刊期:双月刊
主管单位:四川省科学技术协会
主办单位:四川省动物学会/成都大熊猫繁育研究基金会/四川省野生动植物保护协会/四川大学
地址:四川省成都市武侯区望江路29号四川大学生命科学学院内
邮编:610064
电话:028-85410485; 15881112385
传真:028-85410485
E-Mail:scdwzz@vip.163.com & scdwzz001@163.com
刊号:ISSN 1000-7083
        CN 51-1193/Q
国内发行代号:
国际发行代号:
发行范围:国内外公开发布
定价:50元/册
定价:300元/年

您所在位置:首页->过刊浏览->2017年第36卷第2期

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
彭长军1, 牛李丽2, 邓家波2, 余建秋2, 李静1*
点击:590次 下载:0次
DOI:10.11984/j.issn.1000-7083.20160293
作者单位:1. 动物资源与生态环境教育部重点实验室, 四川大学生命科学学院, 成都 610065;
2. 成都动物园, 四川省野生动物研究所, 成都 610081
中文关键字:重复序列;转座子元件;RepeatMasker;RepeatScout;大熊猫
英文关键字:repeat; transposable element; RepeatMasker; RepeatScout; Ailuropoda melanoleura
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. Harnessing transposons for cancer gene discovery[J]. Nature Reviews Cancer, 10(10):696-706.
Fernando A, Huan J, Blumenstiel JP, et al. 2012. Identification of transposable elements of the giant panda (Ailuropoda melanoleuca) genome[C]//IEEE International Conference-on Bioinformatics and Biomedicine Workshops:IEEE Computer Society:674-681.
Kohany O, Gentles AJ, Hankus L, et al. 2006. Annotation, submission and screening of repetitive elements in Repbase:RepbaseSubmitter and Censor[J]. BMC Bioinformatics, 7(7):1-7.
Lander ES, Linton LM, Birren B, et al. 2001. Initial sequencing and analysis of the human genome[J]. Nature, 409(6822):860-921.
Li R, Fan W, Tian G, et al. 2010. The sequence and de novo assembly of the giant panda genome[J]. Nature, 463(7279):311-317.
Li R, Ye J, Li S, et al. 2005. ReAS:recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun[J]. PLoS Computational Biology, 1(4):e43. DOI:10.1371/journal.pcbi.0010043.
Li X, Kahveci T, Settles AM. 2008. A novel genome-scale repeat finder geared towards transposons[J]. Bioinformatics, 24(4):468-476.
Lupski JR. 2011. Retrotransposition and structural variation in the human genome[J]. Cell, 141(7):1110-1112.
Pontius JU, Mullikin JC, Smith DR, et al. 2007. Initial sequence and comparative analysis of the cat genome[J]. Genome Research, 17(11):1675-1689.
Price AL, Jones NC, Pevzner PA. 2005. De novo identification of repeat families in large genomes[J]. Bioinformatics, 21(Suppl 1):i351-i358.
Ray DA, Batzer MA. 2010. Reading TE leaves:new approaches to the identification of transposable element insertions[J]. Genome Research, 21(6):813-820.
Smit A, Hubley R, Green P. 2016. RepeatMasker website and server[CP/OL]. (2016-9-12)[2016-10-15]. http://www.repeatmasker.org/.
Walters-Conte KB, Johnson DL, Allard MW, et al. 2011. Carnivore-specific SINEs (Can-SINEs):distribution, evolution, and genomic impact[J]. Journal of Heredity, 102(Suppl 1):S2-S10.
Walters-Conte KB, Johnson DL, Johnson WE, et al. 2014. The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms[J]. BMC Evolutionary Biology, 14(1):1-15.
Wang W, Kirkness EF. 2005. Short interspersed elements (SINEs) are a major source of canine genomic diversity[J]. Genome Research, 15(12):1798-1808.
读者评论

      读者ID: 密码:   
我要评论:
国内统一连续出版物号:51-1193/Q |国际标准出版物号:1000-7083
主管单位:四川省科学技术协会  主办单位:四川省动物学会/成都大熊猫繁育研究基金会/四川省野生动植物保护协会/四川大学
开户银行:中国工商银行四川分行营业部东大支行(工行成都东大支行营业室)  帐户名:四川省动物学会  帐号:4402 2980 0900 0012 596
版权所有©2018四川动物》编辑部 蜀ICP备08107403号-3
您是本站第6376023名访问者

川公网安备 51010702000173号