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Guillaume Balavoine - One of the best experts on this subject based on the ideXlab platform.
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Extensive Chordate and Annelid Macrosynteny Reveals Ancestral Homeobox Gene Organization.
Molecular Biology and Evolution, 2011Co-Authors: Jerome H L Hui, Detlev Arendt, Guillaume Balavoine, Carmel Mcdougall, Ana S Monteiro, Peter W H Holland, David E K FerrierAbstract:Genes with the homeobox motif are crucial in developmental biology and widely implicated in the evolution of development. The Antennapedia (ANTP)-class is one of the two major classes of animal homeobox genes, and includes the Hox genes, renowned for their role in patterning the anterior-posterior axis of animals. The origin and evolution of the ANTP-class genes are a matter of some debate. A principal guiding hypothesis has been the existence of an ancient gene Mega-cluster deep in animal ancestry. This hypothesis was largely established from linkage data from chordates, and the Mega-cluster hypothesis remains to be seriously tested in Protostomes. We have thus mapped ANTP-class homeobox genes to the chromosome level in a lophotrochozoan Protostome. Our comparison of gene organization in Platynereis dumerilii and chordates indicates that the Mega-cluster, if it did exist, had already been broken up onto four chromosomes by the time of the Protostome-deuterostome ancestor (PDA). These results not only elucidate an aspect of the genome organization of the PDA but also reveal high levels of macrosynteny between P. dumerilii and chordates. This implies a very low rate of interchromosomal genome rearrangement in the lineages leading to P. dumerilii and the chordate ancestor since the time of the PDA.
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features of the ancestral bilaterian inferred from platynereis dumerilii parahox genes
BMC Biology, 2009Co-Authors: Florian Raible, Claire Jubin, Guillaume Balavoine, Nicolas Dray, Natalia Korchagina, Sylvie Samain, Beatrice Segurens, Ghislaine MagdelenatAbstract:BACKGROUND: The ParaHox gene cluster is the evolutionary sister to the Hox cluster. Whilst the role of the Hox cluster in patterning the anterior-posterior axis of bilaterian animals is well established, and the organisation of vertebrate Hox clusters is intimately linked to gene regulation, much less is known about the more recently discovered ParaHox cluster. ParaHox gene clustering, and its relationship to expression, has only been described in deuterostomes. Conventional Protostome models (Drosophila melanogaster and Caenorhabditis elegans) are secondarily derived with respect to ParaHox genes, suffering gene loss and cluster break-up. RESULTS: We provide the first evidence for ParaHox gene clustering from a less-derived Protostome animal, the annelid Platynereis dumerilii. Clustering of these genes is thus not a sole preserve of the deuterostome lineage within Bilateria. This Protostome ParaHox cluster is not entirely intact however, with Pdu-Cdx being on the opposite end of the same chromosome arm from Pdu-Gsx and Pdu-Xlox. From the genomic sequence around the P. dumerilii ParaHox genes the neighbouring genes are identified, compared with other taxa, and the ancestral arrangement deduced. CONCLUSION: We relate the organisation of the ParaHox genes to their expression, and from comparisons with other taxa hypothesise that a relatively complex pattern of ParaHox gene expression existed in the Protostome-deuterostome ancestor, which was secondarily simplified along several invertebrate lineages. Detailed comparisons of the gene content around the ParaHox genes enables the reconstruction of the genome surrounding the ParaHox cluster of the Protostome-deuterostome ancestor, which existed over 550 million years ago.
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hox genes in brachiopods and priapulids and Protostome evolution
Nature, 1999Co-Authors: Renaud De Rosa, Jennifer K Grenier, Tatiana Andreeva, Charles E Cook, Andre Adoutte, Michael Akam, Sean B Carroll, Guillaume BalavoineAbstract:Understanding the early evolution of animal body plans requires knowledge both of metazoan phylogeny and of the genetic and developmental changes involved in the emergence of particular forms. Recent 18S ribosomal RNA phylogenies suggest a three-branched tree for the Bilateria comprising the deuterostomes and two great Protostome clades, the lophotrochozoans1 and ecdysozoans2. Here, we show that the complement of Hox genes in critical Protostome phyla reflects these phylogenetic relationships and reveals the early evolution of developmental regulatory potential in bilaterians. We have identified Hox genes that are shared by subsets of Protostome phyla. These include a diverged pair of posterior (Abdominal-B -like) genes in both a brachiopod and a polychaete annelid, which supports the lophotrochozoan assemblage, and a distinct posterior Hox gene shared by a priapulid, a nematode and the arthropods, which supports the ecdysozoan clade. The ancestors of each of these two major Protostome lineages had a minimum of eight to ten Hox genes. The major period of Hox gene expansion and diversification thus occurred before the radiation of each of the three great bilaterian clades.
Matheus Souza Gomes - One of the best experts on this subject based on the ideXlab platform.
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Characterization of export receptor exportins (XPOs) in the parasite Schistosoma mansoni.
Parasitology research, 2013Co-Authors: Fabiano C. P. De Abreu, Matheus Souza Gomes, Roberta V. Pereira, Victor F. Oliveira, Liana K. Jannotti-passos, William De Castro Borges, Renata Guerra-sáAbstract:Several proteins and different species of RNA that are produced in the nucleus are exported through the nuclear pore complexes, which require a family of conserved nuclear export receptors called exportins (XPOs). It has been reported that the XPOs (XPO1, XPO5, and XPOT) are directly involved in the transport processes of noncoding RNAs from the nucleus to the cytoplasm and/or from cytoplasm to the nucleus. All three genes are present in fungi, plants, and deuterostome metazoans. However, Protostome metazoan species lack one of the three genes across evolution. In this report, we have demonstrated that all three XPO proteins are present in the parasite Protostome Schistosoma mansoni. As this parasite has a complex life cycle presenting several stages in different hosts and environments, implying a differential gene regulation, we proposed a genomic analysis of XPOs to validate their annotation. The results showed the conservation of exportin family members and gene duplication events in S. mansoni. We performed quantitative RT-PCR, which revealed an upregulation of SmXPO1 in 24 h schistosomula (sixfold when compared with cercariae), and similar transcription levels were observed for SmXPO5 and SmXPOT in all the analyzed stages. These three XPO proteins have been identified for the first time in the Protostome clade, which suggests a higher complexity in RNA transport in the parasite S. mansoni. Taken together, these results suggest that RNA transport by exportins might control cellular processes during cercariae, schistosomula, and adult worm development.
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computational identification and evolutionary relationships of the microrna gene cluster mir 71 2 in Protostomes
Journal of Molecular Evolution, 2013Co-Authors: Matheus Souza Gomes, Mark T. A. Donoghue, Mohankumar Muniyappa, Roberta Verciano Pereira, Renata Guerrasa, Charles SpillaneAbstract:MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20–24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computational approach is used to investigate the extent of evolutionary conservation of the miR-71/2 cluster in animals, and to identify novel miRNAs in the miRNA cluster miR-71/2. The miR-71/2 cluster, consisting of copies of the miR-71 and miR-2 (including miR-13) families, was found to be Protostome-specific. Although, this cluster is highly conserved across the Protostomia, the miR-2 family is completely absent from the Deuterostomia species, while miR-71 is absent from the Vertebrata and Urochordata. The evolutionary conservation and clustering propensity of the miR-71/2 family across the Protostomes could indicate the common functional roles across the member species of the Protostomia.
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Computational Identification and Evolutionary Relationships of the MicroRNA Gene Cluster miR-71/2 in Protostomes
Journal of Molecular Evolution, 2013Co-Authors: Matheus Souza Gomes, Mark T. A. Donoghue, Mohankumar Muniyappa, Roberta Verciano Pereira, Renata Guerra-sá, Charles SpillaneAbstract:MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20–24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computational approach is used to investigate the extent of evolutionary conservation of the miR-71/2 cluster in animals, and to identify novel miRNAs in the miRNA cluster miR-71/2. The miR-71/2 cluster, consisting of copies of the miR-71 and miR-2 (including miR-13) families, was found to be Protostome-specific. Although, this cluster is highly conserved across the Protostomia, the miR-2 family is completely absent from the Deuterostomia species, while miR-71 is absent from the Vertebrata and Urochordata. The evolutionary conservation and clustering propensity of the miR-71/2 family across the Protostomes could indicate the common functional roles across the member species of the Protostomia.
Charles Spillane - One of the best experts on this subject based on the ideXlab platform.
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computational identification and evolutionary relationships of the microrna gene cluster mir 71 2 in Protostomes
Journal of Molecular Evolution, 2013Co-Authors: Matheus Souza Gomes, Mark T. A. Donoghue, Mohankumar Muniyappa, Roberta Verciano Pereira, Renata Guerrasa, Charles SpillaneAbstract:MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20–24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computational approach is used to investigate the extent of evolutionary conservation of the miR-71/2 cluster in animals, and to identify novel miRNAs in the miRNA cluster miR-71/2. The miR-71/2 cluster, consisting of copies of the miR-71 and miR-2 (including miR-13) families, was found to be Protostome-specific. Although, this cluster is highly conserved across the Protostomia, the miR-2 family is completely absent from the Deuterostomia species, while miR-71 is absent from the Vertebrata and Urochordata. The evolutionary conservation and clustering propensity of the miR-71/2 family across the Protostomes could indicate the common functional roles across the member species of the Protostomia.
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Computational Identification and Evolutionary Relationships of the MicroRNA Gene Cluster miR-71/2 in Protostomes
Journal of Molecular Evolution, 2013Co-Authors: Matheus Souza Gomes, Mark T. A. Donoghue, Mohankumar Muniyappa, Roberta Verciano Pereira, Renata Guerra-sá, Charles SpillaneAbstract:MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20–24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computational approach is used to investigate the extent of evolutionary conservation of the miR-71/2 cluster in animals, and to identify novel miRNAs in the miRNA cluster miR-71/2. The miR-71/2 cluster, consisting of copies of the miR-71 and miR-2 (including miR-13) families, was found to be Protostome-specific. Although, this cluster is highly conserved across the Protostomia, the miR-2 family is completely absent from the Deuterostomia species, while miR-71 is absent from the Vertebrata and Urochordata. The evolutionary conservation and clustering propensity of the miR-71/2 family across the Protostomes could indicate the common functional roles across the member species of the Protostomia.
Detlev Arendt - One of the best experts on this subject based on the ideXlab platform.
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Extensive Chordate and Annelid Macrosynteny Reveals Ancestral Homeobox Gene Organization.
Molecular Biology and Evolution, 2011Co-Authors: Jerome H L Hui, Detlev Arendt, Guillaume Balavoine, Carmel Mcdougall, Ana S Monteiro, Peter W H Holland, David E K FerrierAbstract:Genes with the homeobox motif are crucial in developmental biology and widely implicated in the evolution of development. The Antennapedia (ANTP)-class is one of the two major classes of animal homeobox genes, and includes the Hox genes, renowned for their role in patterning the anterior-posterior axis of animals. The origin and evolution of the ANTP-class genes are a matter of some debate. A principal guiding hypothesis has been the existence of an ancient gene Mega-cluster deep in animal ancestry. This hypothesis was largely established from linkage data from chordates, and the Mega-cluster hypothesis remains to be seriously tested in Protostomes. We have thus mapped ANTP-class homeobox genes to the chromosome level in a lophotrochozoan Protostome. Our comparison of gene organization in Platynereis dumerilii and chordates indicates that the Mega-cluster, if it did exist, had already been broken up onto four chromosomes by the time of the Protostome-deuterostome ancestor (PDA). These results not only elucidate an aspect of the genome organization of the PDA but also reveal high levels of macrosynteny between P. dumerilii and chordates. This implies a very low rate of interchromosomal genome rearrangement in the lineages leading to P. dumerilii and the chordate ancestor since the time of the PDA.
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the segmental pattern of otx gbx and hox genes in the annelid platynereis dumerilii
Evolution & Development, 2011Co-Authors: Patrick R H Steinmetz, R P Kostyuchenko, Antje H L Fischer, Detlev ArendtAbstract:: SUMMARY Annelids and arthropods, despite their distinct classification as Lophotrochozoa and Ecdysozoa, present a morphologically similar, segmented body plan. To elucidate the evolution of segmentation and, ultimately, to align segments across remote phyla, we undertook a refined expression analysis to precisely register the expression of conserved regionalization genes with morphological boundaries and segmental units in the marine annelid Platynereis dumerilii. We find that Pdu-otx defines a brain region anterior to the first discernable segmental entity that is delineated by a stripe of engrailed-expressing cells. The first segment is a "cryptic" segment that lacks chaetae and parapodia. This and the subsequent three chaetigerous larval segments harbor the anterior expression boundary of gbx, hox1, hox4, and lox5 genes, respectively. This molecular segmental topography matches the segmental pattern of otx, gbx, and Hox gene expression in arthropods. Our data thus support the view that an ancestral ground pattern of segmental identities existed in the trunk of the last common Protostome ancestor that was lost or modified in Protostomes lacking overt segmentation.
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ancient animal micrornas and the evolution of tissue identity
Nature, 2010Co-Authors: Foteini Christodoulou, Florian Raible, Raju Tomer, Oleg Simakov, Kalliopi Trachana, Sebastian Klaus, Heidi Snyman, Gregory J Hannon, Peer Bork, Detlev ArendtAbstract:Recent work suggests that microRNAs, the ubiquitous, small, non-coding genetic elements with important regulatory roles, were important in the evolution of complexity in multicellular animals. What was the role of these microRNAs when they first evolved? A deep sequencing study of the marine ragworm Platynereis dumerilii, and comparison with other bilaterian animals, suggests that the most ancient known microRNA, miR-100, was initially active in neurosecretory cells around the mouth. Other highly conserved varieties were first present in specific tissues and organ systems, such as ciliated cells and parts of the nervous system, musculature and gut. This work suggests that the last common ancestor of bilaterian animals already had all these structures. Recent work suggests that microRNAs might have been important in the evolution of complexity in multicellular animals. Here it is shown that the most ancient known microRNA, miR–100, was initially active in neurosecretory cells around the mouth. Other highly conserved varieties were first present in specific tissues and organ systems. Thus, microRNA expression was initially restricted to an ancient set of ancient animal cell types and tissues. The spectacular escalation in complexity in early bilaterian evolution correlates with a strong increase in the number of microRNAs1,2. To explore the link between the birth of ancient microRNAs and body plan evolution, we set out to determine the ancient sites of activity of conserved bilaterian microRNA families in a comparative approach. We reason that any specific localization shared between Protostomes and deuterostomes (the two major superphyla of bilaterian animals) should probably reflect an ancient specificity of that microRNA in their last common ancestor. Here, we investigate the expression of conserved bilaterian microRNAs in Platynereis dumerilii, a Protostome retaining ancestral bilaterian features3,4, in Capitella, another marine annelid, in the sea urchin Strongylocentrotus, a deuterostome, and in sea anemone Nematostella, representing an outgroup to the bilaterians. Our comparative data indicate that the oldest known animal microRNA, miR-100, and the related miR-125 and let-7 were initially active in neurosecretory cells located around the mouth. Other sets of ancient microRNAs were first present in locomotor ciliated cells, specific brain centres, or, more broadly, one of four major organ systems: central nervous system, sensory tissue, musculature and gut. These findings reveal that microRNA evolution and the establishment of tissue identities were closely coupled in bilaterian evolution. Also, they outline a minimum set of cell types and tissues that existed in the Protostome–deuterostome ancestor.
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the expression of a hunchback ortholog in the polychaete annelid platynereis dumerilii suggests an ancestral role in mesoderm development and neurogenesis
Development Genes and Evolution, 2006Co-Authors: Pierre Kerner, Detlev Arendt, Fabiola Zelada Gonzalez, Martine Le Gouar, Valerie Ledent, Michel VervoortAbstract:Orthologs of the Drosophila gap gene hunchback have been isolated so far only in Protostomes. Phylogenetic analysis of recently available genomic data allowed us to confirm that hunchback genes are widely found in Protostomes (both lophotrochozoans and ecdysozoans). In contrast, no unequivocal hunchback gene can be found in the genomes of deuterostomes and non-bilaterians. We cloned hunchback in the marine polychaete annelid Platynereis dumerilii and analysed its expression during development. In this species, hunchback displays an expression pattern indicative of a role in mesoderm formation and neurogenesis, and similar to the expression found for hunchback genes in arthropods. These data suggest altogether that these functions are ancestral to Protostomes.
Michel Vervoort - One of the best experts on this subject based on the ideXlab platform.
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Coe genes are expressed in differentiating neurons in the central nervous system of Protostomes.
PLoS ONE, 2011Co-Authors: Adrien Demilly, Pierre Kerner, Elena Simionato, David Ohayon, Alain Garcès, Michel VervoortAbstract:Genes of the coe (collier/olfactory/early B-cell factor) family encode Helix-Loop-Helix transcription factors that are widely conserved in metazoans and involved in many developmental processes, neurogenesis in particular. Whereas their functions during vertebrate neural tube formation have been well documented, very little is known about their expression and role during central nervous system (CNS) development in Protostomes. Here we characterized the CNS expression of coe genes in the insect Drosophila melanogaster and the polychaete annelid Platynereis dumerilii, which belong to different subgroups of Protostomes and show strikingly different modes of development. In the Drosophila ventral nerve cord, we found that the Collier-expressing cells form a subpopulation of interneurons with diverse molecular identities and neurotransmitter phenotypes. We also demonstrate that collier is required for the proper differentiation of some interneurons belonging to the Eve-Lateral cluster. In Platynereis dumerilii, we cloned a single coe gene, Pdu-coe, and found that it is exclusively expressed in post mitotic neural cells. Using an original technique of in silico 3D registration, we show that Pdu-coe is co-expressed with many different neuronal markers and therefore that, like in Drosophila, its expression defines a heterogeneous population of neurons with diverse molecular identities. Our detailed characterization and comparison of coe gene expression in the CNS of two distantly-related Protostomes suggest conserved roles of coe genes in neuronal differentiation in this clade. As similar roles have also been observed in vertebrates, this function was probably already established in the last common ancestor of all bilaterians.
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the expression of a hunchback ortholog in the polychaete annelid platynereis dumerilii suggests an ancestral role in mesoderm development and neurogenesis
Development Genes and Evolution, 2006Co-Authors: Pierre Kerner, Detlev Arendt, Fabiola Zelada Gonzalez, Martine Le Gouar, Valerie Ledent, Michel VervoortAbstract:Orthologs of the Drosophila gap gene hunchback have been isolated so far only in Protostomes. Phylogenetic analysis of recently available genomic data allowed us to confirm that hunchback genes are widely found in Protostomes (both lophotrochozoans and ecdysozoans). In contrast, no unequivocal hunchback gene can be found in the genomes of deuterostomes and non-bilaterians. We cloned hunchback in the marine polychaete annelid Platynereis dumerilii and analysed its expression during development. In this species, hunchback displays an expression pattern indicative of a role in mesoderm formation and neurogenesis, and similar to the expression found for hunchback genes in arthropods. These data suggest altogether that these functions are ancestral to Protostomes.
