ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

PLoS Computational Biology

Volumn 1, Issue 4, 2005, Pages 0313-0321

  Li, Ruiqiang ^a,b   Ye, Jia ^a,b   Li, Songgang ^b,c   Wang, Jing ^b   Han, Yujun ^b   Ye, Chen ^b   Wang, Jian ^a,b   Yang, Huanming ^a,b   Yu, Jun ^a,b   Wong, Gane Ka Shu ^a,b,d   Wang, Jun ^a,b,e,f  

^a ZHEJIANG UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c PEKING UNIVERSITY   (China)

^d UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^e AARHUS UNIVERSITY   (Denmark)

^f UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

COPY NUMBER; GENOME SEQUENCES; JAPONICA RICE; RICE GENOMES; TRANSPOSABLE ELEMENTS; WHOLE-GENOME SHOTGUN;

GENES;

ALGORITHM; ARTICLE; GENE DUPLICATION; GENETICS; MOLECULAR EVOLUTION; NUCLEIC ACID DATABASE; PLANT GENOME; RICE; TRANSPOSON;

ALGORITHMS; DATABASES, NUCLEIC ACID; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, PLANT; ORYZA SATIVA;

EID: 55449118548     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010043     Document Type: Article

References (28)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. SanMiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by massive amplification of intergene retrotransposons. Ann Bot 81: 37-44.
3. Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, et al. (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11: 1769-1784.
4. Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11: 1660-1676.
5. Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animal and plants. Proc Natl Acad Sci U S A 94: 7704-7711.
6. Avise JC (2001) Evolving genomic metaphors: A new look at the language of DNA. Science 294: 86-87.
7. Kumar A, Hirochika H (2001) Applications of retro transposons as genetic tools in plant biology. Trends Plant Sci 6: 127-134.
8. Jurka J (1998) Repeats in genomic DNA: Mining and meaning. Curr Opin Struct Biol 8: 333-337.
9. Kurtz S, Choudhuri JV, Ohlebusch E, Scheleiermacher C, Stoye J, et al. (2001) REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29: 4633-4642.
10. Bao Z, Eddy SR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12: 1269-1276.
11. Pevzner PA, Tang H, Tesler G (2004) De novo repeat classification and fragment assembly. Genome Res 14: 1786-1796.
12. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
13. Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
14. Yu J, Wang J, Lin W, Li S, Li H, et al. (2005) The genomes of Oryza sativa: A history of duplications. PLoS Biol 3: e38. DOI: 10.1371/journal.pbio. 0030038
15. Smit AF (1996) The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6: 743-748.
16. Fedoroff N (2000) Transposons and genome evolution in plants. Proc Natl Acad Sci U S A 97: 7002-7007.
17. Goff SA, Ricke D, Lan TH, Presting G, Wang R, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
18. Wang J, Wong GK, Ni P, Han Y, Huang X, et al. (2002) RePS: A sequence assembler that masks exact repeats identified from the shotgun data. Genome Res 12: 824-831.
19. Zhong L, Zhang K, Huang X, Ni P, Han Y, et al. (2003) A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts. Genomics Proteomics Bioinformatics 1: 43-51.
20. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, et al. (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312-316.
21. Feng Q., Zhang Y, Hao P, Wang S, Fu G, et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
22. Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569.
23. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532.
24. McCarthy EM, Liu J, Lizhi G, McDonald JF (2002) Long terminal repeat retrotransposons of Oryza sativa. Genome Biol 3: RESEARCH0053.
25. Kikuchi K, Terauchi K, Wada M, Hirano HY (2003) The plant MITE mPing is mobilized in anther culture. Nature 421: 167-170.
26. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
27. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
28. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE (2001) Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res 11: 1005-1017.