该 Hesperis 分支的基因组大小的巨大变化是由 DNA 重复序列的普遍增殖和罕见的基因组缩小造成的。
The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing.
机构信息
CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic.
Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic.
出版信息
Ann Bot. 2019 Aug 2;124(1):103-120. doi: 10.1093/aob/mcz036.
BACKGROUND AND AIMS
Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing.
METHODS
Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes.
KEY RESULTS
Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species.
CONCLUSIONS
The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.
背景与目的
大多数十字花科物种（十字花科）的核基因组较小（平均 1C 值为 617 Mb）。基因组最大的物种出现在单系的 Hesperis 分支（Mandáková 等人，植物生理学 174:2062-2071；也称为 Clade E 或 Lineage III）中。虽然该分支的大多数染色体数为 6 或 7，但单倍体基因组大小变化了 16 倍（256-4264 Mb）。为了深入了解 Hesperis 分支（约 350 个物种，约 48 个属）的基因组大小进化，我们旨在鉴定、量化并原位定位这些基因组构建所涉及的重复序列。我们通过低通量全基因组测序分析了七个物种的核重复组，这些物种涵盖了分支的系统发育和基因组大小范围。
方法
通过流式细胞术估计基因组大小。将基因组 DNA 在 Illumina 测序仪上测序，并使用 RepeatExplorer 识别和量化 DNA 重复序列；使用荧光原位杂交将最丰富的重复序列定位在染色体上。为了评估基于细菌人工染色体（BAC）的 Hesperis 分支物种比较染色体作图的可行性，使用拟南芥的 BAC 作为作图探针。
主要结果
Hesperis 分支的大多数二年生和多年生物种由于长末端重复逆转录转座子的增殖而具有异常大的核基因组。在短命和一年生物种中，转座元件的清除很少但反复发生，从而抵消了这种普遍的基因组扩张。
结论
Hesperis 分支的最常见祖先由于转座元件扩增而经历了基因组增大。进一步的基因组大小增加，主导了所有 Hesperis 分支部落的多样化，与染色体数目的总体稳定性形成对比。在一些亚分支和物种中，发生了基因组缩小，可能是作为对一年生生活周期的适应性转变。转座元件和串联重复序列的扩增与清除影响了 Hesperis 分支物种的染色体结构。
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