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Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split

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Abstract

Cytoplasmic male-sterility (CMS) conferred by the CMS-S cytoplasm has been most commonly used for onion (Allium cepa L.) F1 hybrid seed production. We first report the complete mitochondrial genome sequence containing CMS-S cytoplasm in this study. Initially, seven contigs were de novo assembled from 150-bp paired-end raw reads produced from the total genomic DNA using the Illumina NextSeq500 platform. These contigs were connected into a single circular genome consisting of 316,363 bp (GenBank accession: KU318712) by PCR amplification. Although all 24 core protein-coding genes were present, no ribosomal protein-coding genes, except rps12, were identified in the onion mitochondrial genome. Unusual trans-splicing of the cox2 gene was verified, and the cox1 gene was identified as part of the chimeric orf725 gene, which is a candidate gene responsible for inducing CMS. In addition to orf725, two small chimeric genes were identified, but no transcripts were detected for these two open reading frames. Thirteen chloroplast-derived sequences, with sizes of 126–13,986 bp, were identified in the intergenic regions. Almost 10 % of the onion mitochondrial genome was composed of repeat sequences. The vast majority of repeats were short repeats of <100 base pairs. Interestingly, the gene encoding ccmFN was split into two genes. The ccmF N gene split is first identified outside the Brassicaceae family. The breakpoint in the onion ccmF N gene was different from that of other Brassicaceae species. This split of the ccmF N gene was also present in 30 other Allium species. The complete onion mitochondrial genome sequence reported in this study would be fundamental information for elucidation of onion CMS evolution.

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Acknowledgments

This study was supported by the Agriculture Research Center program, Golden Seed Project (Center for Horticultural Seed Development, No 213003-04-2-SB910) and a Grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ011034). The authors thank Ji-wha Hur, Jeong-Ahn Yoo, and Su-jung Kim for their dedicated technical assistance.

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

    Bongju Kim & Sunggil Kim

  2. Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Kyunghee Kim & Tae-Jin Yang

  3. Phyzen Genomics Institute, 501-1, Gwanak Century Tower, Gwanak-gu, Seoul, 151-836, Republic of Korea

    Kyunghee Kim

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294_2016_595_MOESM1_ESM.tif

Supplementary Fig. 1. Organization of seven contigs assembled using sequence reads produced by next-generation sequencing. Genes transcribed as forward and reverse complements are indicated as boxes on and beneath the lines, respectively. The filled and empty boxes indicate exons and introns, respectively (TIFF 97 kb)

294_2016_595_MOESM2_ESM.tif

Supplementary Fig. 2. Positions of the seven contigs on the onion mitochondrial genome. A. Onion mitochondrial genome map showing positions of the seven contigs. Bars on the contigs indicate positions of the polymerase chain reaction (PCR) products amplified using primers binding to the end sequences of each contig or chloroplast-derived sequences. B. PCR products amplified using primer pairs binding to the junctions of the contigs. The primer sequences are shown in Supplementary Table 2. Con: PCR product amplified using a primer pair binding to the closely linked nad3 and rps12 genes, respectively (TIFF 334 kb)

294_2016_595_MOESM3_ESM.tif

Supplementary Fig. 3. Structure of three chimeric genes identified in the onion mitochondrial genome. Arrow-shaped boxes indicate the 5′-to-3′ direction. Empty and gray boxes indicate exons and uncharacterized sequences, respectively (TIFF 54 kb)

294_2016_595_MOESM4_ESM.tif

Supplementary Fig. 4. Onion mitochondrial genome map showing the positions and sizes of chloroplast-derived sequences. The detail information of these 13 fragments is shown in Supplementary Table 3 (TIFF 56 kb)

294_2016_595_MOESM5_ESM.tif

Supplementary Fig. 5. Assessment of recombination frequency of two large-sized repeats. A. Diagram showing the positions of primers used to detect normal and recombinant conformations. B. PCR amplification of normal and recombinant conformations. Detail information about the R1 and R2 repeats are shown in Supplementary Table 7. PCR was performed with a 35-cycle condition and primer sequences are shown in Supplementary Table 2 (TIFF 211 kb)

Supplementary Fig. 6. Number of sequence reads mapped onto the onion mitochondrial genome sequence (TIFF 16 kb)

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Supplementary material 9 (DOCX 16 kb)

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Supplementary material 11 (XLSX 32 kb)

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Kim, B., Kim, K., Yang, TJ. et al. Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split. Curr Genet 62, 873–885 (2016). https://doi.org/10.1007/s00294-016-0595-1

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