Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

Mobile DNA

Volumn 4, Issue 1, 2013, Pages

  Lavoie, Christine A ^a,b   Platt, Roy N ^a,b   Novick, Peter A ^c   Counterman, Brian A ^d   Ray, David A ^a,b,e  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b Biocomputing and Biotechnology   (United States)

^c QUEENSBOROUGH COMMUNITY COLLEGE   (United States)

^d MISSISSIPPI STATE UNIVERSITY   (United States)

^e TEXAS TECH UNIVERSITY   (United States)

Author keywords

Butterfly; Genomic deletions; Heliconius melpomene; Lepidopteran; Transposable elements

Indexed keywords

ARTICLE; BOMBYX MORI; BUTTERFLY; HELICONIUS MELPOMENE; LEPIDOPTERA; LONG INTERSPERSED REPEAT; NON LONG TERMINAL REPEAT; NONHUMAN; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; RETROPOSON; SHORT INTERSPERSED REPEAT; TRANSPOSON;

BOMBYX MORI; HELICONIUS; HELICONIUS MELPOMENE; LEPIDOPTERA;

EID: 84884748768     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-4-21     Document Type: Article

References (40)

1. Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Kapitonov V, Tempel S, Jurka J, Gene 2009 448 207 213 10.1016/j.gene.2009.07.019 19651192
2. LINE-mediated retrotransposition of marked Alu Sequences. Dewannieux M, Esnault C, Heidmann T, Nat Genet 2003 35 41 48 10.1038/ng1223 12897783 (Pubitemid 37048594)
3. Junk DNA as an evolutionary force. Biemont C, Vieira C, Nature 2006 443 521 524 10.1038/443521a 17024082 (Pubitemid 44527281)
4. Rolling-circle transposons in eukaryotes. Kapitonov V, Jurka J, Proc Natl Acad Sci U S A 2001 98 8714 8719 10.1073/pnas.151269298 11447285 (Pubitemid 32678093)
5. Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori. Osanai-Futahashi M, Suetsugu Y, Mita K, Fujiwara H, Insect Biochem Mol Biol 2008 38 1046 1057 10.1016/j.ibmb.2008.05.012 19280695
6. A Major Non-LTR Retrotransposon of Bombyx mori, L1Bm. Ichimura S, Mita K, Sugaya K, J Mol Evol 1997 45 253 264 10.1007/PL00006228 9302319 (Pubitemid 27418352)
7. Recent transposition of yabusame, a novel piggyBac-like transposable element in the genome of the silkworm, Bombyx mori. Daimon T, Mitsuhiro M, Katsuma S, Abe H, Mita K, Shimada T, Genome 2010 53 585 593 10.1139/G10-035 20725145
8. A butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Consortium HG, Nature 2012 487 94 98 22722851
9. Parallel race formation and the evolution of mimicry in Heliconius butterflies: A phylogenetic hypothesis from mitochondrial DNA sequences. Brower AVZ, Evolution 1996 50 195 221 10.2307/2410794 (Pubitemid 126517935)
10. The Monarch butterfly genome yields insights into long-distance migration. Zhan S, Merlin C, Boore J, Reppert S, Cell 2011 147 1 15
11. Retroposon Mapping in Molecular Systematics. Okada N, Shedlock A, Nikaido M, Mobile Genetic Elements: Protocols and Genomic Applications, Volume 260 NJ: Humana Press, Miller W, Pierre C, 2004 189 226
12. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Price AL, Eskin E, Pevzner PA, Genome Res 2004 14 2245 2252 10.1101/gr.2693004 15520288 (Pubitemid 39517330)
13. COSEG 0.2.1 http://www.repeatmasker.org
14. A novel web-based TinT application and the chronology of the primate Alu retroposon activity. Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, Schmitz J, BMC Evol Biol 2010 10 376 10.1186/1471-2148-10-376 21126360
15. Cell line fingerprinting using retroelement insertion polymorphism. Ustyugova SV, Amosova AL, Lebedev YB, Sverdlov ED, Biotechniques 2005 38 561 565 10.2144/05384ST02 15884674 (Pubitemid 40529431)
16. Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. Blass E, Bell M, Boissinot S, Genome Biol Evol 2012 4 687 702 10.1093/gbe/evs044 22534163
17. The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals. Novick P, Basta H, Floumanhaft M, McClure M, Boissinot S, Mol Biol Evol 2009 26 1811 1822 10.1093/molbev/msp090 19420048
18. Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori). Jin-Shan X, Qing-You X, Jun L, Guo-Qing P, Ze-Yang Z, Insect Biochem Mol Biol 2005 35 921 929 10.1016/j.ibmb.2005.03.014 15944087 (Pubitemid 41556954)
19. Fruit flies and humans respond differently to retrotransposons. Eickbush T, Furano A, Genomes Evol 2002 12 669 674 (Pubitemid 35335985)
20. Fission yeast Taz1 protein is required for meiotic telomere clustering and recombination. Cooper J, Watanabe Y, Nurse P, Nature 1998 392 828 831 10.1038/33947 9572143 (Pubitemid 28225325)
21. Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination. Song M, Boissinot S, Gene 2007 390 206 213 10.1016/j.gene.2006.09.033 17134851
22. L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Furano A, Duvernell D, Boissinot S, Trends Genet 2004 20 9 14 10.1016/j.tig.2003.11.006 14698614 (Pubitemid 38035206)
23. High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer. Garcia-Fernandez J, Bayascas-Ramirez JR, Marfany G, Munoz-Marmol AM, Casali A, Baguna J, Salo E, Mol Biol Evol 1995 12 421 431 7739384
24. A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Gilbert C, Schaack S, Pace JK 2nd, Brindley PJ, Feschotte C, Nature 2010 464 1347 1350 10.1038/nature08939 20428170
25. Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Novick P, Smith J, Ray D, Boissinot S, Gene 2010 449 85 94 10.1016/j.gene.2009.08.017 19747963
26. Three novel families of miniature inverted-repeat transposable elements are associated with genes of the yellow fever mosquito, Aedes aegypti. Tu Z, Proc Natl Acad Sci U S A 1997 94 7475 7480 10.1073/pnas.94.14.7475 9207116 (Pubitemid 27345340)
27. HIV entry and its inhibition. Chan D, Kim P, Cell 1998 93 681 684 10.1016/S0092-8674(00)81430-0 9630213 (Pubitemid 28257575)
28. RepeatModeler Open-1.0 http://www.repeatmasker.org/RMDownload.html
29. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D, Nucl Acids Res 1997 25 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
30. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC, Nucl Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
31. Annotation, submission and screening of repetitive elements in Repbase: RebaseSubmitter and Censor. Kohany O, Gentles A, Hankus L, Jurka J, BMC Bioinforma 2006 7 107 10.1186/1471-2105-7-107
32. RepeatMasker Open-3.0 http://www.repeatmasker.org
33. PiggyBac-ing on a primate genome: Novel elements, recent activity and horizontal transfer. Pagan H, Smith J, Hubley R, Ray D, Genome Biol Evol 2010 2 293 303 10.1093/gbe/evq021 20624734
34. Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Ray D, Feschotte C, Pagan H, Smith J, Pritham E, Arensburger P, Atkinson P, Craig N, Genome Res 2008 18 717 728 10.1101/gr.071886.107 18340040 (Pubitemid 351645062)
35. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Kimura M, J Mol Evol 1980 16 111 120 10.1007/BF01731581 7463489 (Pubitemid 11166431)
36. Phylogenetics and divergence times of Papilioninae (Lepidoptera) with special reference to the enigmatic genera Teinopalpus and Meandrusa. Simonsen T, Zakharov E, Djernaes M, Cotton A, Vane-Wright R, Sperling F, Cladistics 2010 26 1 25 10.1111/j.1096-0031.2009.00297.x
37. Genbank. Benson DA, Nucleic Acids Res 2010 38 46 D51 10.1093/nar/gkp1024 19910366
38. Repbase Update, a database of eukaryotic repetitive elements. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J, Cytogenet Genome Res 2005 110 462 467 10.1159/000084979 16093699 (Pubitemid 41159923)
39. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Hall TA, Nucleic Acids Symp Ser 1999 41 95 98
40. MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353