Name Description Type
Whole Genome Assembly and Annotation of Oryza glaberrima

Assembly

The genome sequence was generated with PacBio technology and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717, deposited in Genbank with project accession number ADWL02000000.

Annotation

Protein-coding genes were annotated with MAKER-P software in CSHL.

Source : Gramene

Whole Genome Assembly and Annotation of Oryza barthii

Assembly

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using project accession ABRL03000000. The sequence data were generated by PacBio technology.

Annotation

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline at CSHL.

Source : Gramene

Annotation of a genome.
Whole Genome Assembly and Annotation of Asian rice (Zhou et al, 2020)

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR... read more

Genome sequencing and assembly of 12 rice varieties

Genome assemblies from 12 rice varieties (https://doi.org/10.1038/s41597-020-0438-2)

Sequence assembly capable on a very large scale such as assembly of whole genomes. [http://edamontology.org]
Whole Genome Assembly and Annotation for Nerica L19
Whole Genome Assembly and Annotation for Nerica4
Whole Genome Assembly and Annotation of Oryza rufipogon

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 punctata

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 meridionalis

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 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.

Pages