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

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...

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Autores principales: Toda, Takushi, Toriyama, Kinya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer New York 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5394982/
https://www.ncbi.nlm.nih.gov/pubmed/24280589
http://dx.doi.org/10.1186/1939-8433-6-2
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author Toda, Takushi
Toriyama, Kinya
author_facet Toda, Takushi
Toriyama, Kinya
author_sort Toda, Takushi
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1939-8433-6-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-53949822017-04-21 Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare Toda, Takushi Toriyama, Kinya Rice (N Y) Short Report 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1939-8433-6-2) contains supplementary material, which is available to authorized users. Springer New York 2013-01-10 /pmc/articles/PMC5394982/ /pubmed/24280589 http://dx.doi.org/10.1186/1939-8433-6-2 Text en © Toda and Toriyama; licensee Springer. 2013 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Report
Toda, Takushi
Toriyama, Kinya
Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare
title Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare
title_full Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare
title_fullStr Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare
title_full_unstemmed Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare
title_short Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare
title_sort re-sequencing of mitochondrial genes in a standard rice cultivar nipponbare
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5394982/
https://www.ncbi.nlm.nih.gov/pubmed/24280589
http://dx.doi.org/10.1186/1939-8433-6-2
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