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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31 to 40 of 44 Results

MG12 data Apr 21, 2023 - OryzaGenomeData SABOT, Francois, 2023, "MG12 data", https://doi.org/10.23708/1JST4X, DataSuds, V1 This data are the draft genome assembly of MG12 ans its annotation transfered from IRGSP1.0/Nipponbare ference genome. MG12 is a Oryza glaberrima variety involved in some CSSL crosses
Supporting data and code for the African Rice Panreference produced by the frangiPANe software Jan 27, 2023 - DYNADIV Team Tranchant, Christine; Chenal, Clothilde; Blaison, Mathieu; Albar, Laurence; Klein, Valentin; Mariac, Cédric; Wing, Rod; Vigouroux, Yves; Sabot, Francois, 2022, "Supporting data and code for the African Rice Panreference produced by the frangiPANe software", https://doi.org/10.23708/93OQMD, DataSuds, V3, UNF:6:J8wm0efC8Lf7KQQ/txrx4Q== [fileUNF] We present here FrangiPANe (https://github.com/tranchant/frangiPANe), a pipeline developed to build panreference using short reads through a map-then-assemble strategy and a dataset corresponding to 515 Mb of new sequences (484,394 non redundant sequences) in addition to the CG14...
Data for: Varietal mixtures of Sahelian smallholders conciliate enhanced yield and agrobiodiversity conservation Dec 19, 2022 - DYNADIV Team Cisse, Aby; Clermont-Dauphin, Cathy; Sall, Saidou Nourou; Ndir, Khadidiatou; Kane, Ndjido Ardo; Renard, Delphine; Violle, Cyrille; Barnaud, Adeline; Berthouly-Salazar, Cecile, 2022, "Data for: Varietal mixtures of Sahelian smallholders conciliate enhanced yield and agrobiodiversity conservation", https://doi.org/10.23708/SVJS1T, DataSuds, V1, UNF:6:jEDyzHjdv0cMJIPXU7rROw== [fileUNF] This study was co-designed with farmers’ organizations in Senegal with the aim of assessing the impacts of the mixing of early- and late-flowering pearl millet landraces (Cenchrus americanus) on in situ yield, i.e. in poor soil conditions with limited fertilization on smallholder...
v2.2-beta1 version used for the publication data of TrEMOLO Dec 19, 2022 - TrEMOLO software - Data and codes SABOT, Francois; MOHAMED, Mourdas, 2022, "v2.2-beta1 version used for the publication data of TrEMOLO", https://doi.org/10.23708/2FYBUL, DataSuds, V2 This dataset is the locked software version used for the publication of TrEMOLO. It represents the v2.2-beta1 version
Replication data for simulated reads for S1, S2 and S3 genomes for the TrEMOLO paper Dec 19, 2022 - TrEMOLO software - Data and codes SABOT, Francois; MOHAMED, Mourdas, 2022, "Replication data for simulated reads for S1, S2 and S3 genomes for the TrEMOLO paper", https://doi.org/10.23708/N447VS, DataSuds, V1 This dataset contains the simulated reads used to validate TrEMOLO. The reads were created using DeeepSimulator v1.5 (https://github.com/liyu95/DeepSimulator/releases/tag/v1.5) using the options -B 2 -K n -l 20000.
Simulated genome sequences for replication control for TrEMOLO Dec 16, 2022 - TrEMOLO software - Data and codes SABOT, Francois; MOHAMED, Mourdas, 2022, "Simulated genome sequences for replication control for TrEMOLO", https://doi.org/10.23708/DSDTZ0, DataSuds, V1 This dataset contains the simulated genomes based on the G0-F100 initial sequence including the INSIDERs and OUTSIDERs simulated insertions.
Replication Data for Distribution of Quercus ilex subsp. rotundifolia in Tunisia and intraspecific variation of seed morphophysiological traits along climatic gradients Sep 22, 2022 - ADvENS Team Amimi, Nabil; Ghouil, Hana; Zitouna-Chebbi, Rim; Joët, Thierry; Ammari, Youssef, 2022, "Replication Data for Distribution of Quercus ilex subsp. rotundifolia in Tunisia and intraspecific variation of seed morphophysiological traits along climatic gradients", https://doi.org/10.23708/TYFN5U, DataSuds, V1, UNF:6:cHGNf+36WqEUqJV2nD6V3w== [fileUNF] This dataset gathers geographical information for the distribution sites of Quercus ilex subsp. rotundifolia in Tunisia in 2020, as well as climatic data and seed morpho-physiological traits associated with the 18 main populations identified. In order to identify adaptations to l...
Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes Aug 18, 2022 Orjuela, Julie; Comte, Aurore; Ravel, Sébastien; Charriat, Florian; Vi, Tram; Sabot, François; Cunnac, Sébastien, 2022, "Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes", https://doi.org/10.23708/TBPNWJ, DataSuds, V3 CulebrONT is an open-source, scalable, modulable and traceable snakemake pipeline, able to launch multiple assembly tools in parallel and providing help for choosing the best possible assembly. Documentation: https://culebront-pipeline.readthedocs.io/en/2.1.1/ Code development: h...
Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes Aug 18, 2022 Orjuela, Julie; Comte, Aurore; Ravel, Sébastien; Charriat, Florian; Vi, Tram; Sabot, Francois; Cunnac, Sébastien, 2022, "Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes", https://doi.org/10.23708/RJDLCN, DataSuds, V1 Related to CulebrONT software, this dataset includes: - data used to test the software - 2 reports generated by the software : from the test data and from other data - supplementary technical information about CulebrONT pipeline
Fasta files for InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning Feb 1, 2021 - EVOGEC Team Guyot, Romain; Orozco-Arias, Simon; Isaza, Gustavo, 2021, "Fasta files for InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning", https://doi.org/10.23708/QCMOUA, DataSuds, V2 Here, we present InpactorDB a semi-curated dataset composed of 130,511 elements from 195 plant genomes belonging to 108 plant species, classified down to the lineage level. This dataset has been used to train two deep neural networks (one fully connected and one convolutional) fo...

MG12 data

Apr 21, 2023 - OryzaGenomeData

SABOT, Francois, 2023, "MG12 data", https://doi.org/10.23708/1JST4X, DataSuds, V1

This data are the draft genome assembly of MG12 ans its annotation transfered from IRGSP1.0/Nipponbare ference genome. MG12 is a Oryza glaberrima variety involved in some CSSL crosses

Supporting data and code for the African Rice Panreference produced by the frangiPANe software

Jan 27, 2023 - DYNADIV Team

Tranchant, Christine; Chenal, Clothilde; Blaison, Mathieu; Albar, Laurence; Klein, Valentin; Mariac, Cédric; Wing, Rod; Vigouroux, Yves; Sabot, Francois, 2022, "Supporting data and code for the African Rice Panreference produced by the frangiPANe software", https://doi.org/10.23708/93OQMD, DataSuds, V3, UNF:6:J8wm0efC8Lf7KQQ/txrx4Q== [fileUNF]

We present here FrangiPANe (https://github.com/tranchant/frangiPANe), a pipeline developed to build panreference using short reads through a map-then-assemble strategy and a dataset corresponding to 515 Mb of new sequences (484,394 non redundant sequences) in addition to the CG14...

Data for: Varietal mixtures of Sahelian smallholders conciliate enhanced yield and agrobiodiversity conservation

Dec 19, 2022 - DYNADIV Team

Cisse, Aby; Clermont-Dauphin, Cathy; Sall, Saidou Nourou; Ndir, Khadidiatou; Kane, Ndjido Ardo; Renard, Delphine; Violle, Cyrille; Barnaud, Adeline; Berthouly-Salazar, Cecile, 2022, "Data for: Varietal mixtures of Sahelian smallholders conciliate enhanced yield and agrobiodiversity conservation", https://doi.org/10.23708/SVJS1T, DataSuds, V1, UNF:6:jEDyzHjdv0cMJIPXU7rROw== [fileUNF]

This study was co-designed with farmers’ organizations in Senegal with the aim of assessing the impacts of the mixing of early- and late-flowering pearl millet landraces (Cenchrus americanus) on in situ yield, i.e. in poor soil conditions with limited fertilization on smallholder...

v2.2-beta1 version used for the publication data of TrEMOLO

Dec 19, 2022 - TrEMOLO software - Data and codes

SABOT, Francois; MOHAMED, Mourdas, 2022, "v2.2-beta1 version used for the publication data of TrEMOLO", https://doi.org/10.23708/2FYBUL, DataSuds, V2

This dataset is the locked software version used for the publication of TrEMOLO. It represents the v2.2-beta1 version

Replication data for simulated reads for S1, S2 and S3 genomes for the TrEMOLO paper

Dec 19, 2022 - TrEMOLO software - Data and codes

SABOT, Francois; MOHAMED, Mourdas, 2022, "Replication data for simulated reads for S1, S2 and S3 genomes for the TrEMOLO paper", https://doi.org/10.23708/N447VS, DataSuds, V1

This dataset contains the simulated reads used to validate TrEMOLO. The reads were created using DeeepSimulator v1.5 (https://github.com/liyu95/DeepSimulator/releases/tag/v1.5) using the options -B 2 -K n -l 20000.

Simulated genome sequences for replication control for TrEMOLO

Dec 16, 2022 - TrEMOLO software - Data and codes

SABOT, Francois; MOHAMED, Mourdas, 2022, "Simulated genome sequences for replication control for TrEMOLO", https://doi.org/10.23708/DSDTZ0, DataSuds, V1

This dataset contains the simulated genomes based on the G0-F100 initial sequence including the INSIDERs and OUTSIDERs simulated insertions.

Replication Data for Distribution of Quercus ilex subsp. rotundifolia in Tunisia and intraspecific variation of seed morphophysiological traits along climatic gradients

Sep 22, 2022 - ADvENS Team

Amimi, Nabil; Ghouil, Hana; Zitouna-Chebbi, Rim; Joët, Thierry; Ammari, Youssef, 2022, "Replication Data for Distribution of Quercus ilex subsp. rotundifolia in Tunisia and intraspecific variation of seed morphophysiological traits along climatic gradients", https://doi.org/10.23708/TYFN5U, DataSuds, V1, UNF:6:cHGNf+36WqEUqJV2nD6V3w== [fileUNF]

This dataset gathers geographical information for the distribution sites of Quercus ilex subsp. rotundifolia in Tunisia in 2020, as well as climatic data and seed morpho-physiological traits associated with the 18 main populations identified. In order to identify adaptations to l...

Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Aug 18, 2022

Orjuela, Julie; Comte, Aurore; Ravel, Sébastien; Charriat, Florian; Vi, Tram; Sabot, François; Cunnac, Sébastien, 2022, "Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes", https://doi.org/10.23708/TBPNWJ, DataSuds, V3

CulebrONT is an open-source, scalable, modulable and traceable snakemake pipeline, able to launch multiple assembly tools in parallel and providing help for choosing the best possible assembly. Documentation: https://culebront-pipeline.readthedocs.io/en/2.1.1/ Code development: h...

Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Aug 18, 2022

Orjuela, Julie; Comte, Aurore; Ravel, Sébastien; Charriat, Florian; Vi, Tram; Sabot, Francois; Cunnac, Sébastien, 2022, "Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes", https://doi.org/10.23708/RJDLCN, DataSuds, V1

Related to CulebrONT software, this dataset includes: - data used to test the software - 2 reports generated by the software : from the test data and from other data - supplementary technical information about CulebrONT pipeline

Fasta files for InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning

Feb 1, 2021 - EVOGEC Team

Guyot, Romain; Orozco-Arias, Simon; Isaza, Gustavo, 2021, "Fasta files for InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning", https://doi.org/10.23708/QCMOUA, DataSuds, V2

Here, we present InpactorDB a semi-curated dataset composed of 130,511 elements from 195 plant genomes belonging to 108 plant species, classified down to the lineage level. This dataset has been used to train two deep neural networks (one fully connected and one convolutional) fo...

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