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Ricci L, Chaurasia A, Lapébie P, Dru P, Helm RR, Copley RR, Tiozzo S. Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development. Sci Rep 2016; 6:27357. [PMID: 27264734 PMCID: PMC4893630 DOI: 10.1038/srep27357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/17/2016] [Indexed: 11/19/2022] Open
Abstract
Organisms that have evolved alternative modes of reproduction, complementary to the sexual mode, are found across metazoans. The chordate Botryllus schlosseri is an emerging model for asexual development studies. Botryllus can rebuild its entire body from a portion of adult epithelia in a continuous and stereotyped process called blastogenesis. Anatomy and ontogenies of blastogenesis are well described, however molecular signatures triggering this developmental process are entirely unknown. We isolated tissues at the site of blastogenesis onset and from the same epithelia where this process is never triggered. We linearly amplified an ultra-low amount of mRNA (<10ng) and generated three transcriptome datasets. To provide a conservative landscape of transcripts differentially expressed between blastogenic vs. non-blastogenic epithelia we compared three different mapping and analysis strategies with a de novo assembled transcriptome and partially assembled genome as references, additionally a self-mapping strategy on the dataset. A subset of differentially expressed genes were analyzed and validated by in situ hybridization. The comparison of different analyses allowed us to isolate stringent sets of target genes, including transcripts with potential involvement in the onset of a non-embryonic developmental pathway. The results provide a good entry point to approach regenerative event in a basal chordate.
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Affiliation(s)
- Lorenzo Ricci
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Ankita Chaurasia
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Pascal Lapébie
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Philippe Dru
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Rebecca R Helm
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Richard R Copley
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Stefano Tiozzo
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
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Gasparini F, Skobo T, Benato F, Gioacchini G, Voskoboynik A, Carnevali O, Manni L, Dalla Valle L. Characterization of Ambra1 in asexual cycle of a non-vertebrate chordate, the colonial tunicate Botryllus schlosseri, and phylogenetic analysis of the protein group in Bilateria. Mol Phylogenet Evol 2015; 95:46-57. [PMID: 26611831 DOI: 10.1016/j.ympev.2015.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 12/19/2022]
Abstract
Ambra1 is a positive regulator of autophagy, a lysosome-mediated degradative process involved both in physiological and pathological conditions. Nowadays, Ambra1 has been characterized only in mammals and zebrafish. Through bioinformatics searches and targeted cloning, we report the identification of the complete Ambra1 transcript in a non-vertebrate chordate, the tunicate Botryllus schlosseri. Tunicata is the sister group of Vertebrata and the only chordate group possessing species that reproduce also by blastogenesis (asexual reproduction). B. schlosseri Ambra1 deduced amino acid sequence is shorter than vertebrate homologues but still contains the typical WD40 domain. qPCR analyses revealed that the level of B. schlosseri Ambra1 transcription is temporally regulated along the colonial blastogenetic cycle. By means of similarity searches we identified Wdr5 and Katnb1 as proteins evolutionarily associated to Ambra1. Phylogenetic analyses on Bilateria indicate that: (i) Wdr5 is the most related to Ambra1, so that they may derive from an ancestral gene, (ii) Ambra1 forms a group of ancient genes evolved before the radiation of the taxon, (iii) these orthologous Ambra1 share the two conserved WD40/YVTN repeat-like-containing domains, and (iv) they are characterized by ancient duplications of WD40 repeats within the N-terminal domain.
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Affiliation(s)
- Fabio Gasparini
- Department of Biology, University of Padova, Via Ugo Bassi 35131 Padova, Italy.
| | - Tatjana Skobo
- Department of Biology, University of Padova, Via Ugo Bassi 35131 Padova, Italy.
| | - Francesca Benato
- Department of Biology, University of Padova, Via Ugo Bassi 35131 Padova, Italy.
| | - Giorgia Gioacchini
- Department of Life Science and Environment, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Ayelet Voskoboynik
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, 265 Campus Drive, 3rd Floor, CA 94305, Stanford, United States.
| | - Oliana Carnevali
- Department of Life Science and Environment, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi 35131 Padova, Italy.
| | - Luisa Dalla Valle
- Department of Biology, University of Padova, Via Ugo Bassi 35131 Padova, Italy.
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Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader. Dev Genes Evol 2015; 225:149-59. [PMID: 26032664 DOI: 10.1007/s00427-015-0502-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
RNA sequencing analysis was carried out to characterize egg and larval transcriptomes in the appendicularian, Oikopleura dioica, a planktonic chordate, which is characterized by rapid development and short life cycle of 5 days, using a Japanese population of the organism. De novo transcriptome assembly matched with 16,423 proteins corresponding to 95.4% of the protein-encoding genes deposited in the OikoBase, the genome database of the Norwegian population. Nucleotide and amino acid sequence identities between the Japanese and Norwegian O. dioica were estimated to be around 91.0 and 94.8%, respectively. We discovered 175 novel protein-encoding genes: 144 unigenes were common to both the Japanese and Norwegian populations, whereas 31 unigenes were not found in the OikoBase genome reference. Among the total 12,311 unigenes, approximately 63% were detected in egg-stage RNAs, whereas 99% were detected in larval stage RNAs; 3772 genes were up-regulated, and 1336 genes were down-regulated more than four-fold in the larvae. Gene ontology analyses characterized gene activities in these two developmental stages. We found a messenger RNA (mRNA) 5' trans-spliced leader, which was observed in 40.8% of the total unique transcripts. It showed preferential linkage to adenine at the 5' ends of the downstream exons. Trans-splicing was observed more frequently in egg mRNAs compared with larva-specific mRNAs.
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Manni L, Gasparini F, Hotta K, Ishizuka KJ, Ricci L, Tiozzo S, Voskoboynik A, Dauga D. Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri. PLoS One 2014; 9:e96434. [PMID: 24789338 PMCID: PMC4006837 DOI: 10.1371/journal.pone.0096434] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/07/2014] [Indexed: 12/13/2022] Open
Abstract
Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis) of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA) will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements.
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Affiliation(s)
- Lucia Manni
- Department of Biology, University of Padova, Padova, Italy
| | | | - Kohji Hotta
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kouhoku-ku, Yokohama, Japan
| | - Katherine J. Ishizuka
- Institute for Stem Cell Biology and Regenerative Medicine, and Hopkins Marine Station, Stanford, California, United States of America
| | - Lorenzo Ricci
- Centre National de la Recherche Scientifique, Sorbonne Universités, Université Pierre et Marie Curie (University of Paris 06), Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Stefano Tiozzo
- Centre National de la Recherche Scientifique, Sorbonne Universités, Université Pierre et Marie Curie (University of Paris 06), Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, and Hopkins Marine Station, Stanford, California, United States of America
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Nydam ML, Netuschil N, Sanders E, Langenbacher A, Lewis DD, Taketa DA, Marimuthu A, Gracey AY, De Tomaso AW. The candidate histocompatibility locus of a Basal chordate encodes two highly polymorphic proteins. PLoS One 2013; 8:e65980. [PMID: 23826085 PMCID: PMC3691228 DOI: 10.1371/journal.pone.0065980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/29/2013] [Indexed: 01/11/2023] Open
Abstract
The basal chordate Botryllus schlosseri undergoes a natural transplantation reaction governed by a single, highly polymorphic locus called the fuhc. Our initial characterization of this locus suggested it encoded a single gene alternatively spliced into two transcripts: a 555 amino acid–secreted form containing the first half of the gene, and a full-length, 1008 amino acid transmembrane form, with polymorphisms throughout the ectodomain determining outcome. We have now found that the locus encodes two highly polymorphic genes which are separated by a 227 bp intergenic region: first, the secreted form as previously described, and a second gene encoding a 531 amino acid membrane-bound gene containing three extracellular immunoglobulin domains. While northern blotting revealed only these two mRNAs, both PCR and mRNA-seq detect a single capped and polyadenylated transcript that encodes processed forms of both genes linked by the intergenic region, as well as other transcripts in which exons of the two genes are spliced together. These results might suggest that the two genes are expressed as an operon, during which both genes are co-transcribed and then trans-spliced into two separate messages. This type of transcriptional regulation has been described in tunicates previously; however, the membrane-bound gene does not encode a typical Splice Leader (SL) sequence at the 5′ terminus that usually accompanies trans-splicing. Thus, the presence of stable transcripts encoding both genes may suggest a novel mechanism of regulation, or conversely may be rare but stable transcripts in which the two mRNAs are linked due to a small amount of read-through by RNA polymerase. Both genes are highly polymorphic and co-expressed on tissues involved in histocompatibility. In addition, polymorphisms on both genes correlate with outcome, although we have found a case in which it appears that the secreted form may be major allorecognition determinant.
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Affiliation(s)
- Marie L. Nydam
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Nikolai Netuschil
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Erin Sanders
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Adam Langenbacher
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Daniel D. Lewis
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Daryl A. Taketa
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Arumugapradeep Marimuthu
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Andrew Y. Gracey
- Department of Marine Environmental Biology, University of Southern California, Los Angeles, California, United States of America
| | - Anthony W. De Tomaso
- Department of MCD Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail:
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Gasparini F, Degasperi V, Shimeld SM, Burighel P, Manni L. Evolutionary conservation of the placodal transcriptional network during sexual and asexual development in chordates. Dev Dyn 2013; 242:752-66. [DOI: 10.1002/dvdy.23957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 01/14/2023] Open
Affiliation(s)
- Fabio Gasparini
- Dipartimento di Biologia; Università degli Studi di Padova; Padova; Italy
| | | | - Sebastian M. Shimeld
- Department of Zoology; University of Oxford; South Parks Road; Oxford; United Kingdom
| | - Paolo Burighel
- Dipartimento di Biologia; Università degli Studi di Padova; Padova; Italy
| | - Lucia Manni
- Dipartimento di Biologia; Università degli Studi di Padova; Padova; Italy
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Parkinson J, Wasmuth JD, Salinas G, Bizarro CV, Sanford C, Berriman M, Ferreira HB, Zaha A, Blaxter ML, Maizels RM, Fernández C. A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation. PLoS Negl Trop Dis 2012; 6:e1897. [PMID: 23209850 PMCID: PMC3510090 DOI: 10.1371/journal.pntd.0001897] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/25/2012] [Indexed: 01/14/2023] Open
Abstract
Background The cestode Echinococcus granulosus - the agent of cystic echinococcosis, a zoonosis affecting humans and domestic animals worldwide - is an excellent model for the study of host-parasite cross-talk that interfaces with two mammalian hosts. To develop the molecular analysis of these interactions, we carried out an EST survey of E. granulosus larval stages. We report the salient features of this study with a focus on genes reflecting physiological adaptations of different parasite stages. Methodology/Principal Findings We generated ∼10,000 ESTs from two sets of full-length enriched libraries (derived from oligo-capped and trans-spliced cDNAs) prepared with three parasite materials: hydatid cyst wall, larval worms (protoscoleces), and pepsin/H+-activated protoscoleces. The ESTs were clustered into 2700 distinct gene products. In the context of the biology of E. granulosus, our analyses reveal: (i) a diverse group of abundant long non-protein coding transcripts showing homology to a middle repetitive element (EgBRep) that could either be active molecular species or represent precursors of small RNAs (like piRNAs); (ii) an up-regulation of fermentative pathways in the tissue of the cyst wall; (iii) highly expressed thiol- and selenol-dependent antioxidant enzyme targets of thioredoxin glutathione reductase, the functional hub of redox metabolism in parasitic flatworms; (iv) candidate apomucins for the external layer of the tissue-dwelling hydatid cyst, a mucin-rich structure that is critical for survival in the intermediate host; (v) a set of tetraspanins, a protein family that appears to have expanded in the cestode lineage; and (vi) a set of platyhelminth-specific gene products that may offer targets for novel pan-platyhelminth drug development. Conclusions/Significance This survey has greatly increased the quality and the quantity of the molecular information on E. granulosus and constitutes a valuable resource for gene prediction on the parasite genome and for further genomic and proteomic analyses focused on cestodes and platyhelminths. Cestodes are a neglected group of platyhelminth parasites, despite causing chronic infections to humans and domestic animals worldwide. We used Echinococcus granulosus as a model to study the molecular basis of the host-parasite cross-talk during cestode infections. For this purpose, we carried out a survey of the genes expressed by parasite larval stages interfacing with definitive and intermediate hosts. Sequencing from several high quality cDNA libraries provided numerous insights into the expression of genes involved in important aspects of E. granulosus biology, e.g. its metabolism (energy production and antioxidant defences) and the synthesis of key parasite structures (notably, the one exposed to humans and livestock intermediate hosts). Our results also uncovered the existence of an intriguing set of abundant repeat-associated non-protein coding transcripts that may participate in the regulation of gene expression in all surveyed stages. The dataset now generated constitutes a valuable resource for gene prediction on the parasite genome and for further genomic and proteomic studies focused on cestodes and platyhelminths. In particular, the detailed characterization of a range of newly discovered genes will contribute to a better understanding of the biology of cestode infections and, therefore, to the development of products allowing their efficient control.
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Affiliation(s)
- John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - James D. Wasmuth
- Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Gustavo Salinas
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Cristiano V. Bizarro
- Laboratório de Biologia Molecular de Cestódeos and Laboratorio de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Chris Sanford
- Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Matthew Berriman
- Parasite Genomics, The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Henrique B. Ferreira
- Laboratório de Biologia Molecular de Cestódeos and Laboratorio de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Arnaldo Zaha
- Laboratório de Biologia Molecular de Cestódeos and Laboratorio de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mark L. Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rick M. Maizels
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (RMM); (CF)
| | - Cecilia Fernández
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- * E-mail: (RMM); (CF)
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Gasparini F, Shimeld SM, Ruffoni E, Burighel P, Manni L. Expression of a Musashi-like gene in sexual and asexual development of the colonial chordate Botryllus schlosseri and phylogenetic analysis of the protein group. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:562-73. [PMID: 21826788 DOI: 10.1002/jez.b.21431] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 06/24/2011] [Accepted: 06/29/2011] [Indexed: 12/12/2022]
Abstract
Tunicates are the unique chordates to possess species reproducing sexually and asexually. Among them, the colonial ascidian Botryllus schlosseri is a reference model for the study of similarities and differences in these two developmental pathways. We here illustrate the characterization and expression pattern during both pathways of a transcript for a gene orthologous to Dazap1. Dazap1 genes encode for RNA-binding proteins and fall into the Musashi-like (Msi-like) group. Our phylogenetic analysis shows that these are related to other RNA-binding proteins (Tardbp and several heterogeneous nuclear ribonucleoproteins types) that share the same modular domain structure of conserved tandem RNA Recognition Motifs (RRMs). We also classify the whole group as derived from a single ancient duplication of the RRM. Our results also show that Dazap1 is expressed with discrete spatiotemporal pattern during embryogenesis and blastogenesis of B. schlosseri. It is never expressed in wholly differentiated tissues, but it is located in all bud tissues and in different spatiotemporally defined territories of embryos and larva. These expression patterns could indicate different roles in the two processes, but an intriguing relationship appears if aspects of cell division dynamics are taken into account, suggesting that it is related to the proliferative phases in all tissues, and raising a similarity with known Dazap1 orthologs in other metazoans.
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Affiliation(s)
- Fabio Gasparini
- Dipartimento di Biologia, Università degli Studi di Padova, Italy.
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