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Shotgun Assembly Sequences: Genome (WGS) and Transcriptome (TSA)

 

AACV00000000.1 Oryza sativa Japonica Group

Master
# of Contigs: 35,047
# of Proteins: 35,394
# of Scaffolds: 1,436
Total length: 374,226,283 bp
BioProject: PRJNA13139
BioSample: SAMN02953597
Keywords: WGS
Annotation: Scaffolds
Organism: Oryza sativa Japonica Groupshow lineagehide lineage
Biosource:
/cultivar = Nipponbare
/mol_type = genomic genomic
WGS: AACV01000001:AACV01035047
Scaffolds: CH401164:CH402587, CM000138:CM000149
1,436 scaffolds, 35,394 proteins, total length is 717,206,259 bases
Reference:
The Genomes of Oryza sativa: a history of duplications : PLoS Biol. 3 (2), E38 (2005) – show 117 authorshide authors
Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W., Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X., Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J., Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q., Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z., Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P., Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J., Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M., Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y., Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L., Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H., Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L., Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Tian,X., Jiao,Y., Liang,X., Jin,J., Gao,L., Zheng,W., Hao,B., Liu,S., Wang,W., Yuan,L., Cao,M., McDermott,J., Samudrala,R., Wang,J., Wong,G.K., Yang,H.
Submission:
Submitted (12-SEP-2003) Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing Airport Industrial Zone B6, Beijing, Beijing 101300, P.R.China – show 112 authorshide authors
Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W., Hu,S., Zeng,C., Zhang,J., Zhang,Y., Li,R., Xu,Z., Li,S., Li,X., Zheng,H., Cong,L., Lin,L., Yin,J., Geng,J., Li,G., Shi,J., Liu,J., Lv,H., Li,J., Wang,J., Deng,Y., Ran,L., Shi,X., Wang,X., Wu,Q., Li,C., Ren,X., Wang,J., Wang,X., Li,D., Liu,D., Zhang,X., Ji,Z., Zhao,W., Sun,Y., Zhang,Z., Bao,J., Han,Y., Dong,L., Ji,J., Chen,P., Wu,S., Liu,J., Xiao,Y., Bu,D., Tan,J., Yang,L., Ye,C., Zhang,J., Xu,J., Zhou,Y., Yu,Y., Zhang,B., Zhuang,S., Wei,H., Liu,B., Lei,M., Yu,H., Li,Y., Xu,H., Wei,S., He,X., Fang,L., Zhang,Z., Zhang,Y., Huang,X., Su,Z., Tong,W., Li,J., Tong,Z., Li,S., Ye,J., Wang,L., Fang,L., Lei,T., Chen,C., Chen,H., Xu,Z., Li,H., Huang,H., Zhang,F., Xu,H., Li,N., Zhao,C., Li,S., Dong,L., Huang,Y., Li,L., Xi,Y., Qi,Q., Li,W., Zhang,B., Hu,W., Zhang,Y., Zheng,W., Hao,B., Liu,S., Wang,W., Yuan,L., Cao,M.L., McDermott,J., Samudrala,R., Wang,J., Wong,G.K.-S., Yang,H.

The Oryza sativa Japonica Group whole genome shotgun (WGS) project has the project accession AACV00000000. This version of the project (01) has the accession number AACV01000000, and consists of sequences AACV01000001-AACV01035047.

The improved whole-genome shotgun (WGS) sequences for the genomes of indica and japonica rice, AAAA02000000 and AACV01000000, respectively, have multi-megabase contiguity and are nearly 1000-fold improved over the drafts of 2002. Tested against a non-redundant collection of 19,079 full-length cDNAs, 98.1% of the genes are aligned without fragmentation to the mapped super-scaffolds of one or the other genome. Despite having only a small variation in gene content, there is an enormous variation in intergenic regions. At least a quarter of the two sequences could not be aligned, and in the aligned region single-nucleotide-polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions, to 27.6 SNP/kb in the transposable elements. Annotation was updated on the chromosomes, CM000138-CM000149, in February 2009.

Contigs
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GenBank:AACV01.1.gbff.gz 164.8 Mb
FASTA:AACV01.1.fsa_nt.gz 110.2 Mb
ASN.1:AACV01.1.bbs.gz 89.3 Mb