在这项研究中,我们成对比较了多个基因组区域,包括基因,外显子,编码DNA序列(CDS),内含子,和39个动物基因组的基因间区域,包括Deuterostomia(27种)和原口(12种),通过应用建立的基于k聚体的(无对齐)比较方法。我们发现内含子的序列结构和基因间区域之间有很强的相关性,个体有机体,在更广泛的系统发育范围内,表明某些结构在整个被分析生物范围内的保守性。我们通过分解相对于这些词集的相关系数来量化不同DNA单词集对平均相关值的贡献,从而分析了这些序列结构。我们发现内含子中的保守结构,基因间区域,两者之间主要是重复单元≤2bp的保守串联重复的结果(例如,(AT)n),而其他保守的序列结构,比如在外显子和CDS之间发现的那些,由串联重复序列主导,重复单元长度为3bp,DNA单词模式更复杂。我们得出的结论是,内含子和基因间区域之间的保守性表明这些序列结构具有共同的功能。此外,已知起源的保守结构的类似差异,特别是外显子和由DNA密码子产生的CDS之间的保守性,表明内含子和基因间区的基于k聚体组成的功能特性可能不同于外显子和CDS。
In this study, we pairwise-compared multiple genome regions, including genes, exons, coding DNA sequences (CDS), introns, and intergenic regions of 39 Animalia genomes, including Deuterostomia (27 species) and Protostomia (12 species), by applying established k-mer-based (alignment-free) comparison methods. We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by quantifying the contribution of different sets of DNA words to the average correlation value by decomposing the correlation coefficients with respect to these word sets. We found that the conserved structures within introns, intergenic regions, and between the two were mainly a result of conserved tandem repeats with repeat units ≤ 2 bp (e.g., (AT)n), while other conserved sequence structures, such as those found between exons and CDS, were dominated by tandem repeats with repeat unit sizes of 3 bp in length and more complex DNA word patterns. We conclude that the conservation between intron and intergenic regions indicates a shared function of these sequence structures. Also, the similar differences in conserved structures with known origin, especially to the conservation between exons and CDS resulting from DNA codons, indicate that k-mer composition-based functional properties of introns and intergenic regions may differ from those of exons and CDS.