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Passer AR, Clancey SA, Shea T, David-Palma M, Averette AF, Boekhout T, Porcel BM, Nowrousian M, Cuomo CA, Sun S, Heitman J, Coelho MA. Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex. eLife 2022; 11:79114. [PMID: 35713948 PMCID: PMC9296135 DOI: 10.7554/elife.79114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
<title>eLife digest</title>. Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population. Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease. With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility. Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile. Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species. This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.
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Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Terrance Shea
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity InstituteUtrechtNetherlands,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of AmsterdamAmsterdamNetherlands
| | - Betina M Porcel
- Génomique Métabolique, CNRS, University Evry, Université Paris-SaclayEvryFrance
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität BochumBochumGermany
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, Guillou L. Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 2021; 19:209. [PMID: 34551781 PMCID: PMC8459563 DOI: 10.1186/s12915-021-01144-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.,School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Phuong Le
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum national d'Histoire naturelle, CNRS, CP 52, 57 rue Cuvier, 75005, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, UMR 8227, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Jonathan Mercier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tsinda Rukwavu
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France.,Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Pierre Rouzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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3
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, Guillou L. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 2021; 19:1. [PMID: 33407428 PMCID: PMC7789003 DOI: 10.1186/s12915-020-00927-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. RESULTS We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. CONCLUSION These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
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Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Phuong Le
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum national d'Histoire naturelle, CNRS, CP 52, 57 rue Cuvier, 75005, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, UMR 8227, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Jonathan Mercier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tsinda Rukwavu
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Pierre Rouzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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4
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Kayal E, Alves-de-Souza C, Farhat S, Velo-Suarez L, Monjol J, Szymczak J, Bigeard E, Marie D, Noel B, Porcel BM, Corre E, Six C, Guillou L. Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection. Front Microbiol 2020; 11:600823. [PMID: 33424803 PMCID: PMC7793755 DOI: 10.3389/fmicb.2020.600823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya. We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.
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Affiliation(s)
- Ehsan Kayal
- Fédération de Recherche 2424 Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, Roscoff, France
| | - Catharina Alves-de-Souza
- Algal Resources Collection, Center for Marine Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Sarah Farhat
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Lourdes Velo-Suarez
- UMR 1078, Genetics, Functional Genomics and Biotechnology, INSERM. UFR Médecine, Brest, France
| | - Joanne Monjol
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Jeremy Szymczak
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Estelle Bigeard
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Dominique Marie
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Betina M Porcel
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Erwan Corre
- Fédération de Recherche 2424 Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, Roscoff, France
| | - Christophe Six
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
| | - Laure Guillou
- UMR 7144 Sorbonne Université & Centre National pour la Recherche Scientifique, «Adaptation and Diversity in Marine Environment», Team «Ecology of Marine Plankton, ECOMAP», Station Biologique de Roscoff, Roscoff, France
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5
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Cai R, Kayal E, Alves-de-Souza C, Bigeard E, Corre E, Jeanthon C, Marie D, Porcel BM, Siano R, Szymczak J, Wolf M, Guillou L. Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach. Sci Rep 2020; 10:2531. [PMID: 32054950 PMCID: PMC7018713 DOI: 10.1038/s41598-020-59524-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/27/2020] [Indexed: 12/02/2022] Open
Abstract
As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow to intermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton.
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Affiliation(s)
- Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424 ABIMS, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, US
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424 ABIMS, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Christian Jeanthon
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University Evry, Université Paris-Saclay, 91057, Evry, France
| | - Raffaele Siano
- Ifremer-Centre de Bretagne, Département/Unité/Laboratoire ODE/DYNECO/Pelagos, Z.I. Technopôle Brest-Iroise, Pointe du Diable BP70, 29280, Plouzané, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Sci Adv 2019; 5:eaav1110. [PMID: 31032404 PMCID: PMC6482013 DOI: 10.1126/sciadv.aav1110] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/07/2019] [Indexed: 05/30/2023]
Abstract
Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.
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Affiliation(s)
- Uwe John
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Yameng Lu
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sylke Wohlrab
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gurjeet S. Kohli
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Felix C. Mark
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Sarah Farhat
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Marius Felder
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Stephan Frickenhaus
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Hochschule Bremerhaven, Bremerhaven, Germany
| | - Laure Guillou
- CNRS, UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 6, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
| | - Patrick J. Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Betina M. Porcel
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Klaus Valentin
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gernot Glöckner
- Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
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Farhat S, Florent I, Noel B, Kayal E, Da Silva C, Bigeard E, Alberti A, Labadie K, Corre E, Aury JM, Rombauts S, Wincker P, Guillou L, Porcel BM. Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains. Front Microbiol 2018; 9:2251. [PMID: 30333799 PMCID: PMC6176090 DOI: 10.3389/fmicb.2018.02251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/04/2018] [Indexed: 01/31/2023] Open
Abstract
Understanding factors that generate, maintain, and constrain host-parasite associations is of major interest to biologists. Although little studied, many extremely virulent micro-eukaryotic parasites infecting microalgae have been reported in the marine plankton. This is the case for Amoebophrya, a diverse and highly widespread group of Syndiniales infecting and potentially controlling dinoflagellate populations. Here, we analyzed the time-scale gene expression of a complete infection cycle of two Amoebophrya strains infecting the same host (the dinoflagellate Scrippsiella acuminata), but diverging by their host range (one infecting a single host, the other infecting more than one species). Over two-thirds of genes showed two-fold differences in expression between at least two sampled stages of the Amoebophrya life cycle. Genes related to carbohydrate metabolism as well as signaling pathways involving proteases and transporters were overexpressed during the free-living stage of the parasitoid. Once inside the host, all genes related to transcription and translation pathways were actively expressed, suggesting the rapid and extensive protein translation needed following host-cell invasion. Finally, genes related to cellular division and components of the flagellum organization were overexpressed during the sporont stage. In order to gain a deeper understanding of the biological basis of the host-parasitoid interaction, we screened proteins involved in host-cell recognition, invasion, and protection against host-defense identified in model apicomplexan parasites. Very few of the genes encoding critical components of the parasitic lifestyle of apicomplexans could be unambiguously identified as highly expressed in Amoebophrya. Genes related to the oxidative stress response were identified as highly expressed in both parasitoid strains. Among them, the correlated expression of superoxide dismutase/ascorbate peroxidase in the specialist parasite was consistent with previous studies on Perkinsus marinus defense. However, this defense process could not be identified in the generalist Amoebophrya strain, suggesting the establishment of different strategies for parasite protection related to host specificity.
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Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
| | - Isabelle Florent
- Communication Molecules and Adaptation of Microorganisms, National Museum of Natural History, CNRS, Paris, France
| | - Benjamin Noel
- Genoscope, Institut François Jacob, CEA, Evry, France
| | - Ehsan Kayal
- Sorbonne Universités, Université Pierre et Marie Curie-Paris 6, CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | | | - Estelle Bigeard
- Sorbonne Universités, Université Pierre et Marie Curie-Paris 6, CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | | | | | - Erwan Corre
- Sorbonne Universités, Université Pierre et Marie Curie-Paris 6, CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | | | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
| | - Laure Guillou
- Sorbonne Universités, Université Pierre et Marie Curie-Paris 6, CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
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8
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Porcel BM, Denoeud F, Opperdoes F, Noel B, Madoui MA, Hammarton TC, Field MC, Da Silva C, Couloux A, Poulain J, Katinka M, Jabbari K, Aury JM, Campbell DA, Cintron R, Dickens NJ, Docampo R, Sturm NR, Koumandou VL, Fabre S, Flegontov P, Lukeš J, Michaeli S, Mottram JC, Szöőr B, Zilberstein D, Bringaud F, Wincker P, Dollet M. The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants. PLoS Genet 2014; 10:e1004007. [PMID: 24516393 PMCID: PMC3916237 DOI: 10.1371/journal.pgen.1004007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease. Some plant trypanosomes, single-celled organisms living in phloem sap, are responsible for important palm diseases, inducing frequent expensive and toxic insecticide treatments against their insect vectors. Other trypanosomes multiply in latex tubes without detriment to their host. Despite the wide range of behaviors and impacts, these trypanosomes have been rather unceremoniously lumped into a single genus: Phytomonas. A battery of molecular probes has been used for their characterization but no clear phylogeny or classification has been established. We have sequenced the genomes of a pathogenic phloem-specific Phytomonas from a diseased South American coconut palm and a latex-specific isolate collected from an apparently healthy wild euphorb in the south of France. Upon comparison with each other and with human pathogenic trypanosomes, both Phytomonas revealed distinctive compact genomes, consisting essentially of single-copy genes, with the vast majority of genes shared by both isolates irrespective of their effect on the host. A strong cohort of enzymes in the sugar metabolism pathways was consistent with the nutritional environments found in plants. The genetic nuances may reveal the basis for the behavioral differences between these two unique plant parasites, and indicate the direction of our future studies in search of effective treatment of the crop disease parasites.
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Affiliation(s)
- Betina M. Porcel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
- * E-mail: (BMP); (MD)
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
| | - Fred Opperdoes
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Mohammed-Amine Madoui
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Tansy C. Hammarton
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mark C. Field
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Michael Katinka
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Kamel Jabbari
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - David A. Campbell
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Roxana Cintron
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Nicholas J. Dickens
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Nancy R. Sturm
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, United States of America
| | | | - Sandrine Fabre
- CIRAD, TA A-98/F, Campus International de Baillarguet, Montpellier, France
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Shulamit Michaeli
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jeremy C. Mottram
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Balázs Szöőr
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Dan Zilberstein
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques, Université Bordeaux Segalen, CNRS UMR-5536, Bordeaux, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Université d'Evry, UMR 8030, Evry, France
- Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, France
| | - Michel Dollet
- CIRAD, TA A-98/F, Campus International de Baillarguet, Montpellier, France
- * E-mail: (BMP); (MD)
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Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 2010; 330:1381-5. [PMID: 21097902 DOI: 10.1126/science.1194167] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.
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Affiliation(s)
- France Denoeud
- Commissariat à l'Énergie Atomique, Institut de Génomique, Genoscope, Evry, France
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10
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Maheswari U, Jabbari K, Petit JL, Porcel BM, Allen AE, Cadoret JP, De Martino A, Heijde M, Kaas R, La Roche J, Lopez PJ, Martin-Jézéquel V, Meichenin A, Mock T, Schnitzler Parker M, Vardi A, Armbrust EV, Weissenbach J, Katinka M, Bowler C. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biol 2010; 11:R85. [PMID: 20738856 PMCID: PMC2945787 DOI: 10.1186/gb-2010-11-8-r85] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 05/11/2010] [Accepted: 08/25/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. RESULTS We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. CONCLUSIONS The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.
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Affiliation(s)
- Uma Maheswari
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- Current address: EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kamel Jabbari
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Jean-Louis Petit
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Betina M Porcel
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Andrew E Allen
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- Current address: J Craig Venter Institute, 11149 N. Torrey Pines Rd, Suite 220, La Jolla, CA 92037, USA
| | - Jean-Paul Cadoret
- Physiologie et Biotechnologie des Algues, IFREMER, BP 21105, 44311 Nantes, France
| | - Alessandra De Martino
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Marc Heijde
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Raymond Kaas
- Physiologie et Biotechnologie des Algues, IFREMER, BP 21105, 44311 Nantes, France
| | - Julie La Roche
- Marine Biogeochemistry, IFM-GEOMAR Leibniz-Institut für Meereswissenschaften, Düsternbrooker Weg 20, D-24105 Kiel, Germany
| | - Pascal J Lopez
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Véronique Martin-Jézéquel
- Université de Nantes, EA 2160, Laboratoire 'Mer, Molécule, Santé', Faculté des Sciences et Techniques, 2 rue de la Houssinière, 44322, BP 92208, 44322 Nantes Cedex 3, France
| | - Agnès Meichenin
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Thomas Mock
- School of Oceanography, University of Washington, 616 NE Northlake Place, Seattle, WA 98105, USA
- University of East Anglia, School of Environmental Sciences, Norwich Research Park, Norwich NR4 7TJ, UK
| | | | - Assaf Vardi
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - E Virginia Armbrust
- School of Oceanography, University of Washington, 616 NE Northlake Place, Seattle, WA 98105, USA
| | - Jean Weissenbach
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Michaël Katinka
- CEA - Institut de Génomique, Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197 INSERM U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
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Florent I, Porcel BM, Guillaume E, Da Silva C, Artiguenave F, Maréchal E, Bréhélin L, Gascuel O, Charneau S, Wincker P, Grellier P. A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism. BMC Genomics 2009; 10:235. [PMID: 19454033 PMCID: PMC2695484 DOI: 10.1186/1471-2164-10-235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 05/19/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and functional assessments of P. falciparum genes and expression, and polymorphic data are further necessary to exploit genomic information to further qualify therapeutic target candidates. Here, we undertook a large scale analysis of a P. falciparum FcB1-schizont-EST library previously constructed by suppression subtractive hybridization (SSH) to study genes expressed during merozoite morphogenesis, with the aim of: 1) obtaining an exhaustive collection of schizont specific ESTs, 2) experimentally validating or correcting P. falciparum gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains. RESULTS A total of 22,125 clones randomly picked from the SSH library were sequenced, yielding 21,805 usable ESTs that were then clustered on the P. falciparum genome. This allowed identification of 243 protein coding genes, including 121 previously annotated as hypothetical. Statistical analysis of GO terms, when available, indicated significant enrichment in genes involved in "entry into host-cells" and "actin cytoskeleton". Although most ESTs do not span full-length gene reading frames, detailed sequence comparison of FcB1-ESTs versus 3D7 genomic sequences allowed the confirmation of exon/intron boundaries in 29 genes, the detection of new boundaries in 14 genes and identification of protein polymorphism for 21 genes. In addition, a large number of non-protein coding ESTs were identified, mainly matching with the two A-type rRNA units (on chromosomes 5 and 7) and to a lower extent, two atypical rRNA loci (on chromosomes 1 and 8), TARE subtelomeric regions (several chromosomes) and the recently described telomerase RNA gene (chromosome 9). CONCLUSION This FcB1-schizont-EST analysis confirmed the actual expression of 243 protein coding genes, allowing the correction of structural annotations for a quarter of these sequences. In addition, this analysis demonstrated the actual transcription of several remarkable non-protein coding loci: 2 atypical rRNA, TARE region and telomerase RNA gene. Together with other collections of P. falciparum ESTs, usually generated from mixed parasite stages, this collection of FcB1-schizont-ESTs provides valuable data to gain further insight into the P. falciparum gene structure, polymorphism and expression.
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Affiliation(s)
- Isabelle Florent
- FRE3206 CNRS/MNHN, USM504, Biologie Fonctionnelle des Protozoaires, RDDM, Muséum National d'Histoire Naturelle, Paris, France.
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Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Ségurens B, Poulain J, Anthouard V, Grossetete S, Khalili H, Coppin E, Déquard-Chablat M, Picard M, Contamine V, Arnaise S, Bourdais A, Berteaux-Lecellier V, Gautheret D, de Vries RP, Battaglia E, Coutinho PM, Danchin EG, Henrissat B, Khoury RE, Sainsard-Chanet A, Boivin A, Pinan-Lucarré B, Sellem CH, Debuchy R, Wincker P, Weissenbach J, Silar P. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol 2008; 9:R77. [PMID: 18460219 PMCID: PMC2441463 DOI: 10.1186/gb-2008-9-5-r77] [Citation(s) in RCA: 233] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 02/12/2008] [Accepted: 05/06/2008] [Indexed: 12/13/2022] Open
Abstract
A 10X draft sequence of Podospora anserina genome shows highly dynamic evolution since its divergence from Neurospora crassa. Background The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. Results We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown. Conclusion The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.
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Affiliation(s)
- Eric Espagne
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay cedex, France
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Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Ségurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Câmara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouël A, Lepère G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Bétermier M, Weissenbach J, Scarpelli C, Schächter V, Sperling L, Meyer E, Cohen J, Wincker P. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 2006; 444:171-8. [PMID: 17086204 DOI: 10.1038/nature05230] [Citation(s) in RCA: 597] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 08/31/2006] [Indexed: 02/03/2023]
Abstract
The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.
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Affiliation(s)
- Jean-Marc Aury
- Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France
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Porcel BM, Delfour O, Castelli V, De Berardinis V, Friedlander L, Cruaud C, Ureta-Vidal A, Scarpelli C, Wincker P, Schächter V, Saurin W, Gyapay G, Salanoubat M, Weissenbach J. Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection. Genome Res 2004; 14:463-71. [PMID: 14962985 PMCID: PMC353234 DOI: 10.1101/gr.1481104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A collection of 90,000 human cDNA clones generated to increase the fraction of "full-length" cDNAs available was analyzed by sequence alignment on the human genome assembly. Five hundred fifty-two gene models not found in LocusLink, with coding regions of at least 300 bp, were defined by using this collection. Exon composition proposed for novel genes showed an average of 4.7 exons per gene. In 20% of the cases, at least half of the exons predicted for new genes coincided with evolutionary conserved regions defined by sequence comparisons with the pufferfish Tetraodon nigroviridis. Among this subset, CpG islands were observed at the 5' end of 75%. In-frame stop codons upstream of the initiator ATG were present in 49% of the new genes, and 16% contained a coding region comprising at least 50% of the cDNA sequence. This cDNA resource also provided candidate small protein-coding genes, usually not included in genome annotations. In addition, analysis of a sample from this cDNA collection indicates that approximately 380 gene models described in LocusLink could be extended at their 5' end by at least one new exon. Finally, this cDNA resource provided an experimental support for annotations based exclusively on predictions, thus representing a resource substantially improving the human genome annotation.
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Affiliation(s)
- Betina M Porcel
- Genoscope-Centre National de Séquençage and CNRS UMR-8030, 91000 Evry, France
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Porcel BM, Tran AN, Tammi M, Nyarady Z, Rydâker M, Urmenyi TP, Rondinelli E, Pettersson U, Andersson B, Aslund L. Gene survey of the pathogenic protozoan Trypanosoma cruzi. Genome Res 2000; 10:1103-7. [PMID: 10958628 PMCID: PMC310907 DOI: 10.1101/gr.10.8.1103] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/1999] [Accepted: 06/01/2000] [Indexed: 11/24/2022]
Abstract
We have performed a survey of the active genes in the important human pathogen Trypanosoma cruzi by analyzing 5013 expressed sequence tags (ESTs) generated from a normalized epimastigote cDNA library. Clustering of all sequences resulted in 771 clusters, comprising 54% of the ESTs. In total, the ESTs corresponded to 3054 transcripts that might represent one-fourth of the total gene repertoire in T. cruzi. About 33% of the T. cruzi transcripts showed similarity to sequences in the public databases, and a large number of hitherto undiscovered genes predicted to be involved in transcription, cell cycle control, cell division, signal transduction, secretion, and metabolism were identified. More than 140 full-length gene sequences were derived from the ESTs. Comparisons with all open reading frames in yeast and in Caenorhabditis elegans showed that only 12% of the T. cruzi transcripts were shared among diverse eukaryotic organisms. Comparison with other kinetoplastid sequences identified 237 orthologous genes that are shared between these evolutionarily divergent organisms. The generated data are a useful resource for further studies of the biology of the parasite and for development of new means to combat Chagas' disease.
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Affiliation(s)
- B M Porcel
- Department of Genetics & Pathology, Section of Medical Genetics, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
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Porcel BM, Aslund L, Pettersson U, Andersson B. Trypanosoma cruzi: a putative vacuolar ATP synthase subunit and a CAAX prenyl protease-encoding gene, as examples of gene identification in genome projects. Exp Parasitol 2000; 95:176-86. [PMID: 10964645 DOI: 10.1006/expr.2000.4529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An international genome program has been initiated to increase the knowledge about the Trypanosoma cruzi genome and thereby find effective tools to treat Chagas' disease. We here report the molecular characterization of two novel genes found in the course of this project. Two of the open reading frames (ORF) identified in the sequencing of the third smallest chromosome of the CL Brener strain of T. cruzi were selected for further molecular characterization due to their similarity to genes with interesting functions in other organisms and their potential as targets to combat the parasite. The first ORF (402 bp) showed homology to a 14-kDa vacuolar ATP synthase subunit F from a variety of organisms, such as yeast, rat, bovine, human, and a number of prokaryotes. The second ORF (1188 bp) resembled a CAAX prenyl protease-encoding gene, identified in different organisms, including Homo sapiens, Saccharomyces cerevisiae, and Arabidopsis thaliana, as well as several prokaryotes. RT-PCR from T. cruzi total epimastigote RNA allowed us to isolate the complete transcripts of these genes. Furthermore, screening of an available normalized cDNA library derived from the same stage of the parasite confirmed that both genes are expressed at least in the epimastigote stage of T. cruzi. Comparison of the putative T. cruzi proteins to their counterparts in other organisms revealed significant protein sequence conservation over large evolutionary distances. Computer analysis revealed the presence of several motifs in both proteins, possibly related to the regulation and localization of these proteins in the parasite.
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Affiliation(s)
- B M Porcel
- Department of Genetics and Pathology, Section of Medical Genetics, Rudbeck Laboratory, Uppsala, SE-751 85, Sweden
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Sosa Estani S, Segura EL, Ruiz AM, Velazquez E, Porcel BM, Yampotis C. Efficacy of chemotherapy with benznidazole in children in the indeterminate phase of Chagas' disease. Am J Trop Med Hyg 1998; 59:526-9. [PMID: 9790423 DOI: 10.4269/ajtmh.1998.59.526] [Citation(s) in RCA: 254] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A double-blind, randomized, clinical field trial was designed to test the efficacy and tolerance of a specific drug treatment in children in the indeterminate phase of infection by Trypanosoma cruzi. Children were treated with benznidazole at a dose of 5 mg/kg/day for 60 days or placebo and followed-up for 48 months. The treated children showed a significant decrease in geometric mean titers of antibodies against T. cruzi measured by indirect hemagglutination, indirect immunofluorescence, and ELISA. After a four year follow-up, 62% of the benznidazole-treated children and no placebo-treated child were seronegative for T. cruzi when tested by an ELISA using a T. cruzi flagellar calcium-binding protein (F29). Xenodiagnosis carried out after 48 months of follow-up was positive in 4.7% of the benznidazole-treated children and in 51.2% of the placebo-treated children. These results show the tolerance to and efficacy of benznidazole against T. cruzi in seropositive children six to 12 years of age. We used an early serologic marker of cure after treatment, consisting of a recombinant antigen implemented in a rapid, conventional serologic procedure.
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Affiliation(s)
- S Sosa Estani
- Centro Nacional de Diagnóstico e Investigación de Endemo-Epidemias/Administración Nacional de Laboratorios e Institutos de Salud, Dr. Carlos G. Malbrán, Buenos Aires, Argentina
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Silber AM, Búa J, Porcel BM, Segura EL, Ruiz AM. Trypanosoma cruzi: specific detection of parasites by PCR in infected humans and vectors using a set of primers (BP1/BP2) targeted to a nuclear DNA sequence. Exp Parasitol 1997; 85:225-32. [PMID: 9085919 DOI: 10.1006/expr.1996.4141] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the present work we evaluate Trypanosoma cruzi DNA detection by PCR using the nuclear oligonucleotides BP1/BP2 as primers. These primers are targeted to the 5' and 3' ends of the coding region for the flagellar protein F29. An amplification product of BP1/BP2 is a DNA band 692 bp long. Titration assays were performed to evaluate the minimum amount of parasite DNA that can be detected by this assay, resulting in 10 fg (equivalent to about 1/20 of the genome). The assay was also performed using T. cruzi DNA from different strains, clones, and human-derived isolates obtaining, in all cases, amplification products. No DNA amplification was observed when the PCR was performed using DNA from Leishmania braziliensis, but when T. rangeli DNA was used, a 615-bp-long fragment was amplified. Under appropriate gel conditions T. cruzi and T. rangeli DNA amplicons could be differentiated. When both conventional xenodiagnosis and PCR detection of parasite DNA in the feces of insect vectors fed with blood from infected patients were compared, 10 of 20 samples were positive by both techniques. However, 2 other samples with positive serology were also positive by PCR. When PCR was performed on blood samples from infected and uninfected individuals, 62 of 65 serologically positive human samples amplified the BP1/BP2 692-bp T. cruzi DNA fragment (sensitivity >95%). The 3 negative samples were positive when Southern blot hybridization was performed using the radiolabeled PCR amplification product as probe (sensitivity 100%).
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Affiliation(s)
- A M Silber
- Instituto Nacional de Chagas Dr. Mario Fatala Chaben, Ministerio de Salud y Accion Social, Buenos Aires, Argentina
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Porcel BM, Bontempi EJ, Henriksson J, Rydåker M, Aslund L, Segura EL, Pettersson U, Ruiz AM. Trypanosoma rangeli and Trypanosoma cruzi: molecular characterization of genes encoding putative calcium-binding proteins, highly conserved in trypanosomatids. Exp Parasitol 1996; 84:387-99. [PMID: 8948328 DOI: 10.1006/expr.1996.0127] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genes encoding a 29-kDa flagellar calcium-binding protein (F29) in Trypanosoma cruzi, strongly homologous to EF-hand calcium-binding protein-encoding genes previously reported in this parasite, were isolated by immunoscreening. F29 is encoded by a number of very similar genes, highly conserved among different T. cruzi isolates. The genes are located on a pair of homologous chromosomes, arranged in one or two clusters of tandem repeats. PCR amplification of Trypanosoma rangeli genomic DNA, using primers derived from the T. cruzi F29 sequence made it possible to isolate the homologous gene in T. rangeli, encoding a 23-kDa protein called TrCaBP. Gene sequence comparisons showed homology to EF-hand calcium-binding proteins from T. cruzi (82.8%), Trypanosoma brucei brucei (60.2%), and Entamoeba histolytica (28.4%). Northern blot analysis revealed that the TrCaBP gene is expressed in T. rangeli as a polyadenylated transcript. The TrCaBP-encoding genes are present in at least 20 copies per cell, organized in tandem arrays, on large T. rangeli chromosomes in some isolates and on two smaller ones in others. This gene, however, seems to be absent from Leishmania.
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Affiliation(s)
- B M Porcel
- Instituto Nacional de Chagas, Ministerio de Salud y Acción Social, Buenos Aires, Argentina
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Bontempi EJ, Porcel BM, Henriksson J, Carlsson L, Rydåker M, Segura EL, Ruiz AM, Pettersson U. Genes for histone H3 in Trypanosoma cruzi. Mol Biochem Parasitol 1994; 66:147-51. [PMID: 7984178 DOI: 10.1016/0166-6851(94)90046-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- E J Bontempi
- Instituto Nacional de Diagnóstico e Investigación de la Enfermedad de Chagas, Buenos Aires, Argentina
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