Boeke J, Stoye J. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. Retroviruses. Cold Spring Harbor Laboratory Press. 1997.
Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999;9(6):657–63.
Article
CAS
PubMed
Google Scholar
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. The paleontology of intergene retrotransposons of maize. Nat Genet. 1998;20(1):43–5.
Article
CAS
PubMed
Google Scholar
Kumar A, Bennetzen JL. Plant Retrotransposons. Annu Rev Genet. 1999;33(1):479–532.
Article
CAS
PubMed
Google Scholar
Li Y, Tassia MG, Waits DS, Bogantes VE, David KT, Halanych KM. Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biol. 2019;17(1):1–14.
Article
Google Scholar
Bowen NJ, McDonald JF. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 2001;11(9):1527–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiong Y, Eickbush TH. Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol. 1988;5(6):675–90.
CAS
PubMed
Google Scholar
Alzohairy AM, Sabir JSM, Gyulai G, Younis RAA, Jansen RK, Bahieldin A. Environmental stress activation of plant long-terminal repeat retrotransposons. Funct Plant Biol. 2014;41(6):557–67.
Article
CAS
PubMed
Google Scholar
Muszewska A, Hoffman-Sommer M, Grynberg M. LTR Retrotransposons in Fungi. PLoS One. 2011;6(12):e29425 Redfield RJ, editor.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thomas-Bulle C, Piednoël M, Donnart T, Filée J, Jollivet D, Bonnivard É. Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics. BMC Genomics. 2018;19(1):821.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007;8(12):973–82.
Article
CAS
PubMed
Google Scholar
Zhang L, Yan L, Jiang J, Wang Y, Jiang Y, Yan T, et al. The structure and retrotransposition mechanism of LTR-retrotransposons in the asexual yeast Candida albicans. Virulence. 2014;5(6):655–64.
Article
PubMed
PubMed Central
Google Scholar
Steinbauerová V, Neumann P, Novák P, Macas J. A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons. Genetica. 2011;139(11-12):1543–55.
Article
PubMed
CAS
Google Scholar
Neumann P, Novák P, Hoštáková N, Macas J. Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mob DNA. 2019;10:1.
Article
PubMed
PubMed Central
Google Scholar
Carvalho M, Ribeiro T, Viegas W, Morais-Cecilio L, Rocheta M. Presence of env-like sequences in Quercus suber retrotransposons. J Appl Genet. 2010;51(4):461–7.
Article
CAS
PubMed
Google Scholar
Gómez-Orte E, Vicient CM, Martínez-Izquierdo JA. Grande retrotransposons contain an accessory gene in the unusually long 3'-internal region that encodes a nuclear protein transcribed from its own promoter. Plant Mol Biol. 2013;81(6):541–51.
Article
PubMed
CAS
Google Scholar
Steckbeck JD, Kuhlmann AS, Montelaro RC. Structural and functional comparisons of retroviral envelope protein C-terminal domains: still much to learn. Viruses. 2014;6(1):284–300.
Article
PubMed
PubMed Central
CAS
Google Scholar
McLane LM, Pulliam KF, Devine SE, Corbett AH. The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus. Nucleic Acids Res. 2008;36(13):4317–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vicient CM, Casacuberta JM. Additional ORFs in Plant LTR-Retrotransposons. Front Plant Sci. 2020;11:555.
Article
PubMed
PubMed Central
Google Scholar
Gonzalez P, Lessios HA. Evolution of sea urchin retroviral-like (SURL) elements: evidence from 40 echinoid species. Mol Biol Evol. 1999;16(7):938–52.
Article
CAS
PubMed
Google Scholar
Chen JE, Cui G, Wang X, Liew YJ, Aranda M. Recent expansion of heat-activated retrotransposons in the coral symbiont Symbiodinium microadriaticum. ISME J. 2018;12(2):639–43.
Article
CAS
PubMed
Google Scholar
Piednoël M, Donnart T, Esnault C, Graça 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.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang K, Shen Y, Yang Y, Gan X, Liu G, Hu K, et al. Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol. 2019;3(5):823–33.
Article
PubMed
Google Scholar
Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, et al. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nat Ecol Evol. 2017;1(5):121.
Article
PubMed
Google Scholar
Schulze A. Phylogeny of Vestimentifera (Siboglinidae, Annelida) inferred from morphology. Zool Scr. 2003;32(4):321–42.
Article
Google Scholar
Schulze A, Halanych KM. Siboglinid evolution shaped by habitat preference and sulfide tolerance. In: Hydrobiologia: Springer; 2003. p. 199–205.
Google Scholar
Halanych KM. Molecular phylogeny of siboglinid annelids (a.k.a. pogonophorans): a review. In: Morphology, molecules, evolution and phylogeny in polychaeta and related taxa: Springer-Verlag; 2005. p. 297–307.
Chapter
Google Scholar
RepeatModeler Download Page. Available from: http://www.repeatmasker.org/RepeatModeler/. Cited 2021 Feb 20
RepeatMasker Home Page. Available from: http://www.repeatmasker.org/. Cited 2021 Feb 20
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: The protein families database. Nucleic Acids Res. 2014;42(D1):222–30.
Article
CAS
Google Scholar
Marchler-Bauer A, Bryant SH. CD-Search: Protein domain annotations on the fly. Nucleic Acids Res. 2004;32(Web Server issue):W327–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bae YA, Moon SY, Kong Y, Cho SY, Rhyu MG. CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. Mol Biol Evol. 2001;18(8):1474–83.
Article
CAS
PubMed
Google Scholar
Goodwin TJ, Poulter RT. A group of deuterostome Ty3/ gypsy-like retrotransposons with Ty1/ copia-like pol-domain orders. Mol Gen Genomics. 2002;267(4):481–91.
Article
CAS
Google Scholar
Volff J-N, Körting C, Altschmied J, Duschl J, Sweeney K, Wichert K, et al. Jule from the Fish Xiphophorus Is the First Complete Vertebrate Ty3/Gypsy Retrotransposon from the Mag Family. Mol Biol Evol. 2001;18(2):101–11.
Article
CAS
PubMed
Google Scholar
Tubío JM, Naveira H, Costas J. Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. Mol Biol Evol. 2005;22(1):29–39.
Article
PubMed
CAS
Google Scholar
McCarthy EM, Liu J, Lizhi G, McDonald JF. Long terminal repeat retrotransposons of Oryza sativa. Genome Biol. 2002;3(10):research0053.1.
Article
Google Scholar
Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, et al. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2002;3(12):research0084.1.
Article
Google Scholar
Jin-Shan X, Qing-You X, Jun L, Guo-Qing P, Ze-Yang Z. Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori). Insect Biochem Mol Biol. 2005;35(8):921–9.
Article
PubMed
CAS
Google Scholar
Bowen NJ, McDonald JF. Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res. 1999;9(10):924–35.
Article
CAS
PubMed
Google Scholar
Michaille JJ, Mathavan S, Gaillard J, Garel A. The complete sequence of mag, a new retrotransposon in Bombyx mori. Nucleic Acids Res. 1990;18(3):674.
Article
CAS
PubMed
PubMed Central
Google Scholar
Springer MS, Davidson EH, Britten RJ. Retroviral-like element in a marine invertebrate. Proc Natl Acad Sci U S A. 1991;88(19):8401–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Butler M, Goodwin T, Poulter R. An unusual vertebrate LTR retrotransposon from the cod Gadus morhua. Mol Biol Evol. 2001;18(3):443–7.
Article
CAS
PubMed
Google Scholar
Simmen MW, Bird A. Sequence analysis of transposable elements in the sea squirt, Ciona intestinalis. Mol Biol Evol. 2000;17(11):1685–94.
Article
CAS
PubMed
Google Scholar
Abe H, Ohbayashi F, Shimada T, Sugasaki T, Kawai S, Mita K, et al. Molecular structure of a novel gypsy-Ty3-like retrotransposon (Kabuki) and nested retrotransposable elements on the W chromosome of the silkworm Bombyx mori. Mol Gen Genet. 2000;263(6):916–24.
Article
CAS
PubMed
Google Scholar
Copeland CS, Brindley PJ, Heyers O, Michael SF, Johnston DA, Williams DL, et al. Boudicca, a retrovirus-like long terminal repeat retrotransposon from the genome of the human blood fluke Schistosoma mansoni. J Virol. 2003;77(11):6153–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
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 Gen Genomics. 2008;279(1):63–73.
Article
CAS
Google Scholar
De La Chaux N, Wagner A. BEL/Pao retrotransposons in metazoan genomes. BMC Evol Biol. 2011;11:154.
Article
PubMed
PubMed Central
Google Scholar
Copeland CS, Mann VH, Morales ME, Kalinna BH, Brindley PJ. The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements. BMC Evol Biol. 2005;5:20.
Article
PubMed
PubMed Central
CAS
Google Scholar
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(7):1072–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Du C, Swigonová Z, Messing J. Retrotranspositions in orthologous regions of closely related grass species. BMC Evol Biol. 2006;6:62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chénais B, Caruso A, Hiard S, Casse N. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene. 2012;509(1):7–15.
Article
PubMed
CAS
Google Scholar
Halanych KM, Bacheller JD, Aguinaldo AM, Liva SM, Hillis DM, Lake JA. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science. 1995;267(5204):1641–3.
Article
CAS
PubMed
Google Scholar
Metzger MJ, Paynter AN, Siddall ME, Goff SP. Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla. Proc Natl Acad Sci U S A. 2018;115(18):E4227–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
LLUY_1.0 - Genome - Assembly - NCBI. Available from: https://www.ncbi.nlm.nih.gov/assembly/GCA_009193005.1. Cited 2020 Apr 14
Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9(1):18.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007;35(Web Server issue):W265–8.
Article
PubMed
PubMed Central
Google Scholar
Lerat E. Identifying repeats and transposable elements in sequenced genomes: How to find your way through the dense forest of programs. Heredity. 2010;104:520–33 Nature Publishing Group.
Article
CAS
PubMed
Google Scholar
Ou S, Jiang N. LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 2018;176(2):1410–22.
Article
CAS
PubMed
Google Scholar
zhangrengang/TEsorter: TEsorter: lineage-level classification of transposable elements using conserved protein domains. Available from: https://github.com/zhangrengang/TEsorter. Cited 2020 Apr 14
Llorens C, Futami R, Covelli L, Domínguez-Escribá L, Viu JM, Tamarit D, et al. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 2011;39(Database issue):D70–4.
Article
CAS
PubMed
Google Scholar
Vershinin AV, Ellis TH. Heterogeneity of the internal structure of PDR1, a family of Ty1/copia-like retrotransposons in pea. Mol Gen Genet. 1999;262(4-5):703–13.
Article
CAS
PubMed
Google Scholar
Neogi U, Engelbrecht S, Claassen M, Jacobs GB, van Zyl G, Preiser W, et al. Mutational Heterogeneity in p6 Gag Late Assembly (L) Domains in HIV-1 Subtype C Viruses from South Africa. AIDS Res Hum Retrovir. 2016;32(1):80–4.
Article
CAS
PubMed
Google Scholar
Cao L, Yin G, Cao Z, Bing X, Ding W. Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian. Genetica. 2016;144(3):325–33.
Article
CAS
PubMed
Google Scholar
Katoh K, Standley DM. Article Fast Track MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol. 2013;30(4):772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Article
CAS
PubMed
Google Scholar
FigTree. Available from: http://tree.bio.ed.ac.uk/software/figtree/. Cited 2020 May 19.
Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian protein metabolism III. New York: Academic Press; 1969. p. 21–132.
Book
Google Scholar
Ma J, Bennetzen JL. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 2004;101(34):12404–10.
Article
CAS
PubMed
PubMed Central
Google Scholar