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

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

doi:10.1371/journal.pone.0194356

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

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

Authors

Kiwoung Yang¹, Ujjal Kumar Nath^{1

2}, Manosh Kumar Biswas¹, Md Abdul Kayum¹, Go-Eun Yi¹, Jonghoon Lee³, Tae-Jin Yang⁴, Ill-Sup Nou¹

Affiliations

¹ Department of Horticulture, Sunchon National University, Suncheon, Korea.
² Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh.
³ Joeun Seed, Goesan-Gun, Chungcheongbuk-Do, Republic of Korea.
⁴ 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, Republic of Korea.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brassica / classification
Brassica / genetics*
Exome Sequencing / methods*
Gene Expression Profiling / methods
Gene Expression Regulation, Plant
Genes, Mitochondrial / genetics
Genetic Variation*
Genome, Mitochondrial / genetics*
Genome, Plant / genetics*
Phylogeny

Grants and funding

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.