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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Genetics, Epigenetics and Chromosome Biology
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1475064

Assembly and comparative analysis of the first complete mitochondrial genome of Zicaitai (Brassica rapa var. Purpuraria): insights into its genetic architecture and evolutionary relationships

Provisionally accepted
Wanyu Xiao Wanyu Xiao 1*Xian Wu Xian Wu 2*Xianyu Zhou Xianyu Zhou 1*Jing Zhang Jing Zhang 3*Jianghua Huang Jianghua Huang 4*Xiuchun Dai Xiuchun Dai 3*Hailong Ren Hailong Ren 5*Donglin Xu Donglin Xu 1*
  • 1 Guangzhou Academy of Agricultural and Rural Science, Guangzhou, China
  • 2 Northeast Agricultural University, Harbin, Heilongjiang Province, China
  • 3 Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou, China
  • 4 College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
  • 5 Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China

The final, formatted version of the article will be published soon.

    Zicaitai (Brassica rapa var. purpuraria) is a Brassica variety renowned for its distinctive taste and rich nutritional profile. In recent years, the mitochondrial genomes of several Brassica species have been documented, but the mitogenome of Zicaitai remains unreported. In this study, we present the characterization of the Zicaitai mitogenome, achieved through the assembly of sequencing reads derived from both the Oxford Nanopore and Illumina platforms. A detailed comparative analysis was carried out with other Brassica species to draw comparisons and contrasts. The Zicaitai mitogenome is characterized by a circular structure spanning 219,779 base pairs, and it encompasses a total of 59 genes. This gene set includes 33 protein-coding genes, 23 tRNA genes, and 3 rRNA genes, providing a rich foundation for further genomic study. In-depth analyses of codon usage patterns, instances of RNA editing, and the prevalence of sequence repeats within the mitogenome were also conducted to gain a more nuanced understanding of its genetic architecture. An analysis of the Ka/Ks ratios for 30 protein-coding genes shared by the mitogenomes of Zicaitai and seven other Brassica species revealed that most of these genes had undergone purifying selection. Furthermore, a phylogenetic analysis was performed, utilizing the coding sequences (CDS) from the mitochondrial genome of Zicaitai and that of 20 closely related species/varieties to trace evolutionary connections. Additionally, the study explored the migration of genes between the chloroplast and nuclear genomes and the mitogenome, offering insights into the dynamics of genetic exchange within the Brassica genus. The collective results in this study will serve as a foundational resource, aiding future evolutionary studies focused on B. rapa, and contributing to a broader understanding of the complexities of plant evolution.

    Keywords: Zicaitai, Brassica, Mitochondrial Genome, phylogenetic analysis, gene transfer

    Received: 02 Aug 2024; Accepted: 25 Sep 2024.

    Copyright: © 2024 Xiao, Wu, Zhou, Zhang, Huang, Dai, Ren and Xu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Wanyu Xiao, Guangzhou Academy of Agricultural and Rural Science, Guangzhou, China
    Xian Wu, Northeast Agricultural University, Harbin, 150030, Heilongjiang Province, China
    Xianyu Zhou, Guangzhou Academy of Agricultural and Rural Science, Guangzhou, China
    Jing Zhang, Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou, China
    Jianghua Huang, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510100, Guangdong, China
    Xiuchun Dai, Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou, China
    Hailong Ren, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
    Donglin Xu, Guangzhou Academy of Agricultural and Rural Science, Guangzhou, China

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