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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01020

A new algorithm for identifying genome rearrangements in the mammalian evolution

 Juan Wang1*, Bo Cui1, Yulan Zhao1 and Maozu Guo2
  • 1Inner Mongolia University, China
  • 2Beijing University of Civil Engineering and Architecture, China

Genome rearrangements are the evolutionary events on level of genomes. It is a global view on evolution research of species to analyze the genome rearrangements.
We introduce a new method called RGRPT (Recovering the Genome Rearrangements based on Phylogenetic Tree) used to identify the genome rearrangements. We test the RGRPT using simulated data. The results of experiments show that RGRPT has high sensitivity and specificity compared with other tools when to predict rearrangement events. We use RGRPT to predict the rearrangement events of six mammalian genomes (human, chimpanzee, rhesus macaque, mouse, rat, and dog). RGRPT has recognized a total of 1157 rearrangement events for them at 10kb resolution, including 858 reversals, 16 translocations, 249 transpositions, and 34 fusions/fissions. And RGRPT has recognized 475 rearrangement events for them at 50kb resolution, including 332 reversals, 13 translocations, 94 transpositions, and 36 fusions/fissions. The code source of RGRPT is available from https://github.com/wangjuanimu/data-of-genome-rearrangement.

Keywords: Genome rearrangements, Mammal, phylogenetic tree, evolution, algorithm

Received: 02 Jul 2019; Accepted: 24 Sep 2019.

Copyright: © 2019 Wang, Cui, Zhao and Guo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Juan Wang, Inner Mongolia University, Hohhot, China, wangjuan@imu.edu.cn