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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11 to 20 of 996 Results

RiceGraph_MGC_paths.xg Mar 18, 2025 - Output from the analysis described in GrAnnoT paper Unknown - 4.3 GB - MD5: 3ac4d2629fafbc7ffa77ef106d417e84 Data Rice pangenome graph with paths converted in .xg format by VG.
AzucenaRS1.fna Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 368.4 MB - MD5: d621f8e18ef4fce7aef9ddb0b00db2cf Data Fasta file of the genome AzucenaRS1, from the paper from 2020 by Zhou, Y., Chebotarov, D., Kudrna, D. et al., "A platinum standard pan-genome resource that represents the population structure of Asian rice" (doi:10.1038/s41597-020-0438-2).
CHM13_chr1.gff Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 152.4 MB - MD5: 1f0269e5728a0ed5f83188cd08792c41 Data Annotation file of the chromosome 1 of the genome CHM13, adapted from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ to match the pangenome graph.
chm13.draft_v1.1_chr1.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 240.8 MB - MD5: ab2421da8b88a867d087c3f452a6969f Fasta file of the chromosome 1 of the genome CHM13,from https://projects.ensembl.org/hprc/.
EcoliGraph_MGC.gfa Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 112.8 MB - MD5: e5183acfb527fcd7b01ac4386d7be290 Data E.coli pangenome graph built with 12 genomes from the paper available at http://dx.doi.org/10.7554/eLife.78834.
feature_types.txt Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 638 B - MD5: 571dcfb312543edd81dca0524212459a Lists all the feature types in the human annotation (CHM13_chr1.gff), necessary to run Liftoff on all the features.
feature_types.txt Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 104 B - MD5: 6752a18a92500cff53d9d8c4210fc1bc Data Lists all the feature types in the E.coli annotation (sequence_filter_rename_K_12_MG1655_09949b0.gff3), necessary to run Liftoff on all the features.
GCA_000001405.15_GRCh38_chr1.fna Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 240.8 MB - MD5: 90780be24a8555613e6ad0bd2f8a0935 Data Fasta file of the chromosome 1 of the genome GRCh38,from https://projects.ensembl.org/hprc/.
IRGSP_nipponbare.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 363.7 MB - MD5: e923ca38bac7f347ffbf88142b93428f Fasta file of the genome Nipponbare, from the paper from 2013 by Kawahara, Y., de la Bastide, M., Hamilton, J.P. et al., "Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data" (doi:10.1186/1939-8433-6-4).
IRGSP_nipponbare.genome Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 539 B - MD5: 562caffe11637996021726b3d3a2e59b Data Text file necessary to run VG on the rice data.

RiceGraph_MGC_paths.xg

Mar 18, 2025 - Output from the analysis described in GrAnnoT paper

Unknown - 4.3 GB -

Data

Rice pangenome graph with paths converted in .xg format by VG.

AzucenaRS1.fna

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 368.4 MB -

Data

Fasta file of the genome AzucenaRS1, from the paper from 2020 by Zhou, Y., Chebotarov, D., Kudrna, D. et al., "A platinum standard pan-genome resource that represents the population structure of Asian rice" (doi:10.1038/s41597-020-0438-2).

CHM13_chr1.gff

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 152.4 MB -

Data

Annotation file of the chromosome 1 of the genome CHM13, adapted from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ to match the pangenome graph.

chm13.draft_v1.1_chr1.fasta

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 240.8 MB -

Fasta file of the chromosome 1 of the genome CHM13,from https://projects.ensembl.org/hprc/.

EcoliGraph_MGC.gfa

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 112.8 MB -

Data

E.coli pangenome graph built with 12 genomes from the paper available at http://dx.doi.org/10.7554/eLife.78834.

feature_types.txt

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 638 B -

Lists all the feature types in the human annotation (CHM13_chr1.gff), necessary to run Liftoff on all the features.

feature_types.txt

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 104 B -

Data

Lists all the feature types in the E.coli annotation (sequence_filter_rename_K_12_MG1655_09949b0.gff3), necessary to run Liftoff on all the features.

GCA_000001405.15_GRCh38_chr1.fna

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 240.8 MB -

Data

Fasta file of the chromosome 1 of the genome GRCh38,from https://projects.ensembl.org/hprc/.

IRGSP_nipponbare.fasta

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 363.7 MB -

Fasta file of the genome Nipponbare, from the paper from 2013 by Kawahara, Y., de la Bastide, M., Hamilton, J.P. et al., "Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data" (doi:10.1186/1939-8433-6-4).

IRGSP_nipponbare.genome

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 539 B -

Data

Text file necessary to run VG on the rice data.

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