Neighboring genes are closely related to whole genome duplications after their separation

  • Shuaibin Lian
  • Tianliang Liu
  • Zaibao Zhang
  • Hongyu Yuan
  • Lei Wang
  • Lin ChengEmail author
Original Research article



The gene order in a eukaryotic genome is not random. Some neighboring genes show specific similarities, while others become separated during evolution. Whole genome duplication events (WGDs) have been recognized as an important evolutionary force. The potential relationship between the separation of neighboring genes and WGDs needs to be investigated. In this study, we investigated whether there is a potential relationship between separated neighboring gene pairs and WGDs, and the mechanism by which neighboring genes are separated. Additionally, we studied whether neighboring genes tend to show intrachromosomal colocalization after their neighborhood was disrupted and the factors facilitating the intrachromosomal colocalization of separated neighboring genes.


The separation of neighboring gene pairs is closely related to whole genome duplication events. Furthermore, we found that there is a double linear relationship between separated neighboring genes, total genes, and WGDs. The process of separation of neighboring genes caused by WGDs is also not random but abides by the double linear model. Separated neighboring gene pairs tend to show intrachromosomal colocalization. The conservativism of separated neighboring genes and histone modification facilitate the intrachromosomal colocalization of neighboring genes after their separation.


These results provide new insight into the understanding of evolutionary roles of locations and the relationship of neighboring gene pairs with whole genome duplications. Furthermore, understanding the proposed mechanism for intrachromosomal colocalization of separated genes benefits our knowledge of chromosomal interactions in the nucleus.


Gene order Neighboring genes Intrachromosomal colocalization Neighborhood conservation 



Authors thank anonymous reviewers for their comments on the manuscript. The linguistic editing and proofreading provided by TopEdit LLC during the preparation of this manuscript are acknowledged.

Author contributions

SL and TL implemented the algorithms and carried out the experiments. SL and LC drafted the manuscript. SL, LW, and LC designed the study and analyzed the results. LC, LW, and HY participated in the analysis and discussion. SL and TL contributed equally. All authors read and approved the final manuscript.


This work was supported by the National Natural Science Foundation of China (Grant. 61501392, U1604112), Nanhu Scholars Program for Young Scholars of XYNU.

Compliance with ethical standards

Conflict of interest

The authors declare that no competing interests exist.


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Copyright information

© International Association of Scientists in the Interdisciplinary Areas 2019

Authors and Affiliations

  1. 1.College of Physics and Electronic EngineeringXinyang Normal UniversityXinyangChina
  2. 2.College of Life SciencesXinyang Normal UniversityXinyangChina

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