IRGSP statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

IRGSP specifications

Information


Unique identifier OMICS_22297
Name IRGSP
Alternative name International Rice Genome Sequencing Project
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 5.0
Maintained Yes

Maintainer


  • person_outline IRGSP Team

Publication for International Rice Genome Sequencing Project

IRGSP citations

 (134)
library_books

Novel sequences, structural variations and gene presence variations of Asian cultivated rice

2018
Sci Data
PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] y unknown in almost all eukaryotes. In this descriptor, we reported the SV data and gene PAV data of O. sativa, together with the novel sequences absent in the widely used Nipponbare reference genome IRGSP-1.0, as key results of the in-depth analyses of the sequencing data of the 3k RG.In this data descriptor, we present the rice SV data obtained by calling against the Nipponbare reference genome […]

library_books

Development of a quantitative pachytene chromosome map and its unification with somatic chromosome and linkage maps of rice (Oryza sativa L.)

2018
PLoS One
PMCID: 5908146
PMID: 29672536
DOI: 10.1371/journal.pone.0195710

[…] e long arm. The heterochromatic region of Chromosome 4 occupied about 17 Mb from the end of the short arm, based on FISH experiment to pachytene chromosome [] and the revised genome sequence of rice (IRGSP-1.0) []. Nucleotide sequence of Chromosome 4 showed that variety of repetitive sequences were located in the heterochromatic regions including the centromeric region except miniature inverted-re […]

library_books

Identification of a cold tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next generation sequencing strategy

2018
PMCID: 5906412
PMID: 29671148
DOI: 10.1186/s12284-018-0218-1

[…] lumina MiSeq platform using MiSeq Reagent Kit v2 (500 cycles) (Illumina Inc., San Diego, CA, USA). The short reads from both parents and the two DNA pools were aligned to Nipponbare reference genome (IRGSP ) using the BWA software (Li and Durbin ). Reads of the T-pool and S-pool were separately aligned to KY131 and DN422 consensus sequence reads to call SNPs with the SAM tools software (Li and Dur […]

library_books

Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes

2018
Front Plant Sci
PMCID: 5902711
PMID: 29692796
DOI: 10.3389/fpls.2018.00473

[…] (TEJ), and tropical japonica (TRJ), the aromatic (ARO) group was not included due to too limited sample size. The cleaned reads were mapped to the Nipponbare reference genome Os-Nipponbare-Reference-IRGSP-1.0 () using BWA-MEM v0.7.10-r789 () with default parameters. Variants were called using GATK HaplotypeCaller module (), and were filtered by removing variant calls with a quality <50. The popul […]

call_split

Overexpression of OsNAC14 Improves Drought Tolerance in Rice

2018
Front Plant Sci
PMCID: 5855183
PMID: 29593766
DOI: 10.3389/fpls.2018.00310
call_split See protocol

[…] ere prepared using the TruSeq RNA sample Prep Kit (v2) (Macrogen). RNA-sequencing was repeated twice with samples from NT and PGD1::OsNAC14 transgenic plants. Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequences, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., ). To map the re […]

library_books

Comparative Transcriptome Profiling of Rice Near Isogenic Line Carrying Xa23 under Infection of Xanthomonas oryzae pv. oryzae

2018
Int J Mol Sci
PMCID: 5877578
PMID: 29498672
DOI: 10.3390/ijms19030717

[…] oving adapter sequences and low quality reads by cutadapt tool []. Thereafter, clean sequence reads were mapped to the available Japonica rice Nipponbare genome (http://rapdb.dna.affrc.go.jp/download/irgsp1.html) [] using TopHat v2.0.12 (http://ccb.jhu.edu/software/tophat/index.shtml) [], by applying Bowtie2 v2.0.0 []. Afterwards, Cufflinks was applied to measure the transcript abundance and gave […]

Citations

Looking to check out a full list of citations?

IRGSP institution(s)
International Rice Genome Sequencing Project

IRGSP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review IRGSP