Re-sequencing of mitochondrial genes in a standard rice cultivar nipponbare

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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. © 2013 Toda and Toriyama; licensee Springer.

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Toda, T., & Toriyama, K. (2013). Re-sequencing of mitochondrial genes in a standard rice cultivar nipponbare. Rice, 6(1), 1–3. https://doi.org/10.1186/1939-8433-6-2

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