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Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
Sponsored by:Sichuan Society of Zoologists; Chengdu Giant Panda Breeding Research Foundation; Sichuan Association of Wildlife Conservation; Sichuan University
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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
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].
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.
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