LTR retroelements in the genome of Daphnia pulex

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Rho, Mina ^a   Schaack, Sarah ^b   Gao, Xiang ^c   Kim, Sun ^a,c   Lynch, Michael ^c   Tang, Haixu ^a,c  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA DIRECTED DNA POLYMERASE;

ARTICLE; CONTROLLED STUDY; DAPHNIA; GENE IDENTIFICATION; GENE INSERTION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HETEROZYGOSITY; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; REPRODUCTION; RETROPOSON; SEQUENCE ANALYSIS; TRANSPOSON; ANIMAL; FEMALE; GENETICS; GENOME; LABORATORY; MALE;

CRUSTACEA; DAPHNIA PULEX; EUKARYOTA;

ANIMALS; DAPHNIA; FEMALE; GENOME; LABORATORIES; MALE; RETROELEMENTS; TERMINAL REPEAT SEQUENCES; TRANSCRIPTION, GENETIC;

EID: 77954344477     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-425     Document Type: Article

References (45)

1. SanMiguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, et al. Nested Retrotransposons in the Intergenic Regions of the Maize Genome. Science 1996, 274:765-768. 10.1126/science.274.5288.765, 8864112.
2. Consortium IHGS. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. 10.1038/35057062, 11237011.
3. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, et al. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol 2002, 3:research0084.0081-0084.0020.
4. Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D. Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 2005, 1:166-175. 10.1371/journal.pcbi.0010022, 1185648, 16110336.
5. Holmes I. Transcendent elements: whole-genome transposon screens and open evolutionary questions. Genome Res 2002, 12:1152-1155. 10.1101/gr.453102, 12176921.
6. Kidwell MG, Lisch D. Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 1997, 94:7704-7711. 10.1073/pnas.94.15.7704, 33680, 9223252.
7. Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res 2009, 19(2):243-254. 10.1101/gr.083360.108, 2652206, 19029538.
8. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, et al. Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 2006, 16(10):1262-1269. 10.1101/gr.5290206, 1581435, 16963705.
9. Bergman CM, Quesneville H. Discovering and detecting transposable elements in genome sequences. Brief in Bioinform 2007, bbm048.
10. McCarthy EM, McDonald JF. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 2003, 19:362-367. 10.1093/bioinformatics/btf878, 12584121.
11. Rho M, Choi J-H, Kim S, Lynch M, Tang H. De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 2007, 8. doi: 10.1186/1471-2164-1188-1190, 10.1186/1471-2164-8-90, 1858694, 17407597.
12. Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 2009, 461(7267):1130-1134. 10.1038/nature08479, 19847266.
13. Feschotte C. Opinion - Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics 2008, 9(5):397-405. 10.1038/nrg2337, 2596197, 18368054.
14. Arkhipova I, Meselson M. Transposable elements in sexual and ancient asexual taxa. Proc Natl Acad Sci USA 2000, 97(26):14473-14477. 10.1073/pnas.97.26.14473, 18943, 11121049.
15. Dolgin ES, Charlesworth B. The Fate of Transposable Elements in Asexual Populations. Genetics 2006, genetics.106.060434., 1602064, 16888330.
16. Wright S, Finnegan D. Genome evolution: Sex and the transposable element. Curr Biol 2001, 11(8):R296-R299. 10.1016/S0960-9822(01)00168-3, 11369217.
17. Oliver KR, Greene WK. Transposable elements: powerful facilitators of evolution Source. Bioessays 2009, 31(7):703-714. 10.1002/bies.200800219, 19415638.
18. McCarthy EM, Liu J, Lizhi G, McDonald JF. Long terminal repeat retrotransposons of Oryza sativa. Genome Biol 2002, 3(10):research0053.0051-0053.0011.
19. Wicker T, Keller B. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res 2007, 17:1072-1081. 10.1101/gr.6214107, 1899118, 17556529.
20. Massimiliano Marsano R, Caizzi R. A genome-wide screening of BEL-Pao like retrotransposons in Anopheles gambiae by the LTR_STRUC program. Gene 2005, 357(2):115-121. 10.1016/j.gene.2005.06.010, 16102916.
21. JinShan X, QingYou X, Jun L, GuoQing P, ZeYang Z. Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori). Insect Biochemistry and Molecular Biology 2005, 35(8):921-929. 10.1016/j.ibmb.2005.03.014, 15944087.
22. Bowen NJ, McDonald JF. Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside. Genome Res 2001, 11:1527-1540. 10.1101/gr.164201, 311128, 11544196.
23. Tubio JMC, Naveira H, Costas J. Structural and Evolutionary Analyses of the Ty3/gypsy Group of LTR Retrotransposons in the Genome of Anopheles gambiae. Molecular Biology and Evolution 2005, 22(1):29-39. 10.1093/molbev/msh251, 15356275.
24. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, et al. Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes. Science 2002, 297(5585):1301-1310. 10.1126/science.1072104, 12142439.
25. Frame IG, Cutfield JF, Poulter RTM. New BEL-like LTR-retrotransposons in Fugu rubripes, Caenorhabditis elegans, and Drosophila melanogaster. Gene 2001, 263:219-230. 10.1016/S0378-1119(00)00567-9, 11223261.
26. Malik HS, Eickbush TH. NeSL-1, an Ancient Lineage of Site-Specific Non-LTR Retrotransposons From Caenorhabditis elegans. Genetics 2000, 154:193-203. 1460889, 10628980.
27. Cook JM, Martin J, Lewin A, Sinden RE, Tristem M. Systematic screening of Anopheles mosquito genomes yields evidence for a major clade of Pao-like retrotransposons. Insect Mol Biol 2000, 9(1):109-117. 10.1046/j.1365-2583.2000.00167.x, 10672078.
28. Abe H, Ohbayashi F, Sugasaki T, Kanehara M, Terada T, Shimada T, Kawai S, Mita K, Kanamori Y, Yamamoto MT, et al. Two novel Pao-like retrotransposons (Kamikaze and Yamato) from the silkworm species Bombyx mori and B. mandarina: common structural features of Pao-like elements. Mol Genet Genomics 2001, 265:375-385. 10.1007/s004380000428, 11361350.
29. Malik HS, Eickbush TH. Phylogenetic Analysis of Ribonuclease H Domains Suggests a Late, Chimeric Origin of LTR Retrotransposable Elements and Retroviruses. Genome Res 2001, 11(7):1187-1197. 10.1101/gr.185101, 11435400.
30. Goodwin TJD, Poulter RTM, Lorenzen MD, Beeman RW. DIRS retroelements in arthropods: identification of the recently active TcDirs1 element in the red flour beetle Tribolium castaneum. Molecular Genetics and Genomics 2004, 272:47-56. 10.1007/s00438-004-1028-2, 15221458.
31. Goodwin TJD, Poulter RTM. The DIRS1 Group of Retrotransposons. Mol Biol Evol 2001, 18:2067-2082.
32. Rho M, Tang H. MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes. Nucleic Acids Res 2009, 37:e143. 10.1093/nar/gkp752, 2790886, 19762481.
33. Maside X, Bartolome C, Assimacopoulos S, Charlesworth B. Rates of movement and distribution of transposable elements in Drosophila melanogaster: in situ hybridization vs. southern blotting data. Genet Res 2001, 78:121-136. 10.1017/S0016672301005201, 11732090.
34. Papaceit M, Avila V, Aguade M, Garcia-Dorado A. The Dynamics of the roo Transposable Element In Mutation-Accumulation Lines and Segregating Populations of Drosophila melanogaster. Genetics 2007, 177:511-522. 10.1534/genetics.107.076174, 2013678, 17890368.
35. Grandbastien M-A. Activation of plant retrotransposons under stress conditions. Trends Plant Sci 1998, 3(5):181-187.
36. Pourtau N, Lauga V, Audeon C, Grandbastien M, Goulas P, Salvado J. The promoter of the Tnt1A retrotransposon in activated by ozone air pollution in tomato, but not in its natural host tobacco. Plant Science 2003, 165(5):983-992.
37. Muller HJ. The Relation of Recombination to Mutational Advance. Mutat Res 1964, 106:2-9.
38. Lynch M, Burger R, Burcher D, Gabriel W. The Mutational Meltdown in Asexual Populations. Journal of Heredity 1993, 84(5):338-344.
39. Sullender BW, Crease TJ. The behavior of a Daphnia pulex transposable element in cyclically and obligately parthenogenetic populations. J Mol Evol 2001, 53(1):63-69.
40. Valizadeh P, Crease TJ. The association between breeding system and transposable element dynamics in Daphnia pulex. J Mol Evol 2008, 66(6):643-654. 10.1007/s00239-008-9118-0, 18491025.
41. Nuzhdin SV, Petrov DA. Transposable elements in clonal lineages: lethal hangover from sex. Biol J Linn Soc 2003, 79:33-41.
42. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003, 31:3497-3500. 10.1093/nar/gkg500, 168907, 12824352.
43. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092, 17488738.
44. Van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, D'Hauw M, Van Montagu M, Gerats T. Transposon display identifies individual transposable elements in high copy number lines. Plant J 1998, 13(1):121-129. 10.1046/j.1365-313X.1998.00004.x, 17655648.
45. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 1987, 19:11-15.