BACKGROUND The apparent disconnection between biological complexity and both genome size (C-value) and gene number (G-value) is one of the long-standing biological puzzles. Gene-dense genomic sequences in prokaryotes or simple eukaryotes are highly constrained during selection, whereas gene-sparse genomic sequences in higher eukaryotes have low selection constraints. This review discusses the correlations of the C-value and G-value with genome architecture, polyploidy, repeatomes, introns, cell economy and phenomes. DISCUSSION Eukaryotic chromosomes carry an assortment of various repeated DNA sequences (repeatomes). Expansion of copies of repeatomes together with polyploidization or whole-genome duplication (WGD) are major players in genome size (C-value) bloating, but genomes are equipped with counterbalancing systems such as diploidization, illegitimate recombination, and nonhomologous end joining (NHEJ) after double-strand breaks (DSBs). The lack of these efficient purging systems allowed the accumulation of repeat DNA, which resulted in extremely large genomes in several species. However, the correlation between chromosome number and genome size is not clear due to inconsistent results with different sets of species. Positive correlations between genome size and intron size and density were reported in early studies, but these proposals were refuted by the results with increased numbers of species, in which genome-wide features of introns (size, density, gene contents, repeats) were weakly associated with genome size. The assumption of the correlations between C-value and gene number (G-value) and organismal complexity is acceptable in general, but this assumption is often violated in specific lineages or species, suggesting C- and G-value paradoxes. The C-value paradox is partly explained by noncoding repeatomes. The G-value paradox can also be explained by several genomic features: (1) one gene can produce many mature mRNAs by alternative splicing, and eukaryotic gene expression is highly regulated at both the transcriptional and translational levels; (2) many proteins exert multiple functions during development; (3) gene expansion/contraction are frequent events in the gene family among evolutionarily close species; and (4) sets of homeotic genes regulate development such that organismal complexity is sometimes not clear among organisms. A large genome must be burdensome in terms of cell economy, such that a large genome constraint results in the distribution of genome sizes skewed to small genomes. Moreover, the C-value can affect the phenome. A strong positive correlation has been recognized between genome size and cell size, but the relationship is weak or null with higher-level traits. Additional analyses of the relationship between the C-value and phenome should be carried out, because natural selection acts on the phenotype rather than the genotype. CONCLUSIONS Dramatic advancement in genomics has given some answers to the C-value and G-value paradoxes. We know the mechanisms by which the current genomes have been constructed. However, basic questions have not yet been fully resolved. Why have some species retained small genomes yet some closely related species have large genomes? Random genetic drift and mutational pressure might have affected for genome size in the limited population size during evolution; thus, genome size may be quasiadaptable rather than the best adaptive trait.

中文翻译：

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C值和G值悖论具有多倍体，重复组，内含子，现象和细胞经济性。

背景技术生物学复杂性与基因组大小（C值）和基因数目（G值）之间的明显脱节是长期存在的生物学难题之一。在选择过程中，原核生物或简单真核生物中的基因致密基因组序列受到高度限制，而高等真核生物中的基因稀疏基因组序列具有较低的选择约束。这篇评论讨论了C值和G值与基因组结构，多倍体，重复组，内含子，细胞经济性和表型的相关性。讨论真核染色体带有各种重复的DNA序列（重复原子）。重复基因组拷贝的扩展以及多倍体化或全基因组重复（WGD）是导致基因组大小（C值）膨胀的主要因素，但基因组配备了平衡系统，例如二倍体化，非法重组，以及双链断裂（DSB）后的非同源末端连接（NHEJ）。缺乏这些有效的清除系统导致重复DNA的积累，从而导致几个物种中的基因组极大。然而，由于不同物种的结果不一致，染色体数目与基因组大小之间的相关性尚不清楚。早期研究中报道了基因组大小与内含子大小与密度之间存在正相关，但这些提议被物种数量增加的结果所反驳，其中内含子的全基因组特征（大小，密度，基因含量，重复）较弱与基因组大小有关。通常可以接受C值与基因数（G值）与生物复杂性之间的相关性假设，但是这个假设在特定的血统或物种中经常被违反，这暗示了C值和G值的悖论。C值悖论部分地由非编码重复组解释。G值悖论也可以用几个基因组特征来解释：（1）一个基因可以通过选择性剪接产生许多成熟的mRNA，并且真核基因的表达在转录和翻译水平上都受到高度调控；（2）许多蛋白质在发育过程中发挥多种功能；（3）基因扩增/收缩是进化密切的物种中基因家族中的常见事件；（4）各种同源基因调控发育，因此有时在生物体之间尚不清楚生物体的复杂性。大的基因组在细胞经济方面必定是沉重的负担，这样，大的基因组限制会导致偏向小基因组的基因组大小分布。此外，C值会影响现象。基因组大小和细胞大小之间存在很强的正相关性，但与较高水平的性状之间的关系较弱或无效。因为自然选择作用于表型而不是基因型，所以应该对C值与表型之间的关系进行其他分析。结论基因组学的巨大进步为C值和G值悖论提供了一些答案。我们知道构建当前基因组的机制。但是，基本问题尚未完全解决。为什么有些物种保留了较小的基因组，而某些密切相关的物种却保留了较大的基因组？随机遗传漂移和突变压力可能会影响进化过程中有限种群大小的基因组大小；因此，基因组大小可能是准适应的，而不是最佳的适应性状。