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Comparison of mitochondrial and chloroplast genome segments from three onion (Allium cepa L.) cytoplasm types and identification of a trans-splicing intron of cox2

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Abstract

To study genetic relatedness of two male sterility-inducing cytotypes, the phylogenetic relationship among three cytotypes of onions (Allium cepa L.) was assessed by analyzing polymorphisms of the mitochondrial DNA organization and chloroplast sequences. The atp6 gene and a small open reading frame, orf22, did not differ between the normal and CMS-T cytotypes, but two SNPs and one 4-bp insertion were identified in CMS-S cytotype. Partial sequences of the chloroplast ycf2 gene were integrated in the upstream sequence of the cob gene via short repeat sequence-mediated recombination. However, this chloroplast DNA-integrated organization was detected only in CMS-S. Interestingly, disruption of a group II intron of cox2 was identified for the first time in this study. Like other trans-splicing group II introns in mitochondrial genomes, fragmentation of the intron occurred in domain IV. Two variants of each exon1 and exon2 flanking sequences were identified. The predominant types of four variants were identical in both the normal and the CMS-T cytotypes. These predominant types existed as sublimons in CMS-S cytotypes. Altogether, no differences were identified between normal and CMS-T, but significant differences in gene organization and nucleotide sequences were identified in CMS-S, suggesting recent origin of CMS-T male-sterility from the normal cytotype.

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Acknowledgments

This study was supported by the Specific Joint Agricultural Research-Promoting Projects (Project No. 200803A01081219), RDA, Republic of Korea, and by the Biotechnology Research Institute, Chonnam National University, Republic of Korea. We thank Seon Chong and Mi-Young Kim for their dedicated technical assistance.

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  1. Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Korea

    Sunggil Kim

  2. National Institute of Horticultural and Herbal Science, RDA, Suwon, 441-440, Korea

    Moo-Kyoung Yoon

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  1. Sunggil Kim
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  2. Moo-Kyoung Yoon
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Correspondence to Sunggil Kim.

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Communicated by R. Bock.

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Kim, S., Yoon, MK. Comparison of mitochondrial and chloroplast genome segments from three onion (Allium cepa L.) cytoplasm types and identification of a trans-splicing intron of cox2 . Curr Genet 56, 177–188 (2010). https://doi.org/10.1007/s00294-010-0290-6

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