Christine Tranchant‐Dubreuil

Institut de Recherche pour le Développement

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François Sabot

Institut de Recherche pour le Développement

Yves Vigouroux

Université de Montpellier

Alexandre de Kochko

Institut de Recherche pour le Développement

Valérie Poncet

Diversité, adaptation et développement des plantes

Alexis Dereeper

Institut Pasteur

Romain Guyot

Institut de Recherche pour le Développement

Alain Ghesquière

Diversité, adaptation et développement des plantes

Philippe Cubry

Institut de Recherche pour le Développement

Gaëtan Droc

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Hélène Adam

Institut de Recherche pour le Développement

Cooperative Institutions

Université de Montpellier

166

Centre de Coopération Internationale en Recherche Agronomique pour le Développement

162

Institut de Recherche pour le Développement

162

Agropolis International

132

Diversité, adaptation et développement des plantes

112

Centre National de la Recherche Scientifique

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Institut Agro Montpellier

Genetic Improvement and Adaptation of Mediterranean and Tropical Plants

L'Institut Agro

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de novo assemblies of three Oryza glaberrima accessions provide first insights about pan-genome of African rices

Genome Biology and Evolution (2016)

Cécile Monat Bérengère Pera Marie-Noëlle Ndjiondjop Mounirou Sow Christine Tranchant‐Dubreuil

Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific.

Oryza

10.1093/gbe/evw253

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Citations (27)

Plant Pangenome: Impacts on Phenotypes and Evolution

Annual Plant Reviews online (2019)

Christine Tranchant‐Dubreuil Mathieu Rouard François Sabot

Abstract With the emergence of low‐cost high‐throughput sequencing technologies, numerous studies have shown that a single genome is not enough to identify all the genes present in a species. Recently, the pangenome concept has become widely used to investigate genome composition of a collection of individuals. The pangenome consists in the core genome, which encompasses all the sequences shared by all the individuals, and the dispensable genome, composed of sequences present in only some individuals. Pangenomic analyses open new ways to investigate and compare multiple genomes of closely related individuals at once, and more broadly new opportunities for optimising breeding and studying evolution. This emerging concept combined with the power of the third‐generation sequencing technologies gives unprecedented opportunities to uncover new genes, to fully explore genetic diversity and to advance knowledge about the evolutionary forces that shape genome organisation and dynamics.

10.1002/9781119312994.apr0664

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Citations (38)

The south green rice genome hub

Gaëtan Droc Alexis Dereeper Manuel Ruíz Chloé Antoine Maïra Barca

We have developed the Rice Genome Hub (https://rice-genome-hub.southgreen.fr), an integrative genome information system that allows centralized access to genomics and genetics data, and analytical tools to facilitate translational and applied research in rice.Rice is the world's most consumed staple food, especially in Asia. It is also one of the most cultivated crop with maize and wheat. The Hub currently contains seven annotated genome sequences ofOryza sativa(Asian rice), and one ofOryza glaberrima(African rice).The hub is built using the the Content Management System Drupal with the Tripal module that interacts with the Chado database. We opted for GMOD components that are open source, modular, portable and benefiting from a large community support in which we have been involved. The Hub interface provides several functionalities (Blast, DotPlots, Gene Search, JBrowse, Primer Blaster, Primer Designer) to make it easy for querying, visualizing and downloading research data.We also plugged in-house tools developed by the South Green bioinformatics platform such as SNiPlay (detection and analyses of SNPs),Gigwa (filtering on genomic variations), daTALbase (exploration of data related to Xanthomonas TAL effectors), and DiffExDB (differential expression analysis).

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Microsatellite markers for Amborella (Amborellaceae), a monotypic genus endemic to New Caledonia

American Journal of Botany (2012)

Valérie Poncet Marie Couderc Christine Tranchant‐Dubreuil Céline Gomez Perla Hamon

• Premise of the study: Informative markers are required for assessing the diversity of Amborella trichopoda , the only species of its order, endemic to New Caledonia and considered to be the sister species to all flowering plants. Therefore, expressed sequence tag (EST)–based microsatellite markers were developed. • Methods and Results: Fifty‐five microsatellite loci were characterized in 14896 putative unigenes, which were generated by assembling A. trichopoda ESTs from the public sequence database. Seventeen markers revealed polymorphism in 80 adult shrubs from three populations. The number of alleles per locus ranged from two to 12, with a total of 132 alleles scored. The mean expected heterozygosity per population ranged from 0.336 to 0.567. • Conclusions: These markers offer an appropriate amount of variation to investigate genetic diversity structure, gene flow, and other conservation issues.

10.3732/ajb.1200131

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The MooSciTIC project: a booster shot of science for West African research and higher education actors

bioRxiv (Cold Spring Harbor Laboratory) (2018)

Ménonvè Atindehou Kifouli Adéoti Yêyinou Laura Estelle Loko Thierry Beulé Emmanuel Paradis

In this paper, we describe the implementation of the MooSciTIC summer schools, a capacity-building initiative targeting West African research scientists and higher education teachers. Throughout the three years of the project, we provided on-site courses and practicals on cross-disciplinary aspects such as scientific writing, communication and integrity, in the aim of improving the self-reliance of researchers and upgrading research practices throughout the sub-region. We explain how the program was designed and implemented and we show the positive outcomes it generated for our former trainees within a relatively short period, hoping to inspire similar initiatives to follow our steps.

Booster (rocketry)

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One shot

10.1101/504092

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New resources and integrated maps for IR64 x Azucena, a reference population in rice : [P361]

Nourollah Ahmadi Christine Tranchant‐Dubreuil Brigitte Courtois Daniel Foncéka Dominique This

The new resources developed are already used in many fine mapping projects. This integrative genetic map provides a common representation framework and is a potential tool for gene positional cloning, marker-assisted selection and in silico QTL/genes co-localisation. It can also be used for comparative genomic studies by using anchor probes as bridge points to test local synteny and candidate genes of other cereals. The next step will be the integration of markers from other major rice genetic maps (Nipponbare x Kasalath) to enlarge the compilation to other genes and QTLs. (Resume d'auteur)

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Comparison of two African rice species through a new pan-genomic approach on massive data

bioRxiv (Cold Spring Harbor Laboratory) (2018)

Cécile Monat Christine Tranchant‐Dubreuil Stéfan Engelen Karine Labadie Emmanuel Paradis

Abstract Pangenome theory implies that individuals from a given group/species share only a given part of their genome (core-genome), the remaining part being the dispensable one. Domestication process implies a small number of founder individuals, and thus a large core-genome compared to dispensable at the first steps of domestication. We sequenced at high depth 120 cultivated African rice Oryza glaberrima and of 74 wild relatives O. barthii , and mapped them on the external reference from Asian rice O. sativa . We then use a novel DepthOfCoverage approach to identif missing genes. After comparing the two species, we shown that the cultivated species has a smaller core-genome than the wild one, as well as an expected smaller dispensable one. This unexpected output however replaces in perspective the inadequacy of cultivated crops to wilderness.

10.1101/245431

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Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Molecular Ecology (2013)

Valérie Poncet François Munoz Jérôme Munzinger Yohan Pillon Céline Gomez

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range-wide genetic diversity based on nuclear microsatellite data and detected four well-differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum (LGM, c. 21,000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra- and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon.

Refugium (fishkeeping)

10.1111/mec.12554

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Citations (36)

FrangiPANe, a tool for creating a panreference using left behind reads

NAR Genomics and Bioinformatics (2023)

Christine Tranchant‐Dubreuil Clothilde Chenal Blaison Mathieu Laurence Albar Valentin Klein

Abstract We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.

10.1093/nargab/lqad013

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Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Carla de la Fuente Alexandre Grondin Bassirou Sine Marilyne Debieu Christophe Belin

Abstract Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modelling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including GWAS and QTL approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.

Drought Tolerance

Glutaredoxin

10.1101/2023.02.02.526762

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Citations (1)