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Whole-genome sequencing of Brassica oleracea var. capitata reveals new diversity of the mitogenome
PLOS ONE ( IF 3.7 ) Pub Date : 2018-03-16 , DOI: 10.1371/journal.pone.0194356
Kiwoung Yang , Ujjal Kumar Nath , Manosh Kumar Biswas , Md Abdul Kayum , Go-eun Yi , Jonghoon Lee , Tae-Jin Yang , Ill-Sup Nou

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.



中文翻译:

甘蓝变种全基因组测序 实蝇揭示了线粒体基因的新的多元化

植物线粒体基因组(mtDNA)的序列结构各不相同。我们组装了甘蓝型油菜卡塔塔mtDNA的平均覆盖深度为25倍全基因组测序(WGS),并使用先前报道的KJ820683和AP012988 mtDNA作为参考,通过BLASTZ确认存在8个重叠群/片段。mtDNA序列读段的组装产生了219,975 bp的环状结构。我们组装的mtDNA,NCBI认证。不。KU831325包含34个蛋白质编码基因,3个rRNA基因和19个tRNA基因,与KJ820683和AP012988参考mtDNA相似。在KU831325组件中未发现大的重复。但是,与先前报道的mtDNA相比,KU831325在不同区域的碱基排列显示出差异。在参考mtDNA KJ820683和AP012988中,重叠群/片段4被分为两个重叠群/片段4a和4b。但是,重叠群/片段4是单个重叠群/片段,其中29个,KU831325中的661 bp。使用来自重叠群/片段4号分开部分的侧翼标记的PCR和qRT-PCR证实它是单个重叠群/片段。此外,与KU831325相比,质体基因组和mtDNA的基因组重排支持其他mtDNA中存在异质性和异质性区块反向排列,这可能是其多样性的原因之一。因此,我们的结果证实了不同mtDNA在不同领域的存在。与KU831325相比,质体基因组和mtDNA的基因组重排支持了其他mtDNA中异质性区块的异质性和反向排列,这可能是其多样性的原因之一。因此,我们的结果证实了不同mtDNA在不同领域的存在。与KU831325相比,质体基因组和mtDNA的基因组重排支持了其他mtDNA中异质性区块的异质性和反向排列,这可能是其多样性的原因之一。因此,我们的结果证实了不同mtDNA在不同领域的存在。豆科亚种。

更新日期:2018-03-17
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