Department of Horticulture, Sunchon National University, Suncheon, Korea.
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh.
PLoS One. 2018 Mar 16;13(3):e0194356. doi: 10.1371/journal.pone.0194356. eCollection 2018.
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.
植物线粒体基因组（mtDNA）在序列结构上存在差异。我们使用平均覆盖深度为 25X 的全基因组测序（WGS）组装了甘蓝型油菜变种花椰菜的 mtDNA，并通过使用先前报道的 KJ820683 和 AP012988 mtDNA 作为参考的 BLASTZ 证实了存在 8 个连续/片段。组装 mtDNA 序列读取结果得到了一个 219975bp 的圆形结构。我们组装的 mtDNA，NCBI acc. no. KU831325，包含 34 个蛋白编码基因、3 个 rRNA 基因和 19 个 tRNA 基因，与 KJ820683 和 AP012988 参考 mtDNA 具有相似性。在 KU831325 组装中没有发现大的重复序列。然而，与先前报道的 mtDNAs 相比，KU831325 在不同区域的碱基排列上存在差异。在参考 mtDNAs KJ820683 和 AP012988 中，连续/片段 4 被分为两个连续/片段 4a 和 4b。然而，在 KU831325 中，连续/片段 4 是一个单一的连续/片段，长度为 29661bp。使用来自连续/片段 4 不同部分的侧翼标记进行 PCR 和 qRT-PCR 证实它是一个单一的连续/片段。此外，质体基因组和 mtDNAs 的基因组重对齐支持了其他 mtDNAs 中存在异质体和异质体块的反向排列，而与 KU831325 相比，这可能是其多样性的一个原因。我们的结果因此证实了不同甘蓝亚种中存在不同的 mtDNA。
