Разнообразие и распространение мобильных генетических элементов в геномах морских беспозвоночных
https://doi.org/10.18699/VJ16.16-o
Аннотация
Ключевые слова
Об авторах
М. В. ПузаковРоссия
Севастополь
Л. В. Пузакова
Россия
Севастополь
И. К. Захаров
Россия
Новосибирск
Список литературы
1. Бубенщикова Е.В., Антоненко О.В., Васильева Л.В., Ратнер В.А. Индукция транспозиций МГЭ 412 раздельно тепловым и холодовым шоком в сперматогенезе у самцов дрозофилы. Генетика. 2002;38(1):46-55.
2. Васильева Л.А., Ратнер В.А., Антоненко О.В., Лопухова Е.Д., Бубенщикова Е.В. Индукция транспозиций МГЭ 412 различными дозами паров этанола в изогенной линии Drosophila melanogaster. Генетика. 2003;39(5):717-720.
3. Захаренко Л.П., Коваленко Л.В., Перепелкина М.П., Захаров И.К. Влияние γ-радиации на индукцию транспозиций hobo-элемента у Drosophila melanogaster. Генетика. 2006;42(6):763-767.
4. Иващенко Н.И., Гришаева Т.М. Современные представления о роли разных семейств мобильных элементов в геномах эукариот. Успехи современной биологии. 2009;129(2):115-123.
5. Коваленко Л.В., Захаренко Л.П., Волошина М.А., Карамышева Т.В., Рубцов Н.Б., Захаров И.К. Поведение транспозонов hobo и P в нестабильной линии yellow2-717 Drosophila melanogaster и ее производных после скрещиваний с лабораторной линией. Генетика. 2006;42(6):748-756.
6. Ратнер В.А., Васильева Л.А. Индукция транспозиций и эксцизий мобильных генетических элементов у дрозофилы в процессе изогенизации. Генетика. 1996;32(7):933-944.
7. Сергеева Е.М., Салина Е.А. Мобильные элементы и эволюция генома растений. Вавиловский журнал генетики и селекции. 2011;15(2):382-398.
8. Сормачева Н.Д., Блинов А.Г. LTR ретротранспозоны растений. Вавиловский журнал генетики и селекции. 2011;15(2):351-381.
9. Чересиз С.В., Юрченко Н.Н., Иванников А.В., Захаров И.К. Мобильные элементы и стресс. Информационный вестник ВОГиС. 2008;12(1/2):217-242.
10. Юрченко Н.Н., Коваленко Л.В., Захаров И.К. Мобильные генетические элементы: нестабильность генов и геномов. Вавиловский журнал генетики и селекции. 2011;15(2):261-270.
11. Albertin C.B., Simakov O., Mitros T., Wang Z.Y., Pungor J.R., Edsinger-Gonzales E., Brenner S., Ragsdale C.W., Rokhsar D.S. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 2015;524(7564):220-224. https://doi.org/10.1038/nature14668.
12. Arkhipova I., Meselson M. Transposable elements in sexual and ancient asexual taxa. Proc. Natl Acad. Sci. USA. 2000;97(26):14473-14477. https://doi.org/10.1073/pnas.97.26.14473.
13. Bao W., Jurka M.G., Kapitonov V.V., Jurka J. New superfamilies of eukaryotic DNA-transposons and their internal divisions. Mol. Biol. Evol. 2009;26(5):983-993. https://doi.org/10.1093/molbev/msp013.
14. Baughman K.W., McDougall C., Cummins S.F., Hall M., Degnan B.M., Satoh N., Shoguchi E.. Genomic organization of Hox and ParaHox clusters in the echinoderm, Acanthaster planci. Genesis. 2014;52(12):952-958. https://doi.org/10.1002/dvg.22840.
15. Baumgarten S., Simakov O., Esherick L.Y., Liew Y.J., Lehnert E.M., Michell C.T., Li Y., Hambleton E.A., Guse A., Oates M.E., Gough J., Weis V.M., Aranda M., Pringle J.R., Voolstra C.R. The genome of Aiptasia, a sea anemone model for coral symbiosis. Proc. Natl Acad Sci U S A. 2015;112(38):11893-11898. https://doi.org/10.1073/pnas.1513318112.
16. Bui Q.T., Delaurière L., Casse N., Nicolas V., Laulier M., Chénais B. Molecular characterization and phylogenetic position of a new mariner-like element in the coastal crab, Pachygrapsus marmoratus. Gene. 2007;396(2):248-256. https://doi.org/10.1016/j.gene.2007.03.004.
17. Casse N., Bui Q.T., Nicolas V., Renault S., Bigot Y., Laulier M. Species sympatry and horizontal transfers of Mariner transposons in marine crustacean genomes. Mol. Phylogenet. Evol. 2006;40(2):609-619. https://doi.org/10.1016/j.ympev.2006.02.005.
18. Chipman A.D., Ferrier D.E., Brena C., Qu J., Hughes D.S., Schröder R., Torres-Oliva M., Znassi N., Jiang H., Almeida F.C., Alonso C.R., Apostolou Z., Aqrawi P., Arthur W., Barna J.C., Blankenburg K.P., Brites D., Capella-Gutiérrez S., Coyle M., Dearden P.K., Du Pasquier L., Duncan E.J., Ebert D., Eibner C., Erikson G., Evans P.D., Extavour C.G., Francisco L., Gabaldón T., Gillis W.J., GoodwinHorn E.A., Green J.E., Griffiths-Jones S., P. Grimmelikhuijzen C. J., Gubbala S., Guigó R., Han Y., Hauser F., Havlak P., Hayden L., Helbing S., Holder M., Hui J.H.L., Hunn J.P., Hunnekuhl V.S., Jackson L., Javaid M., Jhangiani S.N., Jiggins F.M., Jones T.E., Kaiser T.S., Kalra D., Kenny N.J., Korchina V., Kovar C.L., Kraus F.B., Lapraz F., Lee S.L., Jie Lv, Mandapat C., Manning G., Mariotti M., Mata R., Mathew T., Neumann T., Newsham I., Ngo D.N., ., Pu L.-L., Putman N.H., Rabouille C., Ramos O.M., Rhodes A.C., Robertson H.E., Robertson H.M., Ronshaugen M., Rozas J., Saada N., Sánchez-Gracia A., Scherer S.E., Schurko A.M., Siggens K.W., Simmons D., Stief A., Stolle E., Telford M.J., Tessmar-Raible Ninova M., Okwuonu G., Ongeri F., Palmer W.J., Patil S., Patraquim P., Pham C K., Thornton R., Maurijn van der Zee, Arndt von Haeseler, Williams J.M., Willis J.H., Wu Y., Zou X., Lawson D., Muzny D.M., Worley Kim C., Gibbs R.A., Akam M., Richards S. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biol. 2014;12(11):e1002005. https://doi.org/10.1371/journal.pbio.1002005.
19. Cohen J.B., Liebermann D., Kedes L. Tsp transposons: a heterogeneous family of mobile sequences in the genome of the sea urchin Strongylocentrotus purpuratus. Mol. Cel. Biol. 1985;5(10):2814-2825.
20. Cordaux R., Udit S., Batzer M.A., Feschotte C. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc. Natl Acad. Sci. USA. 2006;103(21):8101-8106. https://doi.org/10.1073/pnas.0601161103.
21. Dehal P., Satou Y., Campbell R.K., Chapman J., Degnan B., De Tomaso A., Davidson B., Di Gregorio A., Gelpke M., Goodstein D.M., Harafuji N., Hastings K.E., Ho I., Hotta K., Huang W., Kawashima T., Lemaire P., Martinez D., Meinertzhagen I.A., Necula S., Nonaka M., Putnam N., Rash S., Saiga H., Satake M., Terry A., Yamada L., Wang H.G., Awazu S., Azumi K., Boore J., Branno M., Chin-Bow S., DeSantis R., Doyle S., Francino P., Keys D.N., Haga S., Hayashi H., Hino K., Imai K.S., Inaba K., Kano S., Kobayashi K., Kobayashi M., Lee B.I., Makabe K.W., Manohar C., Matassi G., Medina M., Mochizuki Y., Mount S., Morishita T., Miura S., Nakayama A., Nishizaka S., Nomoto H., Ohta F., Oishi K., Rigoutsos I., Sano M., Sasaki A., Sasakura Y., Shoguchi E., Shin-i T., Spagnuolo A., Stainier D., Suzuki M.M., Tassy O., Takatori N., Tokuoka M., Yagi K., Yoshizaki F., Wada S., Zhang C., Hyatt P.D., Larimer F., Detter C., Doggett N., Glavina T., Hawkins T., Richardson P., Lucas S., Kohara Y., Levine M., Satoh N., Rokhsar D.S. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002;298(5601):2157-2167.
22. de Koning A.P., Gu W., Castoe T.A., Batzer M.A., Pollock D.D. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011;7(12):e1002384. https://doi.org/10.1371/journal.pgen.1002384.
23. de la Vega E., Hall M.R., Wilson K.J., Reverter A., Woods R.G., Degnan B.M. Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon. Physiol. Genomics. 2007;31(1):126-138. https://doi.org/10.1152/physiolgenomics.00068.2007.
24. Dimitri P., Junakovic N. Revising the selfish DNA hypothesis: new evidence on accumulation of transposable elements in heterochromatin. Trends Genet. 1999;15(4):123-124. https://doi.org/10.1016/S0168-9525(99)01711-4.
25. Fedoroff N.V. Transposable elements, epigenetics, and genome evolution. Science. 2012;338:758-767. https://doi.org/10.1126/science.338.6108.758.
26. Feschotte C., Zhang X., Wessler S.R. Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons, in Mobile DNA II. Washington (DC): Am. Society Microbiol. Press. 2002.
27. Fontdevila A. Hybrid genome evolution by transposition. Cytogenet. Genome Res. 2005;110(1-4):49-55. https://doi.org/10.1159/000084937.
28. Fugmann S.D., Lee A.I., Shockett P.E., Villey I.J., Schatz D.G. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu. Rev. Immunol. 2000;18:495-527. https://doi.org/10.1146/annurev.immunol.18.1.495.
29. Gaffney P.M., Pierce J.C., Mackinley A.G., Titchen D.A., Glenn W.K. Pearl, a novel family of putative transposable elements in bivalve mollusks. J. Mol. Evol. 2003;56(3):308-316. https://doi.org/10.1007/s00239-002-2402-5.
30. Georgiev G.P. Mobile genetic elements in animal cells and their biological significance. Eur. J. Biochem. 1984;145(2):203-220. https://doi.org/10.1111/j.1432-1033.1984.tb08541.x.
31. Gentles A.J., Wakefield M.J., Kohany O., Gu W., Batzer M.A., Pollock D.D., Jurka J. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res. 2007;17(7):992-1004. https://doi.org/10.1101/gr.6070707.
32. Geyer P.K., Spana C., Corces V.G. On the molecular mechanism of gypsy-induced mutations at the yellow locus of Drosophila melanogaster. EMBO J. 1986;5(10):2657-2662.
33. Goodier J.L., Kazazian H.H.Jr. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell. 2008;135(1):23-35. https://doi.org/10.1016/j.cell.2008.09.022.
34. Goodwin T.J., Poulter R.T. The DIRS1 group of retrotransposons. Mol. Biol. Evol. 2001;18(11):2067-2082. https://doi.org/mbev_18_1108.2067_2082.tp.
35. Gonzalez P., Lessios H.A. Evolution of sea urchin retroviral-like (SURL) elements: evidence from 40 Echinoid species. Mol. Biol. Evol. 1999;16(7):938-952. https://doi.org/mbev_16_705.938_952.
36. Guo B., Zou M., Gan X., He S. Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing. BMC Genomics. 2010;11:396. https://doi.org/10.1186/1471-2164-11-396.
37. Halaimia-Toumi N., Casse N., Demattei M.V., Renault S., Pradier E., Bigot Y., Laulier M. The GC-rich transposon Bytmar1 from the deep-sea hydrothermal crab, Bythograea thermydron, may encode three transposase isoforms from a single ORF. J. Mol. Evol. 2004;59(6):747-760. https://doi.org/10.1007/s00239-004-2665-0.
38. Handler A.M., Gomez S.P. P element excision in Drosophila is stimulated by gamma-irradiation in transient embryonic assays. Genet. Res. 1997;70(1):75-78.
39. Hizer S.E., Tamulis W.G., Robertson L.M., Garcia D.K. Evidence of multiple retrotransposons in two litopenaeid species. Anim. Genet. 2008;39(4):363-373. https://doi.org/10.1111/j.1365-2052.2008.01739.x.
40. Hoffman-Liebermann B., Liebermann D., Kedes L.H., Cohen S.N. TU elements: a heterogeneous family of modularly structured eucaryotic transposons. Mol. Cell Biol. 1985;5(5):991-1001.
41. Huang C.R.L., Burns K.H., Boeke J.D. Active transposition in genomes. Annu. Rev. Genet. 2012;46:651-675. https://doi.org/10.1146/annurevgenet-110711-155616.
42. Junakovic N., di Franco C., Barsanti P., Palumbo G. Transpositions of copia-like elements can be induced by heat shock. J. Mol. Evol. 1986;24:89-93.
43. Jurka J., Bao W., Kojima K.K. Families of transposable elements, population structure and the origin of species. Biol. Direct. 2011;6:44. https://doi.org/10.1186/1745-6150-6-44.
44. Jurka J. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 1998;8:333-337.
45. Jurka J. Conserved eukaryotic transposable elements and the evolution of gene regulation. Cell Mol. Life Sci. 2008;65:201-204. https://doi.org/10.1007/s00018-007-7369-3.
46. Kapitonov V.V., Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. 2008;9(5):411-412. https://doi.org/10.1038/nrg2165-c1.
47. Kapitonov V.V., Jurka J. Chapaev - a novel superfamily of DNA transposons. Repbase Reports. 2007;7(9):774-781. http://www.girinst.org/2007/vol7/issue9.
48. Kapitonov V.V., Jurka J. Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc. Natl Acad. Sci. USA. 2003;100(11):6569-6574. https://doi.org/10.1073/pnas.0732024100.
49. Kapitonov V.V., Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol. 2005;3(6):e181. https://doi.org/10.1371/journal.pbio.0030181.
50. Kenny N.J., Sin Y.W., Shen X., Zhe Q., Wang W., Chan T.F., Tobe S.S., Shimeld S.M., Chu K.H., Hui J.H. Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata. Mar Drugs. 2014;12(3):1419-1437. https://doi.org/10.3390/md12031419.
51. Kidwell M.G., Lisch D.R. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution. 2001;55(1):1-24.
52. Kidwell M.G. Transposable elements and the evolution of genome size in eukaryotes. Genetica. 2002;115(1):49-63.
53. Kourtidis A., Drosopoulou E., Pantzartzi C.N., Chintiroglou C.C., Scouras Z.G. Three new satellite sequences and a mobile element found inside HSP70 introns of the mediterranean mussel (Mytilus galloprovincialis). Genome. 2006;49(11):1451-1458. https://doi.org/10.1139/g06-111.
54. Kumar A., Bennetzen J.L. Plant retrotransposons. Annu. Rev. Genet. 1999;33:479-532. https://doi.org/10.1146/annurev.genet.33.1.479.
55. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann Y., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.C., Rives C.M., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe C., Watanabe H., Totoki Y., Taylor T., Weissenbach J., Heilig R., Saurin W., Artiguenave F., Brottier P., Bruls T., Pelletier E., Robert C., Wincker P., Smith D.R., DoucetteStamm L., Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W., Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmutz J., Dickson M., Grimwood J., Cox D.R., Olson M.V., Kaul R., Raymond C., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen F., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie W.R., de la Bastide M., Dedhia N., Blöcker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork P., Brown D.G., Burge C.B., Cerutti L., Chen H.C., Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey T.S., Galagan J., Gilbert J.G., Harmon C., Hayashizaki Y., Haussler D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., Kasif S., Kaspryzk A., Kennedy S., Kent W.J., Kitts P., Koonin E.V., Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen T., Moran J.V., Mulder N., Pollara V.J., Ponting C.P., Schuler G., Schultz J., Slater G., Smit A.F., Stupka E., Szustakowki J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.P., Yeh R.F., Collins F., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., Chen Y.J., Szustakowki J. Initial International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921. https://doi.org/F409_15d 860.921.
56. Liebermann D., Hoffman-Liebermann B., Weinthal J., Childs G., Maxson R., Mauron A., Cohen S.N., Kedes L. An unusual transposon with long terminal inverted repeats in the sea urchin Strongylocentrotus purpuratus. Nature. 1983;306(5941):342-347.
57. Lim J.K., Simmons M.J. Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster. Bioessays. 1994;16(4):269-275. https://doi.org/10.1002/bies.950160410.
58. Llorens C., Muñoz-Pomer A., Bernad L., Botella H., Moya A. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol Direct. 2009;4:41. https://doi.org/10.1186/1745-6150-4-41.
59. Luo Y.J., Takeuchi T., Koyanagi R., Yamada L., Kanda M., Khalturina M., Fujie M., Yamasaki S., Endo K., Satoh N. The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization. Nat Commun. 2015;6:8301. https://doi.org/10.1038/ncomms9301.
60. McClintock B. Controlling elements and the gene. Cold Spring Harbor Sympos. Quant. Biol. 1956;21;197.
61. McInerney C.E., Allcock A.L., Johnson M.P., Bailie D.A., Prodöhl P.A. Comparative genomic analysis reveals speciesdependent complexities that explain difficulties with microsatellite marker development in molluscs. Heredity. 2011;106:78-87. https://doi.org/10.1038/hdy.2010.36.
62. Mobile DNA. Eds. Berg D.E., Howe M.M. Washington D.C.: American Society of Microbiology Press, 1989.
63. Mobile DNA II. Edited by Craig N, Craigie R, Gellert M, Lambowitz A. Washington DC: American Society of Microbiology Press, 2002.
64. Mora C., Tittensor D.P., Adl S., Simpson A.G.B., Worm B. How many species are there on earth and in the ocean? PLoS Biology. 2011;9(8):e1001127. https://doi.org/10.1371/journal.pbio.1001127.
65. Moroz L.L., Kocot K.M., Citarella M.R., Dosung S., Norekian T.P., Povolotskaya I.S., Grigorenko A.P., Dailey C., Berezikov E., Buckley K.M., Ptitsyn A., Reshetov D., Mukherjee K., Moroz T.P., Bobkova Y., Yu F., Kapitonov V.V., Jurka J., Bobkov Y.V., Swore J.J., Girardo D.O., Fodor A., Gusev F., Sanford R., Bruders R., Kittler E., Mills C.E., Rast J.P., Derelle R., Solovyev V.V., Kondrashov F.A., Swalla B.J., Sweedler J.V., Rogaev E.I., Halanych K.M., Kohn A.B.. The ctenophore genome and the evolutionary origins of neural systems. Nature. 2014;510(7503):109-114. https://doi.org/10.1038/nature13400.
66. Nossa C.W., Havlak P., Yue J.X., Lv J., Vincent K.Y., Brockmann H.J., Putnam N.H. Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. Gigascience. 2014;3:9. https://doi.org/10.1186/2047-217X-3-9.
67. Nuzhdin S.V. Sure facts, speculations, and open questions about the evolution of transposable element copy number. Genetica. 1999;107(1-3):129-137.
68. Osborne P.W., Luke G.N., Holland P.W., Ferrier D.E. Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae). Int. J. Biol. Sci. 2006;2(2):54-60. https://doi.org/10.7150/ijbs.2.54.
69. Panchin Y., Moroz L.L. Molluscan mobile elements similar to the vertebrate Recombination-Activating Genes. Biochem. Biophys. Res. Commun. 2008;369(3):818-823. https://doi.org/10.1016/j.bbrc.2008.02.097.
70. Pearce S.R., Pich U., Harrison G., Flavell A.J., Heslop-Harrison J.S., Schubert I., Kumar A. The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 1996;4(5):357-364.
71. Peifer M., Bender W. Sequences of the gypsy transposon of Drosophila necessary for its effects on adjacent genes. Proc. Natl Acad. Sci. USA. 1988;85(24):9650-9654.
72. Permanyer J., Gonzalez-Duarte R., Albalat R. The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes. Genome Biol. 2003;4(11):R73. https://doi.org/10.1186/gb-2003-4-11-r73.
73. Peterson P.A. Historical overview of transposable element research. In: Plant Transposable Elements: Methods and Protocols. Methods in Molecular Biology. Ed. Th. Peterson. 2013;1057:1-9. https://doi.org/10.1007/978-1-62703-568-2_1.
74. Piednoël M., Bonnivard E. DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms. BMC Evol. Biol. 2009;9:86. https://doi.org/10.1186/1471-2148-9-86.
75. Piednoël M., Donnart T., Esnault C., Graḉa P., Higuet D., Bonnivard E. LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like copia elements. PLoS ONE. 2013;8(3):e57675. https://doi.org/10.1371/journal.pone.0057675.
76. Putnam N.H., Butts T., Ferrier D.E., Furlong R.F., Hellsten U., Kawashima T., Robinson-Rechavi M., Shoguchi E., Terry A., Yu J.K., Benito-Gutiérrez E.L., Dubchak I., Garcia-Fernàndez J., GibsonBrown J.J., Grigoriev I.V., Horton A.C., de Jong P.J., Jurka J., Kapitonov V.V., Kohara Y., Kuroki Y., Lindquist E., Lucas S., Osoegawa K., Pennacchio L.A., Salamov A.A., Satou Y., Sauka-Spengler T., Schmutz J., Shin-I T., Toyoda A., Bronner-Fraser M., Fujiyama A., Holland L.Z., Holland P.W., Satoh N., Rokhsar D.S. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008;453(7198):1064-1071. https://doi.org/10.1038/nature06967.
77. Putnam N.H., Srivastava M., Hellsten U., Dirks B., Chapman J., Salamov A., Terry A., Shapiro H., Lindquist E., Kapitonov V.V., Jurka J., Genikhovich G., Grigoriev I.V., Lucas S.M., Steele R.E., Finnerty J.R., Technau U., Martindale M.Q., Rokhsar D.S. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007;317(5834):86-94. https://doi.org/10.1126/science.1139158.
78. Rebollo R., Romanish M.T., Mager D.L. Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev. Genet. 2012;46:21-42. https://doi.org/10.1146/annurev-genet-110711-155621.
79. Robertson H.M. Multiple mariner transposons in flatworms and hydras are related to those of insects. J. Heredity. 1997;88:195-201.
80. Robertson H.M., Zumpano K.L. Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome. Gene. 1997;205:203-217.
81. Ryan J.F., Pang K., Schnitzler C.E., Nguyen A.D., Moreland R.T., Simmons D.K., Koch B.J., Francis W.R., Havlak P., NISC Comparative Sequencing Program, Smith S.A., Putnam N.H., Haddock S.H., Dunn C.W., Wolfsberg T.G., Mullikin J.C., Martindale M.Q., Baxevanis A.D. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013;342(6164):1242592. https://doi.org/10.1126/science.1242592.
82. Sakaew W., Pratoomthai B., Pongtippatee P., Flegel T.W., Withyachumnarnkul B. Discovery and partial characterization of a non-LTR retrotransposon that may be associated with abdominal segment deformity disease (ASDD) in the whiteleg shrimp Penaeus (Litopenaeus) vannamei. BMC Veterinary Research. 2013;9:189. https://doi.org/10.1186/1746-6148-9-189.
83. Sakano H., Huppi K., Heinrich G., Tonegawa S. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature. 1979;280:288-294.
84. SanMiguel P., Tikhonov A., Jin Y.K., Motchoulskaia N., Zakharov D., Melake-Berhan A., Springer P.S., Edwards K.J., Lee M., Avramova Z., Bennetzen J.L. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996;274(5288):765-768. https://doi.org/10.1126/science.274.5288.765.
85. Seo H.C., Kube M., Edvardsen R.B., Jensen M.F., Beck A., Spriet E., Gorsky G., Thompson E.M., Lehrach H., Reinhardt R., Chourrout D. Miniature genome in the marine chordate Oikopleura dioica. Science. 2001;294(5551):2506.
86. Shinzato C., Shoguchi E., Kawashima T., Hamada M., Hisata K., Tanaka M., Fujie M., Fujiwara M., Koyanagi R., Ikuta T., Fujiyama A., Miller D.J., Satoh N. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature. 2011;476(7360):320-323. https://doi.org/10.1038/nature10249.
87. Simakov O., Kawashima T., Marlétaz F., Jenkins J., Koyanagi R., Mitros T., Hisata K., Bredeson J., Shoguchi E., Gyoja F., Yue J.X., Chen Y.C., Freeman R.M. Jr., Sasaki A., Hikosaka-Katayama T., Sato A., Fujie M., Baughman K.W., Levine J., Gonzalez P., Cameron C., Fritzenwanker J.H., Pani A.M., Goto H., Kanda M., Arakaki N., Yamasaki S., Qu J., Cree A., Ding Y., Dinh H.H., Dugan S., Holder M., Jhangiani S.N., Kovar C.L., Lee S.L., Lewis L.R., Morton D., Nazareth L.V., Okwuonu G., Santibanez J., Chen R., Richards S., Muzny D.M., Gillis A., Peshkin L., Wu M., Humphreys T., Su Y.H., Putnam N.H., Schmutz J., Fujiyama A., Yu J.K., Tagawa K., Worley K.C., Gibbs R.A., Kirschner M.W., Lowe C.J., Satoh N., Rokhsar D.S., Gerhart J. Hemichordate genomes and deuterostome origins. Nature. 2015;527(7579):459-465. https://doi.org/10.1038/nature16150.
88. Simakov O., Marletaz F., Cho S.J., Edsinger-Gonzales E., Havlak P., Hellsten U., Kuo D.H., Larsson T., Lv J., Arendt D., Savage R., Osoegawa K., de Jong P., Grimwood J., Chapman J.A., Shapiro H., Aerts A., Otillar R.P., Terry A.Y., Boore J.L., Grigoriev I.V., Lindberg D.R., Seaver E.C., Weisblat D.A., Putnam N.H., Rokhsar D.S. Insights into bilaterian evolution from three spiralian genomes. Nature. 2013;493(7433):526-531. https://doi.org/10.1038/nature11696.
89. Simmen M.W., Bird A. Sequence analysis of transposable elements in the sea squirt, Ciona intestinalis. Mol. Biol. Evol. 2000;17(11):1685-1694. https://doi.org/mbev_17_1102.1685_1694.tp.
90. Small K.S., Brudno M., Hill M.M., Sidow A. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol. 2007;8(3):R41.
91. Sodergren E., Weinstock G.M., Davidson E.H., Cameron R.A., Gibbs R.A., Angerer R.C., Angerer L.M., Arnone M.I., Burgess D.R., Burke R.D., Coffman J.A., Dean M., Elphick M.R., Ettensohn C.A., Foltz K.R., Hamdoun A., Hynes R.O., Klein W.H., Marzluff W., McClay D.R., Morris R.L., Mushegian A., Rast J.P., Smith L.C., Thorndyke M.C., Vacquier V.D., Wessel G.M., Wray G., Zhang L., Elsik C.G., Ermolaeva O., Hlavina W., Hofmann G., Kitts P., Landrum M.J., Mackey A.J., Maglott D., Panopoulou G., Poustka A.J., Pruitt K., Sapojnikov V., Song X., Souvorov A., Solovyev V., Wei Z., Whittaker C.A., Worley K., Durbin K.J., Shen Y., Fedrigo O., Garfield D., Haygood R., Primus A., Satija R., Severson T., Gonzalez-Garay M.L., Jackson A.R., Milosavljevic A., Tong M., Killian C.E., Livingston B.T., Wilt F.H., Adams N., Bellé R., Carbonneau S., Cheung R., Cormier P., Cosson B., Croce J., Fernandez-Guerra A., Genevière A.M., Goel M., Kelkar H., Morales J., Mulner-Lorillon O., Robertson A.J., Goldstone J.V., Cole B., Epel D., Gold B., Hahn M.E., Howard-Ashby M., Scally M., Stegeman J.J., Allgood E.L., Cool J., Judkins K.M., McCafferty S.S., Musante A.M., Obar R.A., Rawson A.P., Rossetti B.J., Gibbons I.R., Hoffman M.P., Leone A., Istrail S., Materna S.C., Samanta M.P., Stolc V., Tongprasit W., Tu Q., Bergeron K.F., Brandhorst B.P., Whittle J., Berney K., Bottjer D.J., Calestani C., Peterson K., Chow E., Yuan Q.A., Elhaik E., Graur D., Reese J.T., Bosdet I., Heesun S., Marra M.A., Schein J., Anderson M.K., Brockton V., Buckley K.M., Cohen A.H., Fugmann S.D., Hibino T., Loza-Coll M., Majeske A.J., Messier C., Nair S.V., Pancer Z., Terwilliger D.P., Agca C., Arboleda E., Chen N., Churcher A.M., Hallböök F., Humphrey G.W., Idris M.M., Kiyama T., Liang S., Mellott D., Mu X., Murray G., Olinski R.P., Raible F., Rowe M., Taylor J.S., Tessmar-Raible K., Wang D., Wilson K.H., Yaguchi S., Gaasterland T., Galindo B.E., Gunaratne H.J., Juliano C., Kinukawa M., Moy G.W., Neill A.T., Nomura M., Raisch M., Reade A., Roux M.M., Song J.L., Su Y.H., Townley I.K., Voronina E., Wong J.L., Amore G., Branno M., Brown E.R., Cavalieri V., Duboc V., Duloquin L., Flytzanis C., Gache C., Lapraz F., Lepage T., Locascio A., Martinez P., Matassi G., Matranga V., Range R., Rizzo F., Röttinger E., Beane W., Bradham C., Byrum C., Glenn T., Hussain S., Manning G., Miranda E., Thomason R., Walton K., Wikramanayke A., Wu S.Y., Xu R., Brown C.T., Chen L., Gray R.F., Lee P.Y., Nam J., Oliveri P., Smith J., Muzny D., Bell S., Chacko J., Cree A., Curry S., Davis C., Dinh H., Dugan-Rocha S., Fowler J., Gill R., Hamilton C., Hernandez J., Hines S., Hume J., Jackson L., Jolivet A., Kovar C., Lee S., Lewis L., Miner G., Morgan M., Nazareth L.V., Okwuonu G., Parker D., Pu L.L., Thorn R., Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006;314(5801):941-952.
92. Specchia V., Piacentini L., Tritto P., Fanti L., D’Alessandro R., Palumbo G., Pimpinelli S., Bozzetti M.P. Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons. Nature. 2010;463(7281):662-665.
93. Springer M.S., Davidson E.H., Britten R.J. Retroviral-like element in a marine invertebrate. Proc. Natl Acad. Sci. USA. 1991;88:8401-8404.
94. Srivastava M., Begovic E., Chapman J., Putnam N.H., Hellsten U., Kawashima T., Kuo A., Mitros T., Salamov A., Carpenter M.L., Signorovitch A.Y., Moreno M.A., Kamm K., Grimwood J., Schmutz J., Shapiro H., Grigoriev I.V., Buss L.W., Schierwater B., Dellaporta S.L., Rokhsar D.S. The Trichoplax genome and the nature of placozoans. Nature. 2008;454(7207):955-60. https://doi.org/10.1038/nature07191.
95. Srivastava M., Simakov O., Chapman J., Fahey B., Gauthier M.E., Mitros T., Richards G.S., Conaco C., Dacre M., Hellsten U., Larroux C., Putnam N.H., Stanke M., Adamska M., Darling A., Degnan S.M., Oakley T.H., Plachetzki D.C., Zhai Y., Adamski M., Calcino A., Cummins S.F., Goodstein D.M., Harris C., Jackson D.J., Leys S.P., Shu S., Woodcroft B.J., Vervoort M., Kosik K.S., Manning G., Degnan B.M., Rokhsar D.S. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010;466(7307):720-726. https://doi.org/10.1038/nature09201.
96. Syvanen M. Evolutionary implications of horizontal gene transfer. Annu. Rev. Genet. 2012;46:341-358. https://doi.org/10.1146/annurev-genet-110711-155529.
97. Terrat Y., Bonnivard E., Higuet D. GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species. Mol. Genet. Genomics. 2008;279:63-73. https://doi.org/10.1007/s00438-007-0295-0.
98. Thompson C.B. New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity. 1995;3:531-539.
99. Vieira C., Nardon C., Arpin C., Lepetit D., Biémont C. Evolution of genome size in Drosophila. Is the invader’s genome being invaded by transposable elements? Mol. Biol. Evol. 2002;19(7):1154-1161. https://doi.org/mbev_19_705.1154_1161.tp.
100. Volff J.N., Lehrach H., Reinhardt R., Chourrout D. Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica. Mol. Biol. Evol. 2004;21(11):2022-2033. https://doi.org/10.1093/molbev/msh207.
101. Wang S., Zhang L., Meyer E., Matz M.V. Characterization of a group of MITEs with unusual features from two coral genomes. PLoS One. 2010;5(5):e10700. https://doi.org/10.1371/journal.pone.0010700.
102. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., Brown S.D., Bult C., Burton J., Butler J., Campbell R.D., Carninci P., Cawley S., Chiaromonte F., Chinwalla A.T., Church D.M., Clamp M., Clee C., Collins F.S., Cook L.L., Copley R.R., Coulson A., Couronne O., Cuff J., Curwen V., Cutts T., Daly M., David R., Davies J., Delehaunty K.D., Deri J., Dermitzakis E.T., Dewey C., Dickens N.J., Diekhans M., Dodge S., Dubchak I., Dunn D.M., Eddy S.R., Elnitski L., Emes R.D., Eswara P., Eyras E., Felsenfeld A., Fewell G.A., Flicek P., Foley K., Frankel W.N., Fulton L.A., Fulton R.S., Furey T.S., Gage D., Gibbs R.A., Glusman G., Gnerre S., Goldman N., Goodstadt L., Grafham D., Graves T.A., Green E.D., Gregory S., Guigó R., Guyer M., Hardison R.C., Haussler D., Hayashizaki Y., Hillier L.W., Hinrichs A., Hlavina W., Holzer T., Hsu F., Hua A., Hubbard T., Hunt A., Jackson I., Jaffe D.B., Johnson L.S., Jones M., Jones T.A., Joy A., Kamal M., Karlsson E.K., Karolchik D., Kasprzyk A., Kawai J., Keibler E., Kells C., Kent W.J., Kirby A., Kolbe D.L., Korf I., Kucherlapati R.S., Kulbokas E.J., Kulp D., Landers T., Leger J.P., Leonard S., Letunic I., Levine R., Li J., Li M., Lloyd C., Lucas S., Ma B., Maglott D.R., Mardis E.R., Matthews L., Mauceli E., Mayer J.H., McCarthy M., McCombie W.R., McLaren S., McLay K., McPherson J.D., Meldrim J., Meredith B., Mesirov J.P., Miller W., Miner T.L., Mongin E., Montgomery K.T., Morgan M., Mott R., Mullikin J.C., Muzny D.M., Nash W.E., Nelson J.O., Nhan M.N., Nicol R., Ning Z., Nusbaum C., O’Connor M.J., Okazaki Y., Oliver K., Overton-Larty E., Pachter L., Parra G., Pepin K.H., Peterson J., Pevzner P., Plumb R., Pohl C.S., Poliakov A., Ponce T.C., Ponting C.P., Potter S., Quail M., Reymond A., Roe B.A., Roskin K.M., Rubin E.M., Rust A.G., Santos R., Sapojnikov V., Schultz B., Schultz J., Schwartz M.S., Schwartz S., Scott C., Seaman S., Searle S., Sharpe T., Sheridan A., Shownkeen R., Sims S., Singer J.B., Slater G., Smit A., Smith D.R., Spencer B., Stabenau A., Stange-Thomann N., Sugnet C., Suyama M., Tesler G., Thompson J., Torrents D., Trevaskis E., Tromp J., Ucla C., Ureta-Vidal A., Vinson J.P., Von Niederhausern A.C., Wade C.M., Wall M., Weber R.J., Weiss R.B., Wendl M.C., West A.P., Wetterstrand K., Wheeler R., Whelan S., Wierzbowski J., Willey D., Williams S., Wilson R.K., Winter E., Worley K.C., Wyman D., Yang S., Yang S.P., Zdobnov E.M., Zody M.C., Lander E.S. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420:520-562. https://doi.org/10.1038/nature01262.
103. Wicker T., Sabot F., Hua-van A., Bennetzen J.L., Capy P., Chalhoub B., Flavell A., Leroy P., Morgante M., Panaud O., Paux E., SanMiguel P., Schulman A.H. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 2007;8:973-982. https://doi.org/10.1038/nrg2165.
104. Zhang G., Fang X., Guo X., Li L., Luo R., Xu F., Yang P., Zhang L., Wang X., Qi H., Xiong Z., Que H., Xie Y., Holland P.W., Paps J., Zhu Y., Wu F., Chen Y., Wang J., Peng C., Meng J., Yang L., Liu J., Wen B., Zhang N., Huang Z., Zhu Q., Feng Y., Mount A., Hedgecock D., Xu Z., Liu Y., Domazet-Lošo T., Du Y., Sun X., Zhang S., Liu B., Cheng P., Jiang X., Li J., Fan D., Wang W., Fu W., Wang T., Wang B., Zhang J., Peng Z., Li Y., Li N., Wang J., Chen M., He Y., Tan F., Song X., Zheng Q., Huang R., Yang H., Du X., Chen L., Yang M., Gaffney P.M., Wang S., Luo L., She Z., Ming Y., Huang W., Zhang S., Huang B., Zhang Y., Qu T., Ni P., Miao G., Wang J., Wang Q., Steinberg C.E., Wang H., Li N., Qian L., Zhang G., Li Y., Yang H., Liu X., Wang J., Yin Y., Wang J. The oyster genome reveals stress adaptation and complexity of shell formation. Nature. 2012;490(7418):49-54. https://doi.org/10.1038/nature11413.