UMR DIADE

DIversity - Adaptation - plant DEvelopment

The DIADE Research Unit aims to understand the diversification of tropical plants, one of the main original reservoirs of biodiversity, and for which conservation, management and exploitation are an important issue for Sustainable Development.

The nine teams forming the Unit belong to IRD, University of Montpellier, CIRAD, and CNRS.

CERES Team

DYNADIV Team

PANEEC Team

EVOGEC Team

ADvENS Team

AgroLD

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1 to 10 of 56 Results

Supporting data and scripts produced by the GraTools software Mar 10, 2026 - gratools Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Supporting data and scripts produced by the GraTools software", https://doi.org/10.23708/M24LJG, DataSuds, V1 Here, we introduce GraTools (https://forge.ird.fr/diade/gratools), a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file. After a one-time graph import, GraTools enables rapid subgraph extraction, fasta sequence retrieval, and comprehensive...
Data used in the gratools paper Mar 6, 2026 - gratools Sabot, Francois, 2026, "Data used in the gratools paper", https://doi.org/10.23708/SOTLQU, DataSuds, V1 These are the data (mostly Pangenome variation graphs) that were used in the gratools paper only. The file is the Zenodo DOI link for the thre graphs.
Code source for GraTools v1.1.0 Mar 6, 2026 - gratools Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Code source for GraTools v1.1.0", https://doi.org/10.23708/DXOP8N, DataSuds, V1 This code is the original source code submitted for GraTools in March 2026. This is a dump of the IRD Forge git, master branch
gratools(IRD - Institut de Recherche pour le Développement) Mar 6, 2026PANEEC Team This dataverse contains codes and data related to the GraTools software
Data used for the analysis described in GrAnnoT paper Oct 29, 2025 - GrAnnoT data and output Marthe, Nina; Sabot, Francois, 2025, "Data used for the analysis described in GrAnnoT paper", https://doi.org/10.23708/DO1RTF, DataSuds, V6 GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the data necessary for these tests is available in this dataset. It includes mainly pangenome graphs, genomes, and annotations.
Output from the analysis described in GrAnnoT paper Oct 29, 2025 - GrAnnoT data and output Marthe, Nina; Sabot, Francois, 2025, "Output from the analysis described in GrAnnoT paper", https://doi.org/10.23708/RRSKRA, DataSuds, V6 GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the outputs from these tests are available in this dataset. It includes mainly transferred annotations.
Testing the impact of environmental variables on the predictive performance of genomic offset statistics: crop-specific metrics computed from the EWEMBI v.1 climate dataset. Sep 17, 2025 - DYNADIV Team Kaczmarek, Thomas; Faye, Adama; Ilmi Ahmed, Aicha; Veltman, Margaretha; Thuillet, Anne-Celine; Scarcelli, Nora; Sultan, Benjamin; Vigouroux, Yves; Cubry, Philippe, 2025, "Testing the impact of environmental variables on the predictive performance of genomic offset statistics: crop-specific metrics computed from the EWEMBI v.1 climate dataset.", https://doi.org/10.23708/M9YGDC, DataSuds, V1, UNF:6:EdX+/x3auhCXDY0Q7OgZ4g== [fileUNF] The ability of species and populations to adapt to their environment faces increasing challenges as climate change accelerates. Recent methods based on genomic offset (GO) statistics aim to quantify the risk of non-adaptation of populations to future climates. While several studi...
Development of new microsatellites markers for Cola acuminata (Malvaceae), a socio-economically important fruit tree species in Central Africa Aug 27, 2025 - DYNADIV Team Duminil, Jerome; Dupiol, Pablo; Chakocha Ngandjui, Armel Franklin; Tientcheu, Avana Marie Louise; Mariac, Cedric; Charahabil, Mohamed Mahamoud; Barnaud, Adeline, 2025, "Development of new microsatellites markers for Cola acuminata (Malvaceae), a socio-economically important fruit tree species in Central Africa", https://doi.org/10.23708/6FCSLF, DataSuds, V1, UNF:6:JjyY2CKXXeBPZvLKRN5hnA== [fileUNF] Data from the publication "Development of new microsatellites markers for Cola acuminata (Malvaceae), a socio-economically important fruit tree species in Central Africa". Manuscript PJS_2_147801 Plant Ecology and Evolution. We developed a new set of nuclear microsatellite marker...
VCF files from the study of low recombining genomic regions in pearl millet Jun 23, 2025 - DYNADIV Team Salson, Marine; Duranton, Maud; Huynh, Stella; Mariac, Cédric; Tranchant-Dubreuil, Christine; Orjuela, Julie; Cubry,Philippe; Thuillet, Anne-Celine; Burgarella, Concetta; De Navascués, Miguel; Zekraouï, Leïla; Couderc, Marie; Arribat, Sandrine; Rodde, Nathalie; Barnaud, Adeline; Adama Faye; Kane, Ndjido; Vigouroux, Yves; Berthouly-Salazar, Cécile, 2025, "VCF files from the study of low recombining genomic regions in pearl millet", https://doi.org/10.23708/SN2T4A, DataSuds, V1 We conducted a comprehensive investigation of large low-recombining regions in cultivated populations of pearl millet, an outcrossing diploid African cereal. We adopted a population genomic approach based on the analysis of single nucleotide polymorphisms. The repository contains...
Taxonomy of the native angiosperm flora of New Caledonia in 1911, 1948, 2001, 2012 and 2024 Jun 20, 2025 - DYNADIV Team Gotty, Karine; Pillon, Yohan, 2025, "Taxonomy of the native angiosperm flora of New Caledonia in 1911, 1948, 2001, 2012 and 2024", https://doi.org/10.23708/TLRYUM, DataSuds, V1, UNF:6:uST0iWeHOy7tvpNpRUnNdw== [fileUNF] The table lists all angiosperm species from New Caledonia cited in five successive checklists published in 1911, 1948, 2001, 2012 and 2024. The table track the fate of each species in the five checklissts and in particular the changes in genus and family.

Supporting data and scripts produced by the GraTools software

Mar 10, 2026 - gratools

Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Supporting data and scripts produced by the GraTools software", https://doi.org/10.23708/M24LJG, DataSuds, V1

Here, we introduce GraTools (https://forge.ird.fr/diade/gratools), a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file. After a one-time graph import, GraTools enables rapid subgraph extraction, fasta sequence retrieval, and comprehensive...

Data used in the gratools paper

Mar 6, 2026 - gratools

Sabot, Francois, 2026, "Data used in the gratools paper", https://doi.org/10.23708/SOTLQU, DataSuds, V1

These are the data (mostly Pangenome variation graphs) that were used in the gratools paper only. The file is the Zenodo DOI link for the thre graphs.

Code source for GraTools v1.1.0

Mar 6, 2026 - gratools

Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Code source for GraTools v1.1.0", https://doi.org/10.23708/DXOP8N, DataSuds, V1

This code is the original source code submitted for GraTools in March 2026. This is a dump of the IRD Forge git, master branch

gratools(IRD - Institut de Recherche pour le Développement)

Mar 6, 2026PANEEC Team

This dataverse contains codes and data related to the GraTools software

Data used for the analysis described in GrAnnoT paper

Oct 29, 2025 - GrAnnoT data and output

Marthe, Nina; Sabot, Francois, 2025, "Data used for the analysis described in GrAnnoT paper", https://doi.org/10.23708/DO1RTF, DataSuds, V6

GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the data necessary for these tests is available in this dataset. It includes mainly pangenome graphs, genomes, and annotations.

Output from the analysis described in GrAnnoT paper

Oct 29, 2025 - GrAnnoT data and output

Marthe, Nina; Sabot, Francois, 2025, "Output from the analysis described in GrAnnoT paper", https://doi.org/10.23708/RRSKRA, DataSuds, V6

GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the outputs from these tests are available in this dataset. It includes mainly transferred annotations.

Testing the impact of environmental variables on the predictive performance of genomic offset statistics: crop-specific metrics computed from the EWEMBI v.1 climate dataset.

Sep 17, 2025 - DYNADIV Team

Kaczmarek, Thomas; Faye, Adama; Ilmi Ahmed, Aicha; Veltman, Margaretha; Thuillet, Anne-Celine; Scarcelli, Nora; Sultan, Benjamin; Vigouroux, Yves; Cubry, Philippe, 2025, "Testing the impact of environmental variables on the predictive performance of genomic offset statistics: crop-specific metrics computed from the EWEMBI v.1 climate dataset.", https://doi.org/10.23708/M9YGDC, DataSuds, V1, UNF:6:EdX+/x3auhCXDY0Q7OgZ4g== [fileUNF]

The ability of species and populations to adapt to their environment faces increasing challenges as climate change accelerates. Recent methods based on genomic offset (GO) statistics aim to quantify the risk of non-adaptation of populations to future climates. While several studi...

Development of new microsatellites markers for Cola acuminata (Malvaceae), a socio-economically important fruit tree species in Central Africa

Aug 27, 2025 - DYNADIV Team

Duminil, Jerome; Dupiol, Pablo; Chakocha Ngandjui, Armel Franklin; Tientcheu, Avana Marie Louise; Mariac, Cedric; Charahabil, Mohamed Mahamoud; Barnaud, Adeline, 2025, "Development of new microsatellites markers for Cola acuminata (Malvaceae), a socio-economically important fruit tree species in Central Africa", https://doi.org/10.23708/6FCSLF, DataSuds, V1, UNF:6:JjyY2CKXXeBPZvLKRN5hnA== [fileUNF]

Data from the publication "Development of new microsatellites markers for Cola acuminata (Malvaceae), a socio-economically important fruit tree species in Central Africa". Manuscript PJS_2_147801 Plant Ecology and Evolution. We developed a new set of nuclear microsatellite marker...

VCF files from the study of low recombining genomic regions in pearl millet

Jun 23, 2025 - DYNADIV Team

Salson, Marine; Duranton, Maud; Huynh, Stella; Mariac, Cédric; Tranchant-Dubreuil, Christine; Orjuela, Julie; Cubry,Philippe; Thuillet, Anne-Celine; Burgarella, Concetta; De Navascués, Miguel; Zekraouï, Leïla; Couderc, Marie; Arribat, Sandrine; Rodde, Nathalie; Barnaud, Adeline; Adama Faye; Kane, Ndjido; Vigouroux, Yves; Berthouly-Salazar, Cécile, 2025, "VCF files from the study of low recombining genomic regions in pearl millet", https://doi.org/10.23708/SN2T4A, DataSuds, V1

We conducted a comprehensive investigation of large low-recombining regions in cultivated populations of pearl millet, an outcrossing diploid African cereal. We adopted a population genomic approach based on the analysis of single nucleotide polymorphisms. The repository contains...

Taxonomy of the native angiosperm flora of New Caledonia in 1911, 1948, 2001, 2012 and 2024

Jun 20, 2025 - DYNADIV Team

Gotty, Karine; Pillon, Yohan, 2025, "Taxonomy of the native angiosperm flora of New Caledonia in 1911, 1948, 2001, 2012 and 2024", https://doi.org/10.23708/TLRYUM, DataSuds, V1, UNF:6:uST0iWeHOy7tvpNpRUnNdw== [fileUNF]

The table lists all angiosperm species from New Caledonia cited in five successive checklists published in 1911, 1948, 2001, 2012 and 2024. The table track the fate of each species in the five checklissts and in particular the changes in genus and family.

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