[Last update: Thu July 30 2022, Dr. Yong Zhou]

IMPORTANT: This page provides nearly telomeres to telomeres genome assemblies for Magic16 accessions and corresponding data, including gene annotations, TEs identification, natural variants detection (PAV, INV, SNPs, InDels) of O. sativa. The data were released on August 30, 2022, last update.

Genome Sequences and Assemblies

The genomes were sequenced by >100x PacBio sequencing reads and assembled using standard PacBio genome assembly (i.e., canu, falcon, mecat2, flye and wtdbg2) and GPM pipeline with Quiver polishing. We also performed >100x Illumina paired-end sequencing to further correct remaining sequencing errors by Pilon (Version2). After manual curation by GPM, the final assemblies reached chromsome-equivalent completeness. Based on each assembly, we conducted base-line annotation for various genomic features, such as centromeres, telomeres, protein-coding genes, transposable elements (TEs).

Data avaliable

Here, we provide all the assembly and annotation files as follows. The assembly files are in FASTA format. The annotation files are in GFF format.


Variety Name/Accession ID Speicies/genome Subpopulation Genome Assembly (NCBI) Annotation (gramene)
IRGSP-1.0/NIPPONBARE O. sativa-AA (Asian rice) GJ-temp GCA_001433935.1 oryza_sativa_core_4_87_7.gff ensemblgenomes/release-48
CHAO MEO::IRGC 80273-1 O. sativa-AA (Asian rice) GJ-subtrp GCA_009831315.1 oryza_sativa132278_core_4_87_1.gff
Azucena O. sativa-AA (Asian rice) GJ-trop1 GCA_009830595.1 oryza_sativaazucena_core_4_87_1.gff
KETAN NANGKA::IRGC 19961-2 O. sativa-AA (Asian rice) GJ-trop2 GCA_009831275.1 oryza_sativa128077_core_4_87_1.gff
ARC 10497::IRGC 12485-1 O. sativa-AA (Asian rice) cB GCA_009831255.1 oryza_sativa117425_core_4_87_1.gff
PR 106::IRGC 53418-1 O. sativa-AA (Asian rice) XI-1B2 GCA_009831045.1 oryza_sativa127742_core_4_87_1.gff
Minghui 63 O. sativa-AA (Asian rice) XI-adm MH63RS2 MH63RS3 oryza_sativamh63.RS3_core_4_87_1.gff
IR 64 O. sativa-AA (Asian rice) XI-1B1 GCA_009914875.1 oryza_sativair64_core_4_87_1.gff
Zhenshan 97 O. sativa-AA (Asian rice) GJ-subtrp ZS97RS2 ZS97RS3 oryza_sativazs97.RS3_core_4_87_1.gff
LIMA::IRGC 81487-1 O. sativa-AA (Asian rice) XI-3A GCA_009829395.1 oryza_sativa127564_core_4_87_1.gff
KHAO YAI GUANG::IRGC 65972-1 O. sativa-AA (Asian rice) XI-3B1 GCA_009831295.1 oryza_sativa127518_core_4_87_1.gff
GOBOL SAIL (BALAM)::IRGC 26624-2 O. sativa-AA (Asian rice) XI-2A GCA_009831025.1 oryza_sativa132424_core_4_87_1.gff
LIU XU::IRGC 109232-1 O. sativa-AA (Asian rice) XI-3B2 GCA_009829375.1 oryza_sativa125827_core_4_87_1.gff
LARHA MUGAD::IRGC 52339-1 O. sativa-AA (Asian rice) XI-2B GCA_009831355.1 oryza_sativa125619_core_4_87_1.gff
N22 (N 22::IRGC 19379-1) O. sativa-AA (Asian rice) cA1 GCA_001952365.2 oryza_aus_core_3_87_2.gff
NATEL BORO::IRGC 34749-1 O. sativa-AA (Asian rice) cA2 GCA_009831335.1 oryza_sativa127652_core_4_87_1.gff
O. rufipogon PNG91-7::IRGC 106523-1 O. rufipogon-AA (Asian rice progenitor) - GCA_023541355.1 CHSL
O. punctataIRGC 105690 O. punctata-BB (Outgroup) - GCA_000573905.2 CHSL

Whole Genomes Metadata

Transcriptome NCBI/BioProject NCBI/BioSample NCBI/Sequence Read Archive (SRA) Publication
Iso-Seq PRJNA760839 SAMN21236499-SAMN21236518 SRR15851177-SRR15851215 Zhou et al., 2022, preprint
RNA-Seq PRJNA659864 SAMN15929528-SAMN15929547 SRR12545183-SRR12545735 Zhou et al., 2022, preprint

Pangenome Graphs

Pangenome Graphs Names Backbone Genome Constitute Genomes Construction methods Publications
RPRP.M16.Pangenome.Graph.Version1 IRGSP-1.0/Nipponbare 16 O. sativa genomes from Whole Genomes Metadata minigraph Zhou et al., 2022, preprint
Pangenome Graphs *.gfa, *.fa and chusum files are avaliable. Password: N9ggtr%61KJD

Pangenome Graphs stats


Raw Reads Accession

The PacBio sequencing reads for this project has been deposed in the National Center for Biotechnology Information (NCBI). All the BioProjects, BioSamples, SRA could be found in Table 3 of our paper "A platinum standard pan-genome resource that represents the population structure of Asian rice".