Abstract
Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.
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Alisch RS, Garcia-Perez JL, Muotri AR, Gage FH, Moran JV (2006) Unconventional translation of mammalian LINE-1 retrotransposons. Genes Dev 20:210–224. doi:10.1101/gad.1380406
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. doi:10.1016/s0022-2836(05)80360-2
Basu VP, Song M, Gao L, Rigby ST, Hanson MN, Bambara RA (2008) Strand transfer events during HIV-1 reverse transcription. Virus Res 134:19–38. doi:10.1016/j.virusres.2007.12.017
Baucom RS et al (2009) Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 5:e1000732. doi:10.1371/journal.pgen.1000732
Beauregard A, Curcio MJ, Belfort M (2008) The take and give between retrotransposable elements and their hosts. Annu Rev Genet 42:587–617. doi:10.1146/annurev.genet.42.110807.091549
Becker KE, Laten HM (2015) A Copia retrotransposon family from Trifolium repens—consensus sequence. Repbase Rep 15:1843
Bennetzen JL, Wang H (2014) The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol 65:505–530. doi:10.1146/annurev-arplant-050213-035811
Casacuberta JM, Santiago N (2003) Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311:1–11. doi:10.1016/S0378-1119(03)00557-2
Casacuberta JM, Vernhettes S, Grandbastien MA (1995) Sequence variability within the tobacco retrotransposon Tnt1 population. EMBO J 14:2670–2678
Dai L, LaCava J, Taylor MS, Boeke JD (2014) Expression and detection of LINE-1 ORF-encoded proteins. Mob Genet Elem. doi:10.4161/mge.29319
De Vega JJ et al (2015) Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Sci Rep 5:17394. doi:10.1038/srep17394
DeBarry JD, Liu R, Bennetzen JL (2008) Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinform 9:235. doi:10.1186/1471-2105-9-235
Dellaporta S, Wood J, Hicks J (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21. doi:10.1007/BF02712670
Devos KM, Brown JK, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12:1075–1079. doi:10.1101/gr.132102
Du J, Grant D, Tian Z, Nelson RT, Zhu L, Shoemaker RC, Ma J (2010a) SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genom 11:113. doi:10.1186/1471-2164-11-113
Du J et al (2010b) Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 63:584–598. doi:10.1111/j.1365-313X.2010.04263.x
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32:1792–1797. doi:10.1093/nar/gkh340
Eickbush TH, Jamburuthugoda VK (2008) The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 134:221–234. doi:10.1016/j.virusres.2007.12.010
Ellinghaus D, Kurtz S, Willhoeft U (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9:1–14. doi:10.1186/1471-2105-9-18
Ellison NW, Liston A, Steiner JJ, Williams WM, Taylor NL (2006) Molecular phylogenetics of the clover genus (Trifolium–Leguminosae). Mol Phylogenet Evol 39:688–705. doi:10.1016/j.ympev.2006.01.004
Ewing A (2015) Transposable element detection from whole genome sequence data. Mob DNA 6:24. doi:10.1186/s13100-015-0055-3
Farabaugh PJ (1996) Programmed translational frameshifting. Annu Rev Genet 30:507–528. doi:10.1146/annurev.genet.30.1.507
Febrer M et al (2007) Construction, characterization, and preliminary BAC-end sequencing analysis of a bacterial artificial chromosome library of white clover (Trifolium repens L.). Genome 50:412–421. doi:10.1139/g07-013
Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368. doi:10.1146/annurev.genet.40.110405.090448
Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering transposable element diversification in De Novo annotation approaches. PLoS ONE 6:e16526. doi:10.1371/journal.pone.0016526
Gabriel A, Willems M, Mules EH, Boeke JD (1996) Replication infidelity during a single cycle of Ty1 retrotransposition. Proc Natl Acad Sci USA 93:7767–7771
Gao C et al (2012) Characterization and functional annotation of nested transposable elements in eukaryotic genomes. Genomics 100:222–230. doi:10.1016/j.ygeno.2012.07.004
Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, Dawe RK (2012) CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res 23:628–637. doi:10.1101/gr.146985.112
Hand ML et al (2008) Identification of homologous, homoeologous and paralogous sequence variants in an outbreeding allopolyploid species based on comparison with progenitor taxa. Mol Genet Genom 280:293–304. doi:10.1007/s00438-008-0365-y
Hand ML, Cogan NO, Sawbridge TI, Spangenberg GC, Forster JW (2010) Comparison of homoeolocus organisation in paired BAC clones from white clover (Trifolium repens L.) and microcolinearity with model legume species. BMC Plant Biol 10:94. doi:10.1186/1471-2229-10-94
Heitkam T, Holtgräwe D, Dohm JC, Minoche AE, Himmelbauer H, Weisshaar B, Schmidt T (2014) Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades. Plant J 79:385–397. doi:10.1111/tpj.12565
Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915–10919
Hoen DR et al (2015) A call for benchmarking transposable element annotation methods. Mob DNA 6:13. doi:10.1186/s13100-015-0044-6
Hong JJ, Wu TY, Chang TY, Chen CY (2013) Viral IRES prediction system—a web server for prediction of the IRES secondary structure in silico. PLoS ONE 8:e79288. doi:10.1371/journal.pone.0079288
Huang CR, Burns KH, Boeke JD (2012) Active transposition in genomes. Annu Rev Genet 46:651–675. doi:10.1146/annurev-genet-110711-155616
Istvanek J, Jaros M, Krenek A, Repkova J (2014) Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae). Am J Bot 101:327–337. doi:10.3732/ajb.1300340
Joly-Lopez Z, Bureau TE (2014) Diversity and evolution of transposable elements in Arabidopsis. Chromosome Res 22:203–216. doi:10.1007/s10577-014-9418-8
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467. doi:10.1159/000084979
Jurka J, Kapitonov VV, Kohany O, Jurka MV (2007) Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genom Hum Genet 8:241–259. doi:10.1146/annurev.genom.8.080706.092416
Koga A (2012) Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element. Genome 55:172–175. doi:10.1139/g11-088
Kohany O, Gentles A, Hankus L, Jurka J (2006) Annotation, submission and screening of repetitive elements in Repbase: Repbasesubmitter and Censor. BMC Bioinform 7:474. doi:10.1186/1471-2105-7-474
Kojima KK, Matsumoto T, Fujiwara H (2005) Eukaryotic translational coupling in UAAUG stop-start codons for the bicistronic RNA translation of the non-long terminal repeat retrotransposon SART1. Mol Cell Biol 25:7675–7686. doi:10.1128/mcb.25.17.7675-7686.2005
Komar AA, Hatzoglou M (2005) Internal ribosome entry sites in cellular mRNAs: mystery of their existence. J Biol Chem 280:23425–23428. doi:10.1074/jbc.R400041200
Laten HM, Mogil LS, Wright LN (2009) A shotgun approach to discovering and reconstructing consensus retrotransposons ex novo from dense contigs of short sequences derived from Genbank Genome Survey Sequence database records. Gene 448:168–173. doi:10.1016/j.gene.2009.06.011
Laten HM, Hand ML, Cogan ROI, Forster JW (2010a) LTR retrotransposons in white clover, Trifolium repens L: TreLTRRT2. Repbase Rep 10:2176–2177
Laten HM, Hand MS, Cogan NO, Forster JW (2010b) LTR retrotransposons in white clover, Trifolium repens L: Copia-1 Tre. Repbase Rep 10:2166–2167
Li R et al (2005) ReAS: recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1:e43. doi:10.1371/journal.pcbi.0010043
Li PWL, Li J, Timmerman SL, Krushel LA, Martin SL (2006) The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition. Nucl Acids Res 34:853–864. doi:10.1093/nar/gkj490
Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60:43–66. doi:10.1146/annurev.arplant.59.032607.092744
Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14:860–869. doi:10.1101/gr.1466204
Marchler-Bauer A et al (2014) CDD: NCBI’s conserved domain database. Nucl Acids Res 43:D222–226. doi:10.1093/nar/gku1221
Martini S, Laten HM (2015) TrepCOPIA3: A Copia retrotransposon family from Trifolium repens—consensus sequence. Repbase Rep 15:1844–1845
Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJM (2007) Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 10:512–519. doi:10.1016/j.pbi.2007.06.007
McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19:362–367. doi:10.1093/bioinformatics/btf878
Mokrejš M, Mašek T, Vopálenský V, Hlubuček P, Delbos P, Pospíšek M (2010) IRESite—a tool for the examination of viral and cellular internal ribosome entry sites. Nucl Acids Res 38:D131–D136. doi:10.1093/nar/gkp981
Noma K, Ohtsubo H, Ohtsubo E (2000) ATLN elements LINEs from Arabidopsis thaliana: identification and characterization. DNA Res 7:291–303. doi:10.1093/dnares/7.5.291
Novák P, Neumann P, Pech J, Steinhaisl J, Macas J (2013) RepeatExplorer: a galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792–793. doi:10.1093/bioinformatics/btt054
Ostertag EM, Kazazian HH Jr (2001) Biology of mammalian L1 retrotransposons. Annu Rev Genet 35:501–538. doi:10.1146/annurev.genet.35.102401.091032
Peterson-Burch BD, Voytas DF (2002) Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol Biol Evol 19:1832–1845
Rebollo R, Romanish MT, Mager DL (2012) Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet 46:21–42. doi:10.1146/annurev-genet-110711-155621
Ronquist F et al (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542. doi:10.1093/sysbio/sys029
Sabot F, Schulman AH (2006) Parasitism and the retrotransposon life cycle in plants: a hitchhiker’s guide to the genome. Heredity 97:381–388. doi:10.1038/sj.hdy.6800903
SanMiguel P et al (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–768. doi:10.1126/science.274.5288.765
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45. doi:10.1038/1695
Schulman AH (2012) Hitching a ride: nonautonomous retrotransposons and parasitism as a lifestyle. In: Grandbastien MA, Casacuberta JM (eds) Plant transposable elements: impact on genome structure and function. Springer, New York, pp 71–88. doi:10.1007/978-3-641-31842-9_5
Senerchia N, Wicker T, Felber F, Parisod C (2013) Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat. Genome Biol Evol 5:1010–1020. doi:10.1093/gbe/evt064
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. doi:10.1093/bioinformatics/btu033
Steinbiss S, Kastens S, Kurtz S (2012) LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Mob DNA 3:18. doi:10.1186/1759-8753-3-18
Tayalé A, Parisod C (2013) Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet Genome Res 140:79–96. doi:10.1159/000351318
Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15:471–478. doi:10.1016/j.tplants.2010.05.003
Thomas MC, Laten HM (2015) TrepLINE1: a LINE retrotransposon family from Trifolium repens. Repbase Rep 15:1847
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucl Acids Res 40:e115. doi:10.1093/nar/gks596
Vitte C, Bennetzen JL (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103:17638–17643. doi:10.1073/pnas.0605618103
Vitte C, Estep MC, Leebens-Mack J, Bennetzen JL (2013) Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Ann Bot 112:881–889. doi:10.1093/aob/mct155
Vitte C, Fustier M-A, Alix K, Tenaillon MI (2014) The bright side of transposons in crop evolution. Brief Funct Genomics 13:276–295. doi:10.1093/bfgp/elu002
Vižintin L, Javornik B, Bohanec B (2006) Genetic characterization of selected Trifolium species as revealed by nuclear DNA content and ITS rDNA region analysis. Plant Sci 170:859–866. doi:10.1016/j.plantsci.2005.12.007
Wenke T, Holtgräwe D, Horn AV, Weisshaar B, Schmidt T (2009) An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris. Plant Mol Biol 71:585–597. doi:10.1007/s11103-009-9542-6
Wicker T, Keller B (2007) 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 17:1072–1081. doi:10.1101/gr.6214107
Wicker T, Matthews DE, Keller B (2002) TREP: a database for Triticeae repetitive elements. Trends Plant Sci 7:561–562. doi:10.1016/S1360-1385(02)02372-5
Wicker T et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982. doi:10.1038/nrg2165
Williams WM (2014) Trifolium interspecific hybridisation: widening the white clover gene pool. Crop Pasture Sci 65:1091–1106. doi:10.1071/CP13294
Williams WM, Ellison NW, Ansari HA, Verry IM, Hussain SW (2012) Experimental evidence for the ancestry of allotetraploid Trifolium repens and creation of synthetic forms with value for plant breeding. BMC Plant Biol 12:55. doi:10.1186/1471-2229-12-55
Xu Z, Wang H (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucl Acids Res 35:W265–W268. doi:10.1093/nar/gkm286
Yamashita H, Tahara M (2006) A LINE-type retrotransposon active in meristem stem cells causes heritable transpositions in the sweet potato genome. Plant Mol Biol 61:79–94. doi:10.1007/s11103-005-6002-9
Acknowledgments
KEB, SM, TS, VD, and RMS were supported by Loyola University undergraduate research fellowships. We thank Emily Welebob and Stephanie Vargas for their experimental contributions, Stefan Kanzok for qPCR guidance, and Haley Luebke for helpful suggestions.
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Kailey E. Becker, Mary C. Thomas, Samer Martini, Tautvydas Shuipys, Howard M. Laten have contributed equally.
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Becker, K.E., Thomas, M.C., Martini, S. et al. Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification. Genetica 144, 577–589 (2016). https://doi.org/10.1007/s10709-016-9926-x
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DOI: https://doi.org/10.1007/s10709-016-9926-x