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

文献类型： 外文期刊

作者： Xiao, Wanyu 1 ; Wu, Xian 2 ; Zhou, Xianyu 1 ; Zhang, Jing 1 ; Huang, Jianghua 3 ; Dai, Xiuchun 1 ; Ren, Hailong 4 ; Xu, Donglin 1 ;

作者机构： 1.Guangzhou Acad Agr & Rural Sci, Guangzhou Municipal Crop Seed Qual Inspect Ctr, Guangzhou, Peoples R China

2.Northeast Agr Univ, Harbin, Peoples R China

3.Zhongkai Univ Agr & Engn, Coll Agr & Biol, Guangzhou, Peoples R China

4.Guangdong Acad Agr Sci, Crops Res Inst, Guangdong Prov Key Lab Crop Genet Improvement, Guangzhou, Peoples R China

关键词： zicaitai; Brassica; mitochondrial genome; phylogenetic analysis; gene transfer

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：4.8； 五年影响因子：5.7 ）

ISSN： 1664-462X

年卷期： 2024 年 15 卷

页码：

收录情况： SCI

摘要： Introduction 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. Methods In this study, we characterized 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. 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. 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. Results 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. 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. 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. Discussion 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.

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