analysis of the cdna and gene encoding a cytoplasmic intermediate filament if protein from the cephalochordate branchiostoma lanceolatum implications for the evolution of the if protein family
European Journal of Cell Biology, 1992Co-Authors: Dieter Riemer, H Dodemont, Klaus WeberAbstract:: We report the molecular cloning of a full-length cDNA encoding a non-neuronal cytoplasmic intermediate filament (IF) protein of the cephalochordate Branchiostoma lanceolatum. Sequence and structural characteristics of IF-1 reveal a close relation to vertebrate IF proteins: they all lack the extended coil 1b version and the lamin tail homology found in protostomic IF proteins. This implies that divergence of type I to IV IF genes from a common ancestor either coincided with the origin of chordates or occurred at an earlier stage in the evolution of deuterostomes. The structural organization of the cephalochordate gene shows a closer relation to vertebrate type III genes than to type I or II genes. The single gene (approximately 19 kb) is composed of 7 exons and 6 introns which are all located within the sequence encoding the rod domain. The positions and phases of the introns show perfect homology to vertebrate type III genes. In line with the absence of protein sequence similarity of the tail domain, the Branchiostoma gene does not possess the introns interrupting this region in type III genes of vertebrates.
Hector Escriva - One of the best experts on this subject based on the ideXlab platform.
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JNK Mediates Differentiation, Cell Polarity and Apoptosis During Amphioxus Development by Regulating Actin Cytoskeleton Dynamics and ERK Signalling
'Frontiers Media SA', 2021Co-Authors: Hector Escriva, Ildiko M.l. Somorjai, Matthias T. Ehebauer, Jordi Garcia-fernàndezAbstract:c-Jun N-terminal kinase (JNK) is a multi-functional protein involved in a diverse array of context-dependent processes, including apoptosis, cell cycle regulation, adhesion, and differentiation. It is integral to several signalling cascades, notably downstream of non-canonical Wnt and mitogen activated protein kinase (MAPK) signalling pathways. As such, it is a key regulator of cellular behaviour and patterning during embryonic development across the animal kingdom. The cephalochordate amphioxus is an invertebrate chordate model system straddling the invertebrate to vertebrate transition and is thus ideally suited for comparative studies of morphogenesis. However, next to nothing is known about JNK signalling or cellular processes in this lineage. Pharmacological inhibition of JNK signalling using SP600125 during embryonic development arrests gastrula invagination and causes convergence extension-like defects in axial elongation, particularly of the notochord. Pharynx formation and anterior oral mesoderm derivatives like the preoral pit are also affected. This is accompanied by tissue-specific transcriptional changes, including reduced expression of six3/6 and wnt2 in the notochord, and ectopic wnt11 in neurulating embryos treated at late gastrula stages. Cellular delamination results in accumulation of cells in the gut cavity and a dorsal fin-like protrusion, followed by secondary Caspase-3-mediated apoptosis of polarity-deficient cells, a phenotype only partly rescued by co-culture with the pan-Caspase inhibitor Z-VAD-fmk. Ectopic activation of extracellular signal regulated kinase (ERK) signalling in the neighbours of extruded notochord and neural cells, possibly due to altered adhesive and tensile properties, as well as defects in cellular migration, may explain some phenotypes caused by JNK inhibition. Overall, this study supports conserved functions of JNK signalling in mediating the complex balance between cell survival, apoptosis, differentiation, and cell fate specification during cephalochordate morphogenesis
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Crosstalk between nitric oxide and retinoic acid pathways is essential for amphioxus pharynx development
'eLife Sciences Publications Ltd', 2021Co-Authors: Filomena Caccavale, Stephanie Bertrand, Hector Escriva, Giovanni Annona, Lucie Subirana, Salvatore D'anielloAbstract:During animal ontogenesis, body axis patterning is finely regulated by complex interactions among several signaling pathways. Nitric oxide (NO) and retinoic acid (RA) are potent morphogens that play a pivotal role in vertebrate development. Their involvement in axial patterning of the head and pharynx shows conserved features in the chordate phylum. Indeed, in the cephalochordate amphioxus, NO and RA are crucial for the correct development of pharyngeal structures. Here, we demonstrate the functional cooperation between NO and RA that occurs during amphioxus embryogenesis. During neurulation, NO modulates RA production through the transcriptional regulation of Aldh1a.2 that irreversibly converts retinaldehyde into RA. On the other hand, RA directly or indirectly regulates the transcription of Nos genes. This reciprocal regulation of NO and RA pathways is essential for the normal pharyngeal development in amphioxus and it could be conserved in vertebrates
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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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Wnt evolution and function shuffling in liberal and conservative chordate genomes
2018Co-Authors: Ildiko M.l. Somorjai, Hector Escriva, Cristian Cañestro, Josep Martí-solans, Miriam Diaz-gracia, Hiroki Nishida, Kaoru S. Imai, Ricard AlbalatAbstract:Additional file 1 (pdf file; 11.8 MB) includes: Figure S1. Evolution of Wnt5 in ascidians. Figure S2. Expression of WntA in two ascidian species. Figure S3. Chordate Wnt expression. Figure S4. Wnt subfamilies in A. lucayanum, P. marinus and C. milii. Table S1. Non-vertebrate chordate Wnt genes. Table S2. Branchiostoma lanceolatum and Halocynthia roretzi primer and probe sequences. Table S3. Genomic coordinates (scaffold or chromosome) for cephalochordate, human and lamprey Wnt genes. Text S1. Branchiostoma lanceolatum Wnt expression as shown in Figure 2. Text S2. References for Figure S3. Additional file 2 (fasta file; 315 KB): Wnt sequence alignement for Figure 1. Additional file 3 (fasta file; 102 KB): Wnt sequence alignment for Figure S4.
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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 Petillon, 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
Linda Z. Holland - One of the best experts on this subject based on the ideXlab platform.
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Laboratory Culture and Mutagenesis of Amphioxus (Branchiostoma floridae).
Methods in Molecular Biology, 2020Co-Authors: Linda Z. HollandAbstract:Cephalochordates (amphioxus) are invertebrate chordates closely related to vertebrates. As they are evolving very slowly, they are proving to be very appropriate for developmental genetics studies aimed at understanding how vertebrates evolved from their invertebrate ancestors. To date, techniques for gene knockdown and overexpression have been developed, but methods for continuous breeding cultures and generating germline mutants have been developed only recently. Here we describe methods for continuous laboratory breeding cultures of the cephalochordate Branchiostoma floridae and the TALEN and Tol2 methods for mutagenesis. Included are strategies for analyzing the mutants and raising successive generations to obtain homozygotes. These methods should be applicable to any warm water species of cephalochordates with a relatively short generation time of 3-4 months and a life span of 3 years or more.
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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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a cdna resource for the cephalochordate amphioxus branchiostoma floridae
Development Genes and Evolution, 2008Co-Authors: Jr-kai Yu, Linda Z. Holland, Mingchih Wang, Tadasu Shini, Noriyuki Satoh, Yuji Kohara, 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, Mingchih Wang, Tadasu Shini, Noriyuki Satoh, Yuji Kohara, 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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the amphioxus genome illuminates vertebrate origins and cephalochordate biology
Genome Research, 2008Co-Authors: Linda Z. Holland, Simona Candiani, Ricard Albalat, Kaoru Azumi, Elia Benitogutierrez, Matthew J Blow, Marianne Bronnerfraser, Frederic Brunet, Thomas Butts, Larry J DishawAbstract:Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates—a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.