The alternative reality of plant mitochondrial DNA: One ring does not rule them all
The alternative reality of plant mitochondrial DNA: One ring does not rule them all
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DOI：
10.1371/journal.pgen.1008373
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发表时间：
2019-08-01
期刊：
影响因子：
4.5
通讯作者：
Christensen, Alan C.
中科院分区：
文献类型：
--
作者：
Kozik, Alexander;Rowan, Beth A.;Christensen, Alan C.
植物线粒体基因组通常被组装并显示为圆形地图，其基础是广泛存在于生命科学家群体中的一种观点，即圆形基因组大小的分子是植物线粒体DNA的主要形式，尽管植物线粒体研究人员认为这是一个不准确和过时的概念。许多植物线粒体基因组有一对或多对大的重复序列，这些重复序列可以作为分子间或分子内重组的位点，导致多种可供选择的排列(亚型)。大多数线粒体基因组的组装使用的方法无法捕获物种内异构体的完整谱，导致对其结构和重组活性的不完全推断。为了记录和研究植物线粒体DNA结构多样性的潜在原因，我们使用了长读(PacBio)和短读(Illumina)测序数据来组装和比较驯化(Lactuca Sativa)和野生(L.saligna和L.serriola)生菜的线粒体基因组。我们描述了每个物种中一套全面、复杂的异构体，并比较了不同物种之间的基因组结构。荧光显微镜下对紫花苜蓿线粒体DNA分子的物理分析表明，线粒体DNA分子具有多种线形、分支和环状结构。美洲斑潜蝇和斑潜蝇的线粒体基因组在序列和排列上是相同的，而与盐生斑潜蝇有很大的差异，说明驯化过程中线粒体基因组结构没有改变。从我们数据中的异构体，我们推断重组发生在不同频率的各种大小的重复中。盐藻和另外两种莴苣在基因组结构上的差异在很大程度上可以用罕见的重组事件来解释。我们的数据表明，将植物线粒体基因组表示为简单的环形分子并不能准确地描述其真实性质，而实际上植物线粒体DNA是一个复杂的、动态的混合形式。作者摘要在研究文章和教科书中，植物线粒体基因组通常被描述为基因组大小的环形分子。尽管过去几十年对线粒体DNA(MtDNA)的研究表明，基因组大小的圆圈非常罕见，而替代形式的mtDNA更常见，但许多生物学家仍然认为圆形图谱代表了一个或多个物理染色体。这种误解可能会导致对线粒体基因组如何组装的偏见，以及对它们的进化关系、共性和历史的误解。在这项研究中，我们提出了一种组装方法，使用短读和长读测序数据来确定三个生菜物种的线粒体基因组结构。我们发现这些线粒体基因组是流动的和动态的，基因组的多个序列排列共存于同一物种的个体内。物种间序列排列的差异可以用罕见的重组事件来解释。对线粒体DNA物理分子的检查发现主要是非环状形式。我们证明了植物线粒体基因组是物理形式和序列安排的复杂混合物。我们的数据表明，植物线粒体基因组应该以多个序列单位的形式呈现，表明它们之间的可变和动态连接，而不是圆圈。
Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across the broad community of life scientists that circular genome-sized molecules are the primary form of plant mitochondrial DNA, despite the understanding by plant mitochondrial researchers that this is an inaccurate and outdated concept. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative arrangements (isoforms). Most mitochondrial genomes have been assembled using methods unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. We characterized a comprehensive, complex set of isoforms within each species and compared genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms in our data, we infer that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other Lactuca species can be largely explained by rare recombination events that rearranged the structure. Our data demonstrate that representations of plant mitochondrial genomes as simple, circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.Author summary Plant mitochondrial genomes are commonly depicted in research articles and textbooks as circular molecules that are the size of the genome. Although research on mitochondrial DNA (mtDNA) over the past few decades has revealed that genome-sized circles are exceedingly rare and that alternative forms of mtDNA are more common, many biologists still perceive circular maps as representing one or more physical chromosomes. This misconception can lead to biases in how mitochondrial genomes are assembled and misinterpretation of their evolutionary relationships, synteny, and histories. In this study, we present an assembly methodology that uses short- and long-read sequencing data to determine the mitochondrial genome structures of three lettuce species. We show that these mitochondrial genomes are fluid and dynamic, with multiple sequence arrangements of the genome coexisting within individuals of the same species. Differences in sequence arrangements between species can be explained by rare recombination events. Inspection of physical molecules of mtDNA reveals primarily non-circular forms. We demonstrate that plant mitochondrial genomes are a complex mixture of physical forms and sequence arrangements. Our data suggest that plant mitochondrial genomes should be presented as multiple sequence units showing their variable and dynamic connections, rather than as circles.