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. 2018 Mar 16;13(3):e0194356.
doi: 10.1371/journal.pone.0194356. eCollection 2018.

Whole-genome Sequencing of Brassica Oleracea Var. Capitata Reveals New Diversity of the Mitogenome

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Free PMC article

Whole-genome Sequencing of Brassica Oleracea Var. Capitata Reveals New Diversity of the Mitogenome

Kiwoung Yang et al. PLoS One. .
Free PMC article

Abstract

Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA. No large repeats were found in the KU831325 assembly. However, KU831325 showed differences in the arrangement of bases at different regions compared to the previously reported mtDNAs. In the reference mtDNAs KJ820683 and AP012988, contig/fragment number 4 is partitioned into two contigs/fragments, 4a and 4b. However, contig/fragment number 4 was a single contig/fragment with 29,661 bp in KU831325. PCR and qRT-PCR using flanking markers from separate parts of contig/fragment number 4 confirmed it to be a single contig/fragment. In addition, genome re-alignment of the plastid genome and mtDNAs supported the presence of heteroplasmy and reverse arrangement of the heteroplasmic blocks within the other mtDNAs compared to KU831325 that might be one of the causal factors for its diversity. Our results thus confirm the existence of different mtDNAs in diverse B. oleracea subspecies.

Conflict of interest statement

Competing Interests: Authors declare that there are no competing interests. Jeon Seed, Republic of Korea provided support in the form of salaries for Jonghoon Lee but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Initially when we started this experiment, Jonghoon Lee was a team member of the group of Prof. TaeJin Yang, Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University. Thereafter, Jonghoon Lee moved to Jeon Seed, Republic of Korea. However, he contributed in this manuscript for helping in sequence trimming and assembly the sequence reads at the time of his stay with Prof. Tae-Jin Yang. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials. The specific roles of authors are articulated in the 'author contributions' section.

Figures

Fig 1
Fig 1. The process for assembling the complete mitochondrial genome sequence using the eight mitochondrial contigs/fragments.
Fig 2
Fig 2. Map of the mitochondrial genome of B. oleracea var. capitata.
Boxes on the inside and outside of the outer circle represent ORF genes. Gene colors correspond to the functional categories listed in the legend. The inner circle displays the GC content represented by dark gray bars. The Fig was created using OGDraw v1.2 (adopted from [45]).
Fig 3
Fig 3. Comparison of KU831325 with the reference mtDNAs KJ820683, AP012988, and JF920286 using the eight related contigs/fragments.
(A) The complete mtDNA assembly of B. oleracea var. capitata using the contig/fragment BLASTZ program compared with reference genome KJ820683. Conserved contigs/fragments between KJ820683 and KU831325 are presented with shadow columns (B) Organization of separate regions in the new mtDNA (KU831325) and reference (KJ820683, AP012988, and JF920286) mtDNAs. Minus (-) sign in parenthesis represent the reverse strand. Arrows indicate the designed primer position for distinguishing the mitochondrial contigs/fragments in different genotypes.
Fig 4
Fig 4
In the left panel (a) identification of variation in the KU831325 mtDNA in various inbred lines. A, B, and E are cabbage, C is broccoli, D is kale, F is cabbage of the Ogura CMS line, G is cauliflower, H is brussels sprouts, I is kohlrabi, and J is kailan and M is the reference ladder with 100 bp. The genotypes with the red asterisks were used for cloning, sequencing, and assemblage of mitochondrial DNA in B. oleracea. There are two bands for contig 2–3, with the lower band being the target amplified according to the primer product size presented in Table 1. In right panel (b) showing relative expression with significant variation of different contigs/fragments present in different genotypes.
Fig 5
Fig 5. A multiple alignment of plastid genome (KR233156) and four mtDNAs (KU831325, KJ820683, JF920286, and AP012988) of Brassica oleracea consists of several rearranged pieces.
Each genome is laid out horizontally with homologous blocks represented as coloured rectangles. Regions inverted relative to plastid are set below those that match in the forward orientation. Lines collate aligned segments between plastid and different mtDNAs. Sections of white within blocks and gaps between blocks indicate lineage specific sequence.
Fig 6
Fig 6. Syntenic block comparative analysis in Brassica oleracea mtDNAs.
The map was generated using Circos. (a) Syntenic block of B. oleracea mtDNA ‘AP012988’ with three other B. oleracea mtDNAs. (b) Syntenic block of B. oleracea mtDNA ‘KJ820683’ with three other B. oleracea mtDNAs. (c) Syntenic block of B. oleracea mtDNA ‘JF920286’ with three other B. oleracea mtDNAs. (d) Syntenic block of B. oleracea mtDNA ‘KU831325’ with three other B. oleracea mtDNAs.
Fig 7
Fig 7. Molecular phylogenetic analysis by Maximum Likelihood method of the four B. oleracea mtDNAs according to the genomic sequences and the distribution of their contigs, the black coloured value is node length and blue coloured one is boost-strap value.

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References

    1. Burger G, Lang BF, Braun HP, Marx S. The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b. Nucleic acids research. 2003;31(9):2353–60. - PMC - PubMed
    1. Knoop V. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Current genetics. 2004;46(3):123–39. doi: 10.1007/s00294-004-0522-8 - DOI - PubMed
    1. Kubo T, Newton KJ. Angiosperm mitochondrial genomes and mutations. Mitochondrion. 2008;8(1):5–14. doi: 10.1016/j.mito.2007.10.006 - DOI - PubMed
    1. Palmer JD, Herbo LA. Unicircular structure of the Brassica hirta mitochondrial genome. Current genetics. 1987;11(6–7):565–70. - PubMed
    1. Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, et al. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 2012;10(1):e1001241 doi: 10.1371/journal.pbio.1001241 - DOI - PMC - PubMed

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Grant support

This research was supported by the Golden Seed Project (Center for Horticultural Seed Development, No. 213007-05-2-CG100), the Ministry of Agriculture, Food and Rural Affairs (MAFRA), the Ministry of Oceans and Fisheries (MOF), the Rural Development Administration (RDA), and the Korea Forest Service (KFS), Republic of Korea (ISN). Jeon Seed, Republic of Korea provided support in the form of salaries for Jonghoon Lee. The funders did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and research materials.
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