Wang Xiaotong, Morton Joseph A, Pellicer Jaume, Leitch Ilia J, Leitch Andrew R
Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK.
Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
Plant J. 2021 Aug;107(4):1003-1015. doi: 10.1111/tpj.15363. Epub 2021 Jul 5.
An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.
对一万多个植物基因组大小（GSs）的分析表明，鉴于其祖先中多倍体的发生率，大多数物种的基因组比预期的要小，这表明存在对基因组缩小的选择。然而，将祖先的基因组大小与祖先多倍体的发生率进行比较表明，多倍体之后的DNA丢失率可能非常低（4 - 70兆碱基/百万年，4 - 482碱基对/代）。这就产生了一个问题。如此小的DNA丢失如何能被选择所察觉，克服遗传漂变的影响并推动基因组缩小呢？在这里，我们探讨这个问题，重点关注双链断裂（DSB）修复途径（非同源末端连接和同源重组）可能发挥的作用。我们还探讨了两个假说，这两个假说可以解释选择如何可能有利于多倍体之后的基因组缩小：一是减少（i）与细胞核和转录组中核酸合成相关的氮（N）和磷（P）成本，二是减少基因组大小的缩放效应对细胞大小的影响，而细胞大小又会影响二氧化碳吸收和水分流失。我们探讨了DNA丢失在多倍体早期世代一定最快的假说。或者，如果DNA丢失在进化时间上是一个更持续的过程，那么我们提出这是其他地方选择的副产品，比如限制重复DNA的破坏活性。如果是这样，那么基因组大小对光合作用、水分利用效率和/或细胞核水平营养成本的影响可能是一些具有优势的新兴特性，但这些优势并非在几代时间尺度上就能被选择出来的。
