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Besnard F, Koutsovoulos G, Dieudonné S, Blaxter M, Félix MA. Toward Universal Forward Genetics: Using a Draft Genome Sequence of the Nematode Oscheius tipulae To Identify Mutations Affecting Vulva Development. Genetics 2017; 206:1747-1761. [PMID: 28630114 PMCID: PMC5560785 DOI: 10.1534/genetics.117.203521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 05/03/2017] [Accepted: 06/15/2017] [Indexed: 12/30/2022] Open
Abstract
Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. Here, we show that a fragmented draft assembly is sufficient to perform mapping-by-sequencing in nonmodel species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae, a distant relative of the model Caenorhabditis elegans We used this draft to identify the likely causative mutations at the O. tipulae cov-3 locus, which affect vulval development. The cov-3 locus encodes the O. tipulae ortholog of C. elegans mig-13, and we further show that Cel-mig-13 mutants also have an unsuspected vulval-development phenotype. In a virtuous circle, we were able to use the linkage information collected during mutant mapping to improve the genome assembly. These results showcase the promise of genome-enabled forward genetics in nonmodel species.
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Affiliation(s)
- Fabrice Besnard
- École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Paris Sciences et Lettres Research University, 75005, France
| | | | - Sana Dieudonné
- École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Paris Sciences et Lettres Research University, 75005, France
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, EH8 9YL, United Kingdom
| | - Marie-Anne Félix
- École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Paris Sciences et Lettres Research University, 75005, France
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Torrini G, Mazza G, Strangi A, Barabaschi D, Landi S, Mori E, Menchetti M, Sposimo P, Giuliani C, Zoccola A, Lazzaro L, Ferretti G, Foggi B, Roversi PF. Oscheius tipulae in Italy: Evidence of an Alien Isolate in the Integral Natural Reserve of Montecristo Island (Tuscany). J Nematol 2016; 48:8-13. [PMID: 27168647 PMCID: PMC4859620 DOI: 10.21307/jofnem-2017-003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 09/24/2015] [Indexed: 11/11/2022] Open
Abstract
Montecristo Island is an integral natural reserve of the Tuscan Archipelago National Park (Central Italy), characterized by a peculiar assemblage of flora and fauna, with several endemic taxa, and also with a high number of alien species. During a soil survey, we found an alien Oscheius tipulae Lam & Webster, 1971 isolate, phylogenetically close to others from South America. In this article, we examined the possible pathways of introduction of this nematode. Because of the high number of alien plants in this protected area and the low desiccation survival ability of O. tipulae, we hypothesized that the presence of this alien nematode isolate may be related to the soil of introduced plants, although historical association with plant-associated invertebrates is also possible. Further studies with more populations and marker molecules are necessary to investigate the distribution of O. tipulae and the possible impact on this natural reserve.
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Affiliation(s)
- Giulia Torrini
- Council for Agricultural Research and Economics-Agrobiology and Pedology Research Centre, Via Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Giuseppe Mazza
- Council for Agricultural Research and Economics-Agrobiology and Pedology Research Centre, Via Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Agostino Strangi
- Council for Agricultural Research and Economics-Agrobiology and Pedology Research Centre, Via Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Delfina Barabaschi
- Council for Agricultural Research and Economics-Genomics Research Centre, Via S. Protaso, 302, 29017 Fiorenzuola d'Arda, Italy
| | - Silvia Landi
- Council for Agricultural Research and Economics-Agrobiology and Pedology Research Centre, Via Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Emiliano Mori
- Department of Agriculture, Forest and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Mattia Menchetti
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Paolo Sposimo
- Nature and Environment Management Operators s.r.l., Piazza M. D'Azeglio 11, 50121 Firenze, Italy
| | - Claudia Giuliani
- Department of Biology, University of Florence, Via La Pira 4, 50121 Firenze, Italy
| | - Antonio Zoccola
- Corpo Forestale dello Stato, Ufficio Territoriale per la Biodiversità di Pratovecchio, via D. Alighieri 41, 52015 Pratovecchio, Italy
| | - Lorenzo Lazzaro
- Department of Biology, University of Florence, Via La Pira 4, 50121 Firenze, Italy
| | - Giulio Ferretti
- Department of Biology, University of Florence, Via La Pira 4, 50121 Firenze, Italy
| | - Bruno Foggi
- Department of Biology, University of Florence, Via La Pira 4, 50121 Firenze, Italy
| | - Pio Federico Roversi
- Council for Agricultural Research and Economics-Agrobiology and Pedology Research Centre, Via Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
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Almenara DP, de Moura JP, Scarabotto CP, Zingali RB, Winter CE. The molecular and structural characterization of two vitellogenins from the free-living nematode Oscheius tipulae. PLoS One 2013; 8:e53460. [PMID: 23308227 PMCID: PMC3538542 DOI: 10.1371/journal.pone.0053460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 08/22/2012] [Accepted: 11/30/2012] [Indexed: 12/03/2022] Open
Abstract
This paper describes the purification of yolk proteins, which are important for the reproduction of egg-laying animals, and the structural characterization of two vitellogenins, VT1 and OTI-VIT-6, of the nematode Oscheius tipulae. O. tipulae is an alternative model organism to its relative, the widely used Caenorhabditis elegans, and is a good model to understand reproduction in insect parasitic nematodes of the genus Heterorhabditis. The native purified O. tipulae vitellogenin is composed of three polypeptides (VT1, VT2 and VT3), whereas in C. elegans, vitellogenin is composed of four polypeptides. The gene (Oti-vit-1) encoding yolk polypeptide VT1 has been recently identified in the genome of O. tipulae. Immunoblotting and N-terminal sequencing confirmed that VT1 is indeed coded by Oti-vit-1. Utilizing the same experimental approaches, we showed that the polypeptides VT2 and VT3 are derived from the proteolytic processing of the C- and N-terminal portions of the precursor OTI-VIT-6, respectively. We also showed that the recombinant polypeptide (P40), corresponding to the N-terminal sequence of OTI-VIT-6, preferentially interacts with a 100-kDa polypeptide found in adult worm extracts, as we have previously shown for the native vitellins of O. tipulae. Using the putative nematode vitellogenin amino acid sequences available in the UniProtKB database, we constructed a phylogenetic tree and showed that the O. tipulae vitellogenins characterized in this study are orthologous to those of the Caenorhabditis spp. Together, these results represent the first structural and functional comparative study of nematode yolk proteins outside the Caenorhabditis genus and provide insight into the evolution of these lipoproteins within the Nematode Phylum.
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Affiliation(s)
- Daniela P. Almenara
- Department of Parasitology, Institute of Biomedical Sciences – University of São Paulo, São Paulo, Brazil
| | - Joselene P. de Moura
- Department of Parasitology, Institute of Biomedical Sciences – University of São Paulo, São Paulo, Brazil
| | - Cristiane P. Scarabotto
- Department of Parasitology, Institute of Biomedical Sciences – University of São Paulo, São Paulo, Brazil
| | - Russolina B. Zingali
- Laboratory of Proteomics and Protein and Peptide Microsequencing, Institute of Medical Biochemistry - UFRJ/CCS/Bloco H, Cid. Universitária – Ilha do Fundão, Rio de Janeiro, Brazil
| | - Carlos E. Winter
- Department of Parasitology, Institute of Biomedical Sciences – University of São Paulo, São Paulo, Brazil
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Zadesenets KS, Katokhin AV, Mordvinov VA, Rubtsov NB. Telomeric DNA in chromosomes of five opisthorchid species. Parasitol Int 2011; 61:81-3. [PMID: 21708281 DOI: 10.1016/j.parint.2011.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/27/2011] [Revised: 06/07/2011] [Accepted: 06/11/2011] [Indexed: 12/21/2022]
Abstract
The analysis of telomere repeat distribution in chromosomes of five opisthorchid species (Opisthorchis felineus (Rivolta, 1884), Opisthorchis viverrini (Poirier, 1886), Metorchis xanthosomus (Creplin, 1846), Metorchis bilis (Braun, 1890), Clonorchis sinensis (Cobbold, 1875)) was performed with fluorescent in situ hybridization (FISH) of labeled (TTAGGG)n DNA-probe and PNA telomere probe on mitotic and meiotic chromosomes of these species. It was shown that chromosome telomeres of all studied species contain large clusters of (TTAGGG)n telomeric repeats. Interstitial clusters of the (TTAGGG)n repeats have not been revealed in the chromosomes of any studied species even when FISH of PNA telomere probe on pachytene chromosomes was performed. Furthermore interstitial clusters of the (TTAGGG)n repeats have not been detected in the chromosomes of O. viverrini, one of chromosomes of this species is the result of a fusion of two ancestral opisthorchid chromosomes.
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Affiliation(s)
- Kira S Zadesenets
- Institute of Cytology and Genetics Siberian Branch of RAS, Novosibirsk, Russia.
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Bombarová M, Vítková M, Špakulová M, Koubková B. Telomere analysis of platyhelminths and acanthocephalans by FISH and Southern hybridization. Genome 2009; 52:897-903. [DOI: 10.1139/g09-063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/22/2022]
Abstract
We examined the composition of telomeres in chromosomes of parasitic worms, representatives of the flatworm groups Monogenea and Cestoda (Platyhelminthes), and thorny-headed worms (Syndermata: Acanthocephala) by fluorescence in situ hybridization (FISH) with different telomeric repeat probes. Our results show that the (TTAGGG)n sequence, supposed to be the ancestral telomeric repeat motif of Metazoa, is conserved in Monogenea ( Paradiplozoon homoion ) and Cestoda ( Caryophyllaeus laticeps , Caryophyllaeides fennica , and Nippotaenia mogurndae ) but not in Acanthocephala ( Pomphorhynchus laevis and Pomphorhynchus tereticollis ). In the Pomphorhynchus species, no hybridization signals were obtained with the “nematode” (TTAGGC)n, “arthropod” (TTAGG)n, and bdelloid (TGTGGG)n telomeric probes using FISH with their chromosomes and Southern hybridization with P. laevis DNA. Therefore, we suggest that parasitic Acanthocephala have evolved yet unknown telomeric repeat motifs or different mechanisms of telomere maintenance.
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Affiliation(s)
- Marta Bombarová
- Parasitological Institute, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Biology Centre of the Academy of Sciences of the Czech Republic (BC ASCR), Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Magda Vítková
- Parasitological Institute, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Biology Centre of the Academy of Sciences of the Czech Republic (BC ASCR), Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Marta Špakulová
- Parasitological Institute, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Biology Centre of the Academy of Sciences of the Czech Republic (BC ASCR), Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Božena Koubková
- Parasitological Institute, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Biology Centre of the Academy of Sciences of the Czech Republic (BC ASCR), Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Akamine RN, Winter CE. Oscheius tipulae as an example of eEF1A gene diversity in nematodes. J Mol Evol 2008; 67:278-90. [PMID: 18696027 DOI: 10.1007/s00239-008-9147-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/21/2008] [Revised: 04/15/2008] [Accepted: 07/14/2008] [Indexed: 10/21/2022]
Abstract
We characterized four eEF1A genes in the alternative rhabditid nematode model organism Oscheius tipulae. This is twice the copy number of eEF1A genes in C. elegans, C. briggsae, and, probably, many other free-living and parasitic nematodes. The introns show features remarkably different from those of other metazoan eEF1A genes. Most of the introns in the eEF1A genes are specific to O. tipulae and are not shared with any of the other genes described in metazoans. Most of the introns are phase 0 (inserted between two codons), and few are inserted in protosplice sites (introns inserted between the nucleotide sequence A/CAG and G/A). Two of these phase 0 introns are conserved in sequence in two or more of the four eEF1A gene copies, and are inserted in the same position in the genes. Neither of these characteristics has been detected in any of the nematode eEF1A genes characterized to date. The coding sequences were also compared with other eEF1A cDNAs from 11 different nematodes to determine the variability of these genes within the phylum Nematoda. Parsimony and distance trees yielded similar topologies, which were similar to those created using other molecular markers. The presence of more than one copy of the eEF1A gene with nearly identical coding regions makes it difficult to define the orthologous cDNAs. As shown by our data on O. tipulae, careful and extensive examination of intron positions in the eEF1A gene across the phylum is necessary to define their potential for use as valid phylogenetic markers.
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Affiliation(s)
- Rubens N Akamine
- Departmento de Parasitologia, Instituto de Ciências Biomédicas/Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, 05508-900, Sao Paulo, SP, Brazil
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Baïlle D, Barrière A, Félix MA. Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans. Mol Ecol 2008; 17:1523-34. [PMID: 18284567 DOI: 10.1111/j.1365-294x.2008.03697.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/28/2022]
Abstract
The nematode Oscheius tipulae belongs to the same family (Rhabditidae) as the model species Caenorhabditis elegans. Both species reproduce through self-fertilizing hermaphrodites and facultative males. Recent studies have shown that the self-fertile C. elegans and C. briggsae displayed a 20-fold lower genetic diversity than the male-female species C. remanei. Several explanations have been put forward to account for this difference, including their mode of reproduction and dynamic population structure. Here, we present the results of extensive worldwide sampling of O. tipulae, which we previously used as a laboratory organism for developmental genetics. We found that O. tipulae is much more widespread and common in soil throughout the world than Caenorhabditis species. We analysed 63 O. tipulae isolates from several continents using amplified fragment length polymorphism (AFLP). We found that O. tipulae harbours a 5-fold higher genetic diversity than C. elegans and C. briggsae. As in C. elegans, a high proportion of this diversity was found locally. Yet, we detected significant geographical differentiation, both at the worldwide scale with a latitudinal structure and between three localities in France. In summary, O. tipulae exhibited significantly higher levels of genetic diversity and large-scale geographical structure than C. elegans, despite their shared mode of reproduction. This species difference in genetic diversity may be explained by a number of other differences, such as population size, distribution, migration and dynamics. Due to its widespread occurrence and relatively high genetic diversity, O. tipulae may be a promising study species for evolutionary studies.
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Affiliation(s)
- Dorothée Baïlle
- Institut Jacques Monod, CNRS-Universities of Paris 6 and 7, Tour 43, 2 place Jussieu, 75251 Paris cedex 05, France
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Traut W, Szczepanowski M, Vítková M, Opitz C, Marec F, Zrzavý J. The telomere repeat motif of basal Metazoa. Chromosome Res 2007; 15:371-82. [PMID: 17385051 DOI: 10.1007/s10577-007-1132-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 02/04/2007] [Revised: 02/13/2007] [Accepted: 02/13/2007] [Indexed: 11/29/2022]
Abstract
In most eukaryotes the telomeres consist of short DNA tandem repeats and associated proteins. Telomeric repeats are added to the chromosome ends by telomerase, a specialized reverse transcriptase. We examined telomerase activity and telomere repeat sequences in representatives of basal metazoan groups. Our results show that the 'vertebrate' telomere motif (TTAGGG)( n ) is present in all basal metazoan groups, i.e. sponges, Cnidaria, Ctenophora, and Placozoa, and also in the unicellular metazoan sister group, the Choanozoa. Thus it can be considered the ancestral telomere repeat motif of Metazoa. It has been conserved from the metazoan radiation in most animal phylogenetic lineages, and replaced by other motifs-according to our present knowledge-only in two major lineages, Arthropoda and Nematoda.
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Affiliation(s)
- Walther Traut
- Institut für Biologie, Zentrum für Medizinische Struktur- und Zellbiologie, Universität zu Lübeck, D-23538, Lübeck, Germany.
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