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| De Carvalho Augusto, Ronaldo; Rey, Oliver; Cosseau, Céline; Chaparro, Cristian; Vidal-dupiol, Jeremie; Allienne, Jean-françois; Duval, David; Pinaud, Silvain; Tönges, Sina; Andriantsoa, Ranja; Luquet, Emilien; Aubret, Fabien; Dia Sow, Mamadou; David, Patrice; Thomson, Vicki; Joly, Dominique; Gomes Lima, Mariana; Federico, Déborah; Danchin, Etienne; Minoda, Aki; Grunau, Christoph. |
| We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise. |
| Tipo: Text |
Palavras-chave: Epigenetics; Epigenomics; ATAC-seq; Daphnia pulex; Schistosoma mansoni. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00681/79353/81859.pdf |
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| De Lorgeril, Julien; Petton, Bruno; Lucasson, Aude; Perez, Valérie; Stenger, Pierre-louis; Degremont, Lionel; Montagnani, Caroline; Escoubas, Jean Michel; Haffner, Philippe; Allienne, Jean-françois; Leroy, Marc; Lagarde, Franck; Vidal Dupiol, Jeremie; Gueguen, Yannick; Mitta, Guillaume. |
| Background: As a major threat to the oyster industry, Pacific Oyster Mortality Syndrome (POMS) is a polymicrobial disease affecting the main oyster species farmed across the world. POMS affects oyster juveniles and became panzootic this last decade, but POMS resistance in some oyster genotypes has emerged. While we know some genetic loci associated with resistance, the underlying mechanisms remained uncharacterized. So, we developed a comparative transcriptomic approach using basal gene expression profiles between different oyster biparental families with contrasted phenotypes when confronted to POMS (resistant or susceptible). Results: We showed that POMS resistant oysters show differential expression of genes involved in stress responses, protein... |
| Tipo: Text |
Palavras-chave: Pacific oyster; Oyster disease; Resistance; OsHV-1; Antiviral molecular pathways; Invertebrate immunity. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00602/71369/69811.pdf |
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| Rey, Olivier; Toulza, Eve; Chaparro, Cristian; Allienne, Jean-françois; Kincaid-smith, Julien; Mathieu-begné, Eglantine; Allan, Fiona; Rollinson, David; Webster, Bonnie L.; Boissier, Jérôme. |
| Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here, we conducted a genomic comparative study and investigated the genomic relationships between S. haematobium, S. bovis and their hybrids using 19 isolates originating from a wide geographical range over Africa, including samples... |
| Tipo: Text |
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| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00678/79020/81421.pdf |
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| Oleaga, Ana; Rey, Olivier; Polack, Bruno; Grech-angelini, Sébastien; Quilichini, Yann; Pérez-sánchez, Ricardo; Boireau, Pascal; Mulero, Stephen; Brunet, Aimé; Rogon, Anne; Vallée, Isabelle; Kincaid-smith, Julien; Allienne, Jean-françois; Boissier, Jérôme. |
| Environmental and anthropogenic changes are expected to promote emergence and spread of pathogens worldwide. Since 2013, human urogenital schistosomiasis is established in Corsica island (France). Schistosomiasis is a parasitic disease affecting both humans and animals. The parasite involved in the Corsican outbreak is a hybrid form between Schistosoma haematobium, a human parasite, and Schistosoma bovis, a livestock parasite. S. bovis has been detected in Corsican livestock few decades ago raising the questions whether hybridization occurred in Corsica and if animals could behave as a reservoir for the recently established parasite lineage. The latter hypothesis has huge epidemiological outcomes since the emergence of a zoonotic lineage of schistosomes... |
| Tipo: Text |
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| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00504/61566/65491.pdf |
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| Kebede, Tadesse; Bech, Nicolas; Allienne, Jean-françois; Olivier, Rey; Erko, Berhanu; Boissier, Jerome. |
| Background Schistosomiasis is a chronic parasitic disease, that affects over 207 million people and causes over 200,000 deaths annually, mainly in sub-Saharan Africa. Although many health measures have been carried out to limit parasite transmission, significant numbers of non-human primates such as Chlorocebus aethiops (Ch. aethiops) (vervet) and Papio anubis (baboon) are infected with S. mansoni, notably in Ethiopia, where they are expected to have potentially significant implications for transmission and control efforts. Objective The objective of this study was to assess and compare the genetic diversity and population structure of S. mansoni isolates from human and non-human primates free-ranging in close proximity to villages in selected endemic... |
| Tipo: Text |
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| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00653/76484/77558.pdf |
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| Mulero, Stephen; Toulza, Eve; Loisier, Anaïs; Zimmerman, Meryl; Allienne, Jean-françois; Foata, Joséphine; Quilichini, Yann; Pointier, Jean-pierre; Rey, Olivier; Boissier, Jérôme. |
| To assess the effect of anthropogenic activities on ecosystems, it is of prime importance to develop new tools enabling a rapid characterization of ecological communities. Freshwater ecosystems are particularly impacted and threatened by human activities and need thorough attention to preserve their biodiversity and the ecological services they provide. Studying such ecosystems is generally difficult because the associated organisms are hard to sample and to monitor. We present a ready-to-use environmental metabarcoding protocol to characterize and monitor the freshwater gastropods communities from water samples. The efficiency of this new tool was compared to a classical malacological survey at 19 sampled sites from 10 distinct rivers distributed over... |
| Tipo: Text |
Palavras-chave: Biomonitoring; Corsica; Environmental DNA; Malacology; Metabarcoding; Snail communities. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00666/77777/79917.docx |
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