Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes
Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes
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DOI：
10.1101/gr.104372.109
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发表时间：
2010-08-01
期刊：
影响因子：
7
通讯作者：
Galtier, Nicolas
中科院分区：
文献类型：
--
作者：
Romiguier, Jonathan;Ranwez, Vincent;Galtier, Nicolas
GC含量的基因组变异的起源、进化和功能相关性是一个长期争论的话题，特别是在哺乳动物中。然而，大多数现有文献都集中在少数模式物种和/或有限的序列数据集上。我们分析了33个完整测序的哺乳动物基因组中的1000多个直向同源基因，在最大似然框架下重建了它们的祖先等容线组织，并探讨了16个目和27个家族代表的第三密码子位置GC含量的进化。我们发现，以前报道的GC丰富的等容线的侵蚀是不是一个普遍的趋势。几个物种（例如，鼩、鼠蝠、天蚕、兔）的GC含量独立地显著增加，GC最少和GC最多的基因类别之间的差距扩大。深入研究的猿类和（特别是）鼠科动物并不反映一般的胎盘模式。我们相关的GC含量的演变与物种的生活史特征和细胞学。检测到体重和基因组大小的显著影响，每个都与GC偏向的基因转换模型一致。
The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconstructed their ancestral isochore organization in the maximum likelihood framework, and explored the evolution of third-codon position GC content in representatives of 16 orders and 27 families. We showed that the previously reported erosion of GC-rich isochores is not a general trend. Several species (e.g., shrew, microbat, tenrec, rabbit) have independently undergone a marked increase in GC content, with a widening gap between the GC-poorest and GC-richest classes of genes. The intensively studied apes and (especially) murids do not reflect the general placental pattern. We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene conversion model.