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Comparative Study
. 2024 Jun 1;25(1):546.
doi: 10.1186/s12864-024-10457-1.

Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria

Yihui Gong  1 , Xin Xie  2 , Guihua Zhou  2 , Meiyu Chen  2 , Zhiyin Chen  2 , Peng Li  3 , Hua Huang  4
Affiliations
Comparative Study

Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria

Yihui Gong et al. BMC Genomics. .

Abstract

Background: Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed.

Results: The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution.

Conclusions: The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.

Keywords: Brassica rapa var. Purpuraria; Mitochondrial genome; Phylogenetic analysis; RNA editing; Repeat sequence.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The circular map of the B. rapa var. Purpuraria mt genome
Fig. 2
Fig. 2
RSCU analysis of the B. rapa var. Purpuraria mt genome
Fig. 3
Fig. 3
The distribution and comparison of RNA-editing sites in the PCGs of B. rapa var. Purpuraria mt genome and three closely related Brassica mt genomes
Fig. 4
Fig. 4
Dispersed repeats analysis in the B. rapa var. Purpuraria mt genome
Fig. 5
Fig. 5
Ka/Ks ratios of 33 PCGs between B. rapa var. Purpuraria and six species
Fig. 6
Fig. 6
Nucleotide diversity of B. rapa var. Purpuraria mt genome
Fig. 7
Fig. 7
Maximum-likelihood phylogenetic tree based on 31 conserved PCGs among 25 species. Ginkgo biloba (NC_027976) used as the out group
See this image and copyright information in PMC

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