Whole-genome sequencing of Brassica oleracea var. capitata reveals new diversity of the mitogenome.

Kiwoung Yang,Ill-Sup Nou,Ujjal Kumar Nath,Md Abdul Kayum,Manosh Kumar Biswas,Jonghoon Lee,Go-Eun Yi,Tae-Jin Yang,Yong Pyo Lim

doi:10.1371/journal.pone.0194356

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.

Highlights

Several features of plant mitochondrial genomes that distinguish them from animal and fungal mtDNAs, include larger genome size, frequent rearrangements, and an extremely low rate of point mutations [1,2,3]
Our whole genome sequencing (WGS) and assembly showed contig/fragment number 1–2 connected to contig/fragment number 2–6, and contig/fragment number 2–6 connected to contig/fragment number 5–3 (Fig 3B), which differed from the reference mitochondrial genomes KJ820683, AP012988, and JF920286
Mitochondria contribute to energy production; metabolism and cell homeostasis depend on the performance of the mitochondrial genetic system [53]

Summary

Introduction

Several features of plant mitochondrial genomes (mtDNAs) that distinguish them from animal and fungal mtDNAs, include larger genome size, frequent rearrangements, and an extremely low rate of point mutations [1,2,3]. Plant mtDNAs are relatively stable but complex, and variable in size compared to animal mtDNAs [4,5], their DNA evolves rapidly in structure, but slowly in sequence [6]. The mtDNAs of flowering plants are variable among. Whole genome sequencing reveals mitogenome diversity in cabbage (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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Conclusion