Unknown

Dataset Information

0

Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare.


ABSTRACT: BACKGROUND:Genomic sequence of a rice cultivar Nipponbare has been often used as a reference sequence since a whole-genomic sequence was first determined in 2005 by the International Rice Genome Sequencing Project. As for mitochondrial genomic sequence of Nipponbare, two groups have deposited their sequences into DDBJ/EMBL/GenBank under the accession numbers BA000029 and DQ167400. However, there are 19 discrepancies in the nucleotide sequences of 7 genes between BA000029 and DQ167400. FINDINGS:We performed PCR to amplify these 7 genes and to perform direct sequencing. Nucleotides of the discrepant sites were all identical to those in DQ167400.1. The sequence in BA000029.3 is thought to contain sequencing errors. CONCLUSION:Nucleotide sequences of the mitochondrial genes in BA000029.3 need to be updated using the data in this study when used as a reference genome.

SUBMITTER: Toda T 

PROVIDER: S-EPMC5394982 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

altmetric image

Publications

Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare.

Toda Takushi T   Toriyama Kinya K  

Rice (New York, N.Y.) 20130110 1


<h4>Background</h4>Genomic sequence of a rice cultivar Nipponbare has been often used as a reference sequence since a whole-genomic sequence was first determined in 2005 by the International Rice Genome Sequencing Project. As for mitochondrial genomic sequence of Nipponbare, two groups have deposited their sequences into DDBJ/EMBL/GenBank under the accession numbers BA000029 and DQ167400. However, there are 19 discrepancies in the nucleotide sequences of 7 genes between BA000029 and DQ167400.<h4  ...[more]

Similar Datasets

2012-10-02 | GSE31775 | GEO
| S-EPMC6567010 | biostudies-literature
2012-10-02 | E-GEOD-31775 | biostudies-arrayexpress
2013-12-31 | GSE48202 | GEO
| S-EPMC8563964 | biostudies-literature
| S-EPMC5613164 | biostudies-literature
| S-EPMC5507442 | biostudies-literature
| S-EPMC5569538 | biostudies-literature
| S-EPMC4958085 | biostudies-literature
| S-EPMC8141088 | biostudies-literature