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Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
Department of Biology, Washington University in St. Louis, St. Louis, MO 63130.
G3 (Bethesda). 2017 Aug 7;7(8):2439-2460. doi: 10.1534/g3.117.040907.
The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in , but it is substantially larger (>18.7 Mb) in To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while sequences integrated into the genome are minor contributors (0.02%). Both and F-element genes exhibit distinct characteristics compared to D-element genes (, larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in Compared to , the codon bias observed in F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.
基因组大小与真核生物复杂性之间的不一致部分可归因于重复序列密度的差异。缪勒F元素（约5.2兆碱基）是[某物种]中最小的染色体，但在[另一物种]中它要大得多（>18.7兆碱基）。为了确定F元素扩张的主要贡献因素并评估其影响，我们改进了基因组序列，并注释了F元素1.4兆碱基区域以及用于比较的来自D元素的1.7兆碱基区域中的基因。我们发现转座子（特别是长末端重复序列和长散在核元件逆转座子）是这种扩张的主要贡献因素（78.6%），而整合到[某物种]基因组中的[特定序列名称]序列贡献较小（0.02%）。与D元素基因相比，[两个物种]的F元素基因都表现出不同的特征（[具体特征列举]，更大的编码跨度、更大的内含子、更多的编码外显子以及更低的密码子偏好性），但在[某物种]中这些差异更为明显。与[另一物种]相比，[某物种]F元素基因中观察到的密码子偏好性主要可归因于突变偏好而非选择。两个物种中F元素基因的5'端富含组蛋白3赖氨酸4二甲基化（H3K4me2），而编码跨度富含H3K9me2。尽管重复序列密度和基因特征存在差异，但与常染色质区域的基因相比，[某物种]F元素基因的表达水平范围相似。这项研究增进了我们对转座子如何影响基因组大小以及基因如何在高度重复区域内发挥功能的理解。
