College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China.
College of Life Sciences, Xinyang Normal University, Xinyang, China.
BMC Genomics. 2018 Jun 13;19(1):455. doi: 10.1186/s12864-018-4844-1.
Gene order and location in chromosomes of species are non-random. Neighboring gene pairs tend to display some similarities, such as co-expression and co-modification. However, the contribution of linear proximity, spatial proximity, and evolutionary proximity to these similarities remain unclear, together with whether the presence of several types of proximity can strengthens the similarities.
In this study, we investigated the properties of three kinds of colocalized gene pairs: intrachromosomal colocalized gene pairs, always-neighboring gene pairs, and evolutionary neighboring gene pairs. Our analysis showed that (1) Different types of colocalized genes differentially contribute to co-expression, co-modifications and conservation across species; (2) Intrachromosomal colocalization can strengthen co-expression and co-modification of neighboring gene pairs and their conservation across species; (3) The combination of the three kinds of colocalization can lead to the strongest co-modification and is most strongly conserved across species. (4) Colocalized gene pairs are indicative of phylogenetic relationships and whole genome duplications (WGDs).
These results provide valuable clues for future efforts to understand the characteristics of colocalized gene pairs and how the neighborhood affects their interactions.
物种染色体中的基因顺序和位置并非随机排列。相邻的基因对往往表现出某些相似性，如共表达和共修饰。然而，线性接近、空间接近和进化接近对这些相似性的贡献尚不清楚，以及是否存在多种接近类型可以增强相似性。
在这项研究中，我们研究了三种共定位基因对的特性：染色体内共定位基因对、始终相邻基因对和进化相邻基因对。我们的分析表明：（1）不同类型的共定位基因对在不同程度上有助于物种间的共表达、共修饰和保守性；（2）染色体内共定位可以增强相邻基因对的共表达和共修饰及其在物种间的保守性；（3）三种共定位的组合可以导致最强的共修饰，并且在物种间的保守性最强。（4）共定位基因对与系统发育关系和全基因组复制（WGDs）有关。
这些结果为未来理解共定位基因对的特征以及邻域如何影响它们的相互作用提供了有价值的线索。
