Datasets
| Name | Description | Type |
|---|---|---|
| Whole Genome Assembly and Annotation of Oryza nivara |
Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing |
Annotation of a genome. |
| Whole Genome Assembly and Annotation of Oryza glumipatula |
Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. |
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. |
| 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 of Oryza brachyantha |
Protein-coding genes were annotated using an evidence-based approach as implemented in the Gramene gene-build pipeline by collaboration with Dr. Chengzhi Liang at IGDB. Transposable elements were annotated by collaboration with Dr. Scott A. Jackson at University of Georgia. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. |
Annotation of a genome. |
| Dynamic and Coordinated Expression Changes of Rice Small RNAs in Response to Xanthomonas oryzae pv. oryzae |
Examine the small RNA expression profiles of rice leaves at 2, 6, 12, and 24 hours post infection of Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99, the causal agent of rice bacterial blight disease. |
|
| Small RNA sequencing of Rice leaves infected with strains of the oryzae or oryzicola pathovars of Xanthomonas oryzae |
The sRNA-seq data for the Diversity dataset was generated by the Novogene company (Hong Kong, China) from total RNA extracted from triplicate samples collected at 24 hpi using a NEBNext Small RNA Library Prep Set for Illumina kit optimized by Novogene on the supplied total RNAs. Ultimately, size selected 18–47 bp inserts were sequenced on a Illumina HiSeq (1 × 50 bp). |
|
| Small RNA sequencing of Rice leaves infected with the African Xanthomonas oryzae pv. oryzae strain BAI3 |
The sRNA-seq data for the BAI3 dataset was generated by the Fasteris company (Geneva, Switzerland). Briefly, sRNA libraries were prepared with total RNA extracted from duplicate samples collected at 24 hpi using the Illumina TruSeq small RNA kit with polyacrylamide gel purified 18–25 nt sRNA fractions and sequenced on a portion of a Illumina HiSeq 2000 lane, 1 × 50 single-reads. |
|
| Genome sequencing and assembly of Oryza barthii | 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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