Gene Expression Unit, Dept of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
Tissue Engineering Laboratory, Dept of Development and Regeneration, KU Leuven, Kortrijk, Belgium.
BMC Evol Biol. 2019 Jul 16;19(1):144. doi: 10.1186/s12862-019-1469-1.
Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depends on the analysis of sequence homology at the nucleotide or protein level.
We analyzed mRNA GC content, codon usage and divergence of orthologous proteins in 55 vertebrate genomes. Data were visualized in genome-wide landscapes using a sliding window approach. Landscapes of GC content reveal both evolutionary conservation of clustered genes, and lineage-specific changes, so that it was possible to construct a phylogenetic tree that closely matched the classic "tree of life". Landscapes of GC content also strongly correlated to landscapes of amino acid usage: positive correlation with glycine, alanine, arginine and proline and negative correlation with phenylalanine, tyrosine, methionine, isoleucine, asparagine and lysine. Peaks of GC content correlated strongly with increased protein divergence.
Landscapes of base- and amino acid composition of the coding genome opens a new approach in comparative genomics, allowing identification of discrete regions in which protein evolution accelerated over deep evolutionary time. Insight in the evolution of genome structure may spur novel studies assessing the evolutionary benefit of genes in particular genomic regions.
脊椎动物基因组序列的快速积累使得比较基因组学成为研究宏观进化事件的有力方法。物种之间系统发育关系的评估通常依赖于核苷酸或蛋白质水平的序列同源性分析。
我们分析了 55 个脊椎动物基因组中 mRNA 的 GC 含量、密码子使用和同源蛋白的分歧。使用滑动窗口方法在全基因组景观中可视化数据。GC 含量景观揭示了聚类基因的进化保守性和谱系特异性变化，因此可以构建与经典的“生命之树”密切匹配的系统发育树。GC 含量景观也与氨基酸使用景观强烈相关：与甘氨酸、丙氨酸、精氨酸和脯氨酸呈正相关，与苯丙氨酸、酪氨酸、蛋氨酸、异亮氨酸、天冬酰胺和赖氨酸呈负相关。GC 含量的峰值与蛋白质分歧的增加密切相关。
编码基因组碱基和氨基酸组成的景观为比较基因组学开辟了一条新途径，允许识别在深层进化时间内蛋白质进化加速的离散区域。对基因组结构进化的深入了解可能会激发新的研究，评估特定基因组区域中基因的进化优势。
