Annotations of the Repeat Elements in Giant Panda Genome Based on two Strategies
Author of the article:PENG Changjun1, DENG Jiabo,YU Jianqiu,LI Jing,Niu
Author's Workplace：1. Key Laboratory of Bio-resources and Eco-environment, Ministry of Education，College of life and Science, Sichuan University, Chengdu 610064, China;
2. Sichuan wild animal research institute, Sichuan Chengdu Zoo, Chengdu 610081, China
Key Words：Repeat elements; Transposable elements; RepeatMasker; RepeatScout; Giant panda
Abstract：Abstract: Repeat elements, especially the transposable elements (TE) are very important in the eukaryotic genomes contributing to the variation in genome architecture and being involved in wide ranges of biological processes such as gene mutation or activation and various types of diseases. In the present study, the TE content, type, copy number, subfamily, divergence rate and average length were investigated in the panda genome based on two strategies: the library based strategy of RepeatMasker (RM) and the de nove based strategy of RepeatScout (RS), respectively. The two strategies were compared and it was found that the copy number of most TE annotated by RM were significantly more than that by RS, whereas in some TE subfamilies RM identified less copy number than RS. Moreover, RM successfully identified much more TE subfamilies than RS, and the average length of each type of TE annotated by RM was longer than that annotated by RS. In addition, we constructed 3,400 consensus sequences of giant panda repeat elements using RS, and 20% of which were different from consensus sequences of those elements in the database, thus might include panda lineage specific repeat elements.
Keywords: Repeat elements; Transposable elements; RepeatMasker; RepeatScout; Giant panda