两种方法对大熊猫基因组重复序列的注释比较
Annotations of the Repeat Elements in Ailuropoda melanoleura Genome Based on Two Strategies

中文摘要：重复序列是动物基因组的重要组分，对于基因组结构多样性、调节基因表达和介导多种遗传疾病具有重要影响。本研究采用了2种策略：基于序列比对的RepeatMasker（RM）和从头预测的RepeatScout（RS），对大熊猫 Ailuropoda melanoleura基因组中的重复序列进行鉴定与注释，详细阐明了其转座子元件（TE）的组成、类型、数量、亚家族、长度分布、分化率等。比较2种注释方法的结果，RM注释到的TE数量在绝大部分亚家族中均多于RS，而在某些亚家族中则少于RS；RS注释到的TE亚家族类型及平均长度均小于RM。此外，RS构建的大熊猫TE一致性序列中，有20%不属于现有的重复序列类型，可能包含大熊猫特有的TE类型。研究结果对于阐明大熊猫重复序列的特征及其生物学功能奠定了重要基础。
英文摘要：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 参考文献： Bao Z, Eddy SR. 2002. Automated de novo identification of repeat sequence families in sequenced genomes[J]. Genome Research, 12(8):1269-1276. Bedell JA, Korf I, Gish W. 2000. MaskerAid:a performance enhancement to RepeatMasker[J]. Bioinformatics, 16(11):1040-1041. Belancio VP, Deininger PL, Roy-Engel AM. 2009. LINE dancing in the human genome:transposable elements and disease[J]. Genome Medicine, 1(10):97. Bergman CM, Quesneville H. 2007. Discovering and detecting transposable elements in genome sequences[J]. Briefings in Bioinformatics, 8(6):382-392. Clark LA, Wahl JM, Rees CA, et al. 2006. Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog[J]. Proceedings of the National Academy of Sciences of the United States of America, 103(5):1376-1381. Copeland NG, Jenkins NA. 2010.