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Article ; Online: Imputed genomes of historical horses provide insights into modern breeding

Evelyn T. Todd / Aurore Fromentier / Richard Sutcliffe / Yvette Running Horse Collin / Aude Perdereau / Jean-Marc Aury / Camille Èche / Olivier Bouchez / Cécile Donnadieu / Patrick Wincker / Ted Kalbfleisch / Jessica L. Petersen / Ludovic Orlando

iScience, Vol 26, Iss 7, Pp 107104- (2023)

2023

Abstract: Summary: Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, ... ...

Abstract	Summary: Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski’s horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski’s horse following a century of captive breeding.
Keywords	Equine genetics ; Genomics ; Phylogenetics ; Science ; Q
Subject code	630
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae)

Van de Paer, Céline / Olivier Bouchez / Guillaume Besnard

Molecular ecology resources. 2018 May, v. 18, no. 3

2018

Abstract: The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic ... ...

Abstract	The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high‐throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid‐derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.
Keywords	Chionanthus ; case studies ; chimerism ; chloroplast genome ; cytoplasmic male sterility ; metagenomics ; mitochondria ; mitochondrial DNA ; mitochondrial genes ; mitochondrial genome ; mitogenomics ; olives ; phylogeny ; phylogeography ; topology ; Mediterranean region
Language	English
Dates of publication	2018-05
Size	p. 407-423.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.12742
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands

Madeleine Bossaert / Angélique Pipier / Jean-Francois Riou / Céline Noirot / Linh-Trang Nguyên / Remy-Felix Serre / Olivier Bouchez / Eric Defrancq / Patrick Calsou / Sébastien Britton / Dennis Gomez

eLife, Vol

2021 Volume 10

Abstract: G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double- ... ...

Abstract	G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double-strand breaks. Through the use of an unbiased genetic approach, we identify here topoisomerase 2α (TOP2A) as a major effector of cytotoxicity induced by two clastogenic G4 ligands, pyridostatin and CX-5461, the latter molecule currently undergoing phase I/II clinical trials in oncology. We show that both TOP2 activity and transcription account for DNA break production following G4 ligand treatments. In contrast, clastogenic activity of these G4 ligands is countered by topoisomerase 1 (TOP1), which limits co-transcriptional G4 formation, and by factors promoting transcriptional elongation. Altogether our results support that clastogenic G4 ligands act as DNA structure-driven TOP2 poisons at transcribed regions bearing G4 structures.
Keywords	G-quadruplex ; CX-5461 ; topoisomerase 2 ; DNA breaks ; transcription ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A secreted WY-domain-containing protein present in European isolates of the oomycete Plasmopara viticola induces cell death in grapevine and tobacco species.

Maud Combier / Edouard Evangelisti / Marie-Christine Piron / David Rengel / Ludovic Legrand / Liron Shenhav / Olivier Bouchez / Sebastian Schornack / Pere Mestre

PLoS ONE, Vol 14, Iss 7, p e

2019 Volume 0220184

Abstract: Plasmopara viticola is a biotrophic oomycete pathogen causing grapevine downy mildew. We characterized the repertoire of P. viticola effector proteins which may be translocated into plants to support the disease. We found several secreted proteins that ... ...

Abstract	Plasmopara viticola is a biotrophic oomycete pathogen causing grapevine downy mildew. We characterized the repertoire of P. viticola effector proteins which may be translocated into plants to support the disease. We found several secreted proteins that contain canonical dEER motifs and conserved WY-domains but lack the characteristic RXLR motif reported previously from oomycete effectors. We cloned four candidates and showed that one of them, Pv33, induces plant cell death in grapevine and Nicotiana species. This activity is dependent on the nuclear localization of the protein. Sequence similar effectors were present in seven European, but in none of the tested American isolates. Together our work contributes a new type of conserved P. viticola effector candidates.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines

Amaury Payelleville / Ludovic Legrand / Jean-Claude Ogier / Céline Roques / Alain Roulet / Olivier Bouchez / Annabelle Mouammine / Alain Givaudan / Julien Brillard

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 14

Abstract: Abstract DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been ... ...

Abstract	Abstract DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (>94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium’s lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2018-08-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Early Introduction of Solid Feeds

Charlotte Paës / Thierry Gidenne / Karine Bébin / Joël Duperray / Charly Gohier / Emeline Guené-Grand / Gwénaël Rebours / Olivier Bouchez / Céline Barilly / Patrick Aymard / Sylvie Combes

Frontiers in Veterinary Science, Vol

Ingestion Level Matters More Than Prebiotic Supplementation for Shaping Gut Microbiota

2020 Volume 7

Abstract: Early introduction of a nutritional substrate is a promising biomimetic strategy for controlling the implantation of the microbiota and preserving the health of young animals. In this study, we provided experimental solid substrate in a gel form to ... ...

Abstract	Early introduction of a nutritional substrate is a promising biomimetic strategy for controlling the implantation of the microbiota and preserving the health of young animals. In this study, we provided experimental solid substrate in a gel form to stimulate suckling rabbits' intake and to investigate its effects on microbiota implantation and colonization. All the rabbits had access to solid feed outside the nest as of 15 days of age. Except for the control group, rabbits were offered starter feed gels inside the nests from 3 to 18 days of age. These gels were either free of additives (AF_GEL) or contained 4% of fructo-oligosaccharides (FOS_GEL) or 4% of mannan-oligosaccharides and β-glucans mixtures (MOS_GEL). The cecal content of 160 rabbits was sampled at 18, 29, 38, and 57 days of age and analyzed using 16S rRNA gene sequencing. Pups consumed an average of 3.95 ± 1.07 g of starter feed gel with a higher intake when it was supplemented with fructo-oligosaccharides (+1.2 g; P < 0.05). Starter feed gel consumption increased the ensuing intake of pellets (+17 g from 15 to 21 days; P < 0.05). Alpha-diversity indexes were similar between groups and prebiotic supplementation did not induce a clear shift in microbiota pattern. Conversely, when considering rabbits that consumed more starter feed, the highest proportions of bacteria with plant-degrading abilities, such as species from the Lachnospiraceae and Ruminococcaceae families, were observed at 18 days of age. However, fermentative activities were not affected by starter feed intake at 29, 38, and 57 days of age. By providing comprehensive results on the regulation of microbial community structure at the onset of solid feed intake, this research paves the way for further studies on digestive ecosystem maturation.
Keywords	early life ; rabbit ; microbiome ; weaning ; gel starter diet ; oligosaccharide ; Veterinary medicine ; SF600-1100
Subject code	630
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola)

Ngan Thi Phan / Julie Orjuela / Etienne G. J. Danchin / Christophe Klopp / Laetitia Perfus‐Barbeoch / Djampa K. Kozlowski / Georgios D. Koutsovoulos / Céline Lopez‐Roques / Olivier Bouchez / Margot Zahm / Guillaume Besnard / Stéphane Bellafiore

Ecology and Evolution, Vol 10, Iss 20, Pp 11006-

2020 Volume 11021

Abstract: Abstract Discovered in the 1960s, Meloidogyne graminicola is a root‐knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have ... ...

Abstract	Abstract Discovered in the 1960s, Meloidogyne graminicola is a root‐knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well‐assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published for Meloidogyne genomes. We predicted 10,284 protein‐coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of M. graminicola parasitism. This high‐quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of Meloidogyne species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of M. graminicola and its closest relatives.
Keywords	cereals ; horizontal gene transfer ; pest ; reference genome ; root‐knot nematode ; transposable element ; Ecology ; QH540-549.5
Subject code	580
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: First 1-M Resolution Land Cover Map Labeling the Overlap in the 3rd Dimension

Céline Bassine / Julien Radoux / Benjamin Beaumont / Taïs Grippa / Moritz Lennert / Céline Champagne / Mathilde De Vroey / Augustin Martinet / Olivier Bouchez / Nicolas Deffense / Eric Hallot / Eléonore Wolff / Pierre Defourny

Data, Vol 5, Iss 117, p

The 2018 Map for Wallonia

2020 Volume 117

Abstract: Land cover maps contribute to a large diversity of geospatial applications, including but not limited to land management, hydrology, land use planning, climate modeling and biodiversity monitoring. In densely populated and highly fragmented landscapes as ...

Abstract	Land cover maps contribute to a large diversity of geospatial applications, including but not limited to land management, hydrology, land use planning, climate modeling and biodiversity monitoring. In densely populated and highly fragmented landscapes as observed in the Walloon region (Belgium), very high spatial resolution is required to depict all the infrastructures, buildings and most of the structural elements of the semi-natural landscapes (like hedges and small water bodies). Because of the resolution, the vertical dimension needs explicit handling to avoid discontinuities incompatible with many applications. For example, how to map a river flowing under a bridge? The particularity of our data is to provide a two-digit land cover code to label all the overlapping items. The identification of all the overlaps resulted from the combination of remote sensing image analysis and decision rules involving ancillary data. The final product is therefore semantically precise and accurate in terms of land cover description thanks to the addition of 24 classes on top of the 11 pure land cover classes. The quality of the map has been assessed using a state-of-the-art validation scheme. Its overall accuracy is as high as 91.5%, with an average producer’s accuracy of 86% and an average user’s accuracy of 91%.
Keywords	land cover ; map ; landscape ; remote sensing ; Bibliography. Library science. Information resources ; Z
Subject code	710
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Rv0180c contributes to Mycobacterium tuberculosis cell shape and to infectivity in mice and macrophages.

Delphine Payros / Henar Alonso / Wladimir Malaga / Arnaud Volle / Serge Mazères / Sébastien Déjean / Sophie Valière / Flavie Moreau / Stéphanie Balor / Alexandre Stella / Lucie Combes-Soia / Odile Burlet-Schiltz / Olivier Bouchez / Jérôme Nigou / Catherine Astarie-Dequeker / Christophe Guilhot

PLoS Pathogens, Vol 17, Iss 11, p e

2021 Volume 1010020

Abstract: Mycobacterium tuberculosis, the main causative agent of human tuberculosis, is transmitted from person to person via small droplets containing very few bacteria. Optimizing the chance to seed in the lungs is therefore a major adaptation to favor survival ...

Abstract	Mycobacterium tuberculosis, the main causative agent of human tuberculosis, is transmitted from person to person via small droplets containing very few bacteria. Optimizing the chance to seed in the lungs is therefore a major adaptation to favor survival and dissemination in the human population. Here we used TnSeq to identify genes important for the early events leading to bacterial seeding in the lungs. Beside several genes encoding known virulence factors, we found three new candidates not previously described: rv0180c, rv1779c and rv1592c. We focused on the gene, rv0180c, of unknown function. First, we found that deletion of rv0180c in M. tuberculosis substantially reduced the initiation of infection in the lungs of mice. Next, we established that Rv0180c enhances entry into macrophages through the use of complement-receptor 3 (CR3), a major phagocytic receptor for M. tuberculosis. Silencing CR3 or blocking the CR3 lectin site abolished the difference in entry between the wild-type parental strain and the Δrv0180c::km mutant. However, we detected no difference in the production of both CR3-known carbohydrate ligands (glucan, arabinomannan, mannan), CR3-modulating lipids (phthiocerol dimycocerosate), or proteins in the capsule of the Δrv0180c::km mutant in comparison to the wild-type or complemented strains. By contrast, we established that Rv0180c contributes to the functionality of the bacterial cell envelope regarding resistance to toxic molecule attack and cell shape. This alteration of bacterial shape could impair the engagement of membrane receptors that M. tuberculosis uses to invade host cells, and open a new perspective on the modulation of bacterial infectivity.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rv0180c contributes to Mycobacterium tuberculosis cell shape and to infectivity in mice and macrophages

PLoS Pathogens, Vol 17, Iss

2021 Volume 11

Abstract	Mycobacterium tuberculosis, the main causative agent of human tuberculosis, is transmitted from person to person via small droplets containing very few bacteria. Optimizing the chance to seed in the lungs is therefore a major adaptation to favor survival and dissemination in the human population. Here we used TnSeq to identify genes important for the early events leading to bacterial seeding in the lungs. Beside several genes encoding known virulence factors, we found three new candidates not previously described: rv0180c, rv1779c and rv1592c. We focused on the gene, rv0180c, of unknown function. First, we found that deletion of rv0180c in M. tuberculosis substantially reduced the initiation of infection in the lungs of mice. Next, we established that Rv0180c enhances entry into macrophages through the use of complement-receptor 3 (CR3), a major phagocytic receptor for M. tuberculosis. Silencing CR3 or blocking the CR3 lectin site abolished the difference in entry between the wild-type parental strain and the Δrv0180c::km mutant. However, we detected no difference in the production of both CR3-known carbohydrate ligands (glucan, arabinomannan, mannan), CR3-modulating lipids (phthiocerol dimycocerosate), or proteins in the capsule of the Δrv0180c::km mutant in comparison to the wild-type or complemented strains. By contrast, we established that Rv0180c contributes to the functionality of the bacterial cell envelope regarding resistance to toxic molecule attack and cell shape. This alteration of bacterial shape could impair the engagement of membrane receptors that M. tuberculosis uses to invade host cells, and open a new perspective on the modulation of bacterial infectivity. Author summary The epidemic efficiency of tuberculosis bacilli is determined by their capacity to transmit via aerosol. Currently, the bacterial functions that favor Mycobacterium tuberculosis seeding in the lung of naïve host remain mostly unknown. Here we implemented a genome-wide approach to identify M. tuberculosis mutants deficient for ...
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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