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

Takushi Toda, Kinya Toriyama

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number2
Pages (from-to)1-3
Number of pages3
JournalRice
Volume6
Issue number1
DOIs
Publication statusPublished - 2013 Jan 1

Keywords

  • Mitochondria
  • Re-sequencing
  • Rice
  • SNP

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Soil Science
  • Plant Science

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