Datasets
| Name | Description | Type |
|---|---|---|
| Whole Genome Assembly and Annotation for Basmati334 |
Gene annotation was conducted using the MAKER program. An in-depth description of running MAKER can be found on the website: https://gist.github.com/darencard/bb1001ac1532dd4225b030cf0cd61ce2 |
Annotation of a genome. |
| Whole Genome Assembly and Annotation for Dom Sufid |
Gene annotation was conducted using the MAKER program. An in-depth description of running MAKER can be found on the website: https://gist.github.com/darencard/bb1001ac1532dd4225b030cf0cd61ce2 |
Annotation of a genome. |
| Transcriptome of Oryza glaberrima in response to Meloidogyne graminicola |
Gene expression profiling of the resistant rice Oryza glaberrima (TOG5681) in response to the root-knot nematode Meloidogyne graminicola, a major pest of rice (Oryza sativa L.) in Asia and in Central America. Dual RNA-seq, that is the simultaneous sequencing of the two organisms, was performed on M. graminicola-infected rice plants. RNA-seq data were obtained from 8 libraries coming from two biological replicates (1 and 2) of the following samples: mock-inoculated rice root tips (Oryza glaberrima... read more |
The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. |
| Transcriptome of Oryza sativa in response to Meloidogyne graminicola |
Gene expression profiling of the susceptible rice Oryza sativa (Nipponbare) in response to the root-knot nematode Meloidogyne graminicola, a major pest of rice (Oryza sativa L.) in Asia and in Central America. Dual RNA-seq, that is the simultaneous sequencing of the two organisms, was performed on M. graminicola-infected rice plants. RNA-seq data were obtained from 10 libraries coming from two biological replicates (1 and 2) of the following samples: mock-inoculated rice root tips (Oryza sativa... read more |
The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. |
| Genome-wide association mapping for agronomic and environmental traits in a panel of O. glaberrima rice accessions |
A panel of 163 accessions of O. glaberrima from West Africa were used to performed a genome-wide-association study for flowering time, panicle morphological traits, RYMV resistance and climatic variation |
Genome-wide association study experiments. |
| Genome-wide association mapping for shoot growth and water uptake dynamics in a panel of O. glaberrima rice accessions |
147 O. glaberrima genotypes were phenotyped in a high-throughput phenotyping platform for shoot growth and water uptake dynamics at early vegetative stage. |
Genome-wide association study experiments. |
| Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam |
This GWAS project for root traits is a collaboration between IRD (UMR DIADE) and LMI RICE (Vietnam). A panel of 180 Vietnamese rice varieties originating from provinces from North to South Vietnaman and from different agrosystems characterized by contrasted water regimes were used to perform a genome-wide association study for different root parameters. |
Genome-wide association study experiments. |
| Genome sequencing and assembly of Oryza barthii | Annotation of a genome. | |
| Whole Genome Assembly and Annotation of Oryza longistaminata |
Protein-coding genes, annotation of repeats and transposable elements were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. MAKER-P was used as evidence-based genome annotation pipeline. RepeatMasker was used to annotate repeats and transposable elements using species-specific de novo repeat libraries. Non coding RNA genes were predicted by AGI with Infernal, tRNA genes with tRNAScan. |
Annotation of a genome. |
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Rice GH is a collaborative project among rice teams from IRD & CIRAD. Funding has been provided by CRP Rice, IRD and CIRAD
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