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Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
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Your Position :Home->Past Journals Catalog->2017 Vol.36 No.2

Annotations of the Repeat Elements in Ailuropoda melanoleura Genome Based on Two Strategies
Author of the article:PENG Changjun1, NIU Lili2, DENG Jiabo2, YU Jianqiu2, LI Jing1*
Author's Workplace:1. Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, Sichuan University, Chengdu 610065, China;
2. Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu 610081, China
Key Words:repeat; transposable element; RepeatMasker; RepeatScout; Ailuropoda melanoleura
Abstract:Repeat elements, especially the transposable elements (TEs) 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 2 strategies:the library based strategy of RepeatMasker (RM) and the de novo based strategy of RepeatScout (RS). The 2 strategies were compared and the results showed that the copy number of most TEs annotated by RM were significantly more than that by RS, whereas RM identified less copy number than RS in some TE subfamilies. Moreover, RM successfully identified much more TE subfamilies than RS, and the average length of each type of TEs 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.
2017,36(2): 121-130 收稿日期:2016-10-26
DOI:10.11984/j.issn.1000-7083.20160293
分类号:R857.3;Q959.838
基金项目:成都大熊猫繁育研究基金会项目(CPF2014-13)
作者简介:彭长军,男,硕士研究生,研究方向:哺乳动物基因组遗传信息分析,E-mail:jj-5380682@163.com
*通讯作者:彭长军,E-mail:ljtjf@126.com
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