Zhang Yue, Xu Yang, Chen Hao, Wang Liuyang, Yin Kangquan, Du Fang K
School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, United States.
Front Genet. 2020 Jan 14;10:1295. doi: 10.3389/fgene.2019.01295. eCollection 2019.
Inverted repeat (IR) regions in the plastomes from land plants induce homologous recombination, generating isomeric plastomes. While the plastomes of Taxaceae species often lose one of the IR regions, considerable isomeric plastomes were created in Taxaceae species with a hitherto unclarified mechanism. To investigate the detailed mechanism underpinning the IR-independent genesis of plastomic diversity, we sequenced four Taxaceae plastomes, including Siebold & Zuccarini, Nan Li & R. R. Mill, and two individuals of Zuccarini. Then we compared these structures with those of previously reported Taxaceae plastomes. Our analysis identified four distinct plastome forms that originated from the rearrangements of two IR-flanking inverted fragments. The presence of isomeric plastomes was then verified in individuals. Both rearrangement analyses and phylogenetic results indicated that Taxaceae were separated into two clades, one including and and another formed by and . Our reconstructed scenario suggests that the minimum number of inversion events required for the transformation of the plastome of Masters into the diversified Taxaceae plastomes ranged from three to six. To sum up, our study reveals a distinct pattern and the mechanism driving the structural diversification of Taxaceae plastomes, which will advance our understanding of the maintenance of plastomic diversity and complexity in conifers.
陆地植物质体基因组中的反向重复（IR）区域会引发同源重组，产生异构质体基因组。虽然红豆杉科物种的质体基因组通常会丢失其中一个IR区域，但在红豆杉科物种中却产生了相当数量的异构质体基因组，其机制迄今尚未阐明。为了研究质体基因组多样性的IR非依赖性起源的详细机制，我们对四个红豆杉科质体基因组进行了测序，包括东北红豆杉、南方红豆杉和两个欧洲红豆杉个体。然后我们将这些结构与先前报道的红豆杉科质体基因组结构进行了比较。我们的分析确定了四种不同的质体基因组形式，它们起源于两个IR侧翼反向片段的重排。随后在个体中验证了异构质体基因组的存在。重排分析和系统发育结果均表明，红豆杉科分为两个分支，一个包括东北红豆杉和南方红豆杉，另一个由欧洲红豆杉形成。我们重建的情景表明，将台湾红豆杉的质体基因组转化为多样化的红豆杉科质体基因组所需的最小倒位事件数为三到六个。总之，我们的研究揭示了红豆杉科质体基因组结构多样化的独特模式和驱动机制，这将增进我们对针叶树质体基因组多样性和复杂性维持的理解。
