Oryza rufipogon ASM81722v2 Assembly & Annotation

Overview

Analysis Name Oryza rufipogon ASM81722v2 Assembly & Annotation
Sequencing technology Illumina
Assembly method Genome Puzzle Master
Release Date 2014-12-30
Reference Publication(s)

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. 2018 Feb;50(2):285-296. doi: 10.1038/s41588-018-0040-0.

Abstract

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago.

Assembly statistics

Genome size339.2 Mb
Total ungapped length332.7 Mb
Number of scaffolds3,819
Scaffold N5027.8 Mb
Scaffold L506
Number of contigs68,482
Contig N5034.2 kb
Contig L502,765
GC percent42.5
Assembly levelScaffold

Assembly

The Oryza rufipogon ASM81722v2 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) GCA_000817225.2_ASM81722v2_genomic.fna.gz

Gene Predictions

The Oryza rufipogon ASM81722v2 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) Oryza_rufipogon.maker.gff.gz
CDS sequences (FASTA file) Oryza_rufipogon.coding.fasta.gz
Protein sequences (FASTA file) Oryza_rufipogon.protein.fasta.gz

Functional Analysis

Functional annotation for the Oryza rufipogon ASM81722v2 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Oryza_rufipogon.Pfam.tsv.gz

S genes

Summary

QueryScaffoldSize(bp)CoordinatestBLASTn HittBLASTn %IDDomain
DUF247I-SΨHG417169.1266527785391548-5391697LpSDUF247-I_chromosome167DUF247
DUF247II-SHG417169.1266527785378027-5379688LpSDUF247-II_chromosome168DUF247
HPS10-SHG417169.1266527785381623-5381725,
5381828-5381964
LpsS_contig1102937-
DUF247I-ZΨHG417168.13052168628078371-28078724Olongistaminata62DUF247
DUF247II-ZHG417168.13052168628084831-28086447AlongiglumisDUF247II-Z75DUF247
HPS10-ZHG417168.13052168628083282-28083379,
28083509-28083629
Osativa64-

Nucleotide

Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences