TY - JOUR AU - Bennetzen, J. L. AU - Ma, J. AU - Devos, K. M. PY - 2005 DA - 2005// TI - Mechanisms of recent genome size variation in flowering plants JO - Annu Bot VL - 95 UR - https://doi.org/10.1093/aob/mci008 DO - 10.1093/aob/mci008 ID - Bennetzen2005 ER - TY - STD TI - GT V, Schmutzer T, Bull F, Cao HX, Fuchs J, Tran TD, et al. Comparative genome analysis reveals divergent genome size evolution in a carnivorous plant genus. Plant Genome. 2015;8(3) ID - ref2 ER - TY - JOUR AU - Yin, H. AU - Du, J. AU - Li, L. AU - Jin, C. AU - Fan, L. AU - Li, M. PY - 2014 DA - 2014// TI - Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent Interelement recombination for Cassandra Retrotransposon in pear (Pyrus bretschneideri Rehd.) JO - Genome Biol Evol. VL - 6 UR - https://doi.org/10.1093/gbe/evu114 DO - 10.1093/gbe/evu114 ID - Yin2014 ER - TY - JOUR AU - Wu, J. AU - Wang, Z. AU - Shi, Z. AU - Zhang, S. AU - Ming, R. AU - Zhu, S. PY - 2013 DA - 2013// TI - The genome of the pear (Pyrus bretschneideri Rehd.) JO - Genome Res VL - 23 UR - https://doi.org/10.1101/gr.144311.112 DO - 10.1101/gr.144311.112 ID - Wu2013 ER - TY - JOUR AU - Velasco, R. AU - Zharkikh, A. AU - Affourtit, J. AU - Dhingra, A. AU - Cestaro, A. AU - Kalyanaraman, A. PY - 2010 DA - 2010// TI - The genome of the domesticated apple (Malus × domestica Borkh.) JO - Nature Genet. VL - 42 UR - https://doi.org/10.1038/ng.654 DO - 10.1038/ng.654 ID - Velasco2010 ER - TY - JOUR AU - Verde, I. AU - Abbott, A. G. AU - Scalabrin, S. AU - Jung, S. AU - Shu, S. AU - Marroni, F. PY - 2013 DA - 2013// TI - The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution JO - Nature Genet VL - 45 UR - https://doi.org/10.1038/ng.2586 DO - 10.1038/ng.2586 ID - Verde2013 ER - TY - JOUR AU - Paterson, A. H. AU - Wendel, J. F. AU - Gundlach, H. AU - Guo, H. AU - Jenkins, J. AU - Jin, D. PY - 2012 DA - 2012// TI - Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres JO - Nature VL - 492 UR - https://doi.org/10.1038/nature11798 DO - 10.1038/nature11798 ID - Paterson2012 ER - TY - JOUR AU - Schnable, P. S. AU - Ware, D. AU - Fulton, R. S. AU - Stein, J. C. AU - Wei, F. AU - Pasternak, S. PY - 2009 DA - 2009// TI - The B73 maize genome: complexity, diversity, and dynamics JO - Science VL - 326 UR - https://doi.org/10.1126/science.1178534 DO - 10.1126/science.1178534 ID - Schnable2009 ER - TY - JOUR AU - Kumar, A. AU - Bennetzen, J. L. PY - 1999 DA - 1999// TI - Plant retrotransposons JO - Annu Rev Genet VL - 33 UR - https://doi.org/10.1146/annurev.genet.33.1.479 DO - 10.1146/annurev.genet.33.1.479 ID - Kumar1999 ER - TY - JOUR AU - Kalendar, R. AU - Vicient, C. M. AU - Peleg, O. AU - Anamthawat-Jonsson, K. AU - Bolshoy, A. AU - Schulman, A. H. PY - 2004 DA - 2004// TI - Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes JO - Genetics VL - 166 UR - https://doi.org/10.1534/genetics.166.3.1437 DO - 10.1534/genetics.166.3.1437 ID - Kalendar2004 ER - TY - JOUR AU - Witte, C. -. P. AU - Le, Q. H. AU - Bureau, T. AU - Kumar, A. PY - 2001 DA - 2001// TI - Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes JO - P Natl Acad Sci USA. VL - 98 UR - https://doi.org/10.1073/pnas.241341898 DO - 10.1073/pnas.241341898 ID - Witte2001 ER - TY - JOUR AU - Hirochika, H. AU - Sugimoto, K. AU - Otsuki, Y. AU - Tsugawa, H. AU - Kanda, M. PY - 1996 DA - 1996// TI - Retrotransposons of rice involved in mutations induced by tissue culture JO - P Natl Acad Sci USA. VL - 93 UR - https://doi.org/10.1073/pnas.93.15.7783 DO - 10.1073/pnas.93.15.7783 ID - Hirochika1996 ER - TY - JOUR AU - Yin, H. AU - Liu, J. AU - Xu, Y. AU - Liu, X. AU - Zhang, S. AU - Ma, J. PY - 2013 DA - 2013// TI - TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0068587 DO - 10.1371/journal.pone.0068587 ID - Yin2013 ER - TY - JOUR AU - Kim, S. AU - Park, J. Y. AU - Yang, T. -. J. PY - 2015 DA - 2015// TI - Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the pink allele of the ANS gene in onion (Allium cepa L.) JO - Mol Gen Genomics VL - 290 UR - https://doi.org/10.1007/s00438-014-0973-7 DO - 10.1007/s00438-014-0973-7 ID - Kim2015 ER - TY - JOUR AU - Hartl, D. L. AU - Lohe, A. R. AU - Lozovskaya, E. R. PY - 1997 DA - 1997// TI - Regulation of the transposable element mariner JO - Genetica VL - 100 UR - https://doi.org/10.1023/A:1018333629222 DO - 10.1023/A:1018333629222 ID - Hartl1997 ER - TY - JOUR AU - Daniels, S. B. AU - Peterson, K. R. AU - Strausbaugh, L. D. AU - Kidwell, M. G. AU - Chovnick, A. PY - 1990 DA - 1990// TI - Evidence for horizontal transmission of the P transposable element between Drosophila species JO - Genetics VL - 124 ID - Daniels1990 ER - TY - JOUR AU - Roulin, A. AU - Piegu, B. AU - Wing, R. A. AU - Panaud, O. PY - 2008 DA - 2008// TI - Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza JO - Plant J VL - 53 UR - https://doi.org/10.1111/j.1365-313X.2007.03388.x DO - 10.1111/j.1365-313X.2007.03388.x ID - Roulin2008 ER - TY - JOUR AU - Roulin, A. AU - Piegu, B. AU - Fortune, P. M. AU - Sabot, F. AU - D’Hont, A. AU - Manicacci, D. PY - 2009 DA - 2009// TI - Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae JO - BMC Evol Biol VL - 9 UR - https://doi.org/10.1186/1471-2148-9-58 DO - 10.1186/1471-2148-9-58 ID - Roulin2009 ER - TY - JOUR AU - El Baidouri, M. AU - Carpentier, M. -. C. AU - Cooke, R. AU - Gao, D. AU - Lasserre, E. AU - Llauro, C. PY - 2014 DA - 2014// TI - Widespread and frequent horizontal transfers of transposable elements in plants JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.164400.113 DO - 10.1101/gr.164400.113 ID - El Baidouri2014 ER - TY - JOUR AU - Feschotte, C. AU - Jiang, N. AU - Wessler, S. R. PY - 2002 DA - 2002// TI - Plant transposable elements: where genetics meets genomics JO - Nat Rev Genet. VL - 3 UR - https://doi.org/10.1038/nrg793 DO - 10.1038/nrg793 ID - Feschotte2002 ER - TY - JOUR AU - Paszkowski, J. PY - 2015 DA - 2015// TI - Controlled activation of retrotransposition for plant breeding JO - Curr Opin Biotech VL - 32 UR - https://doi.org/10.1016/j.copbio.2015.01.003 DO - 10.1016/j.copbio.2015.01.003 ID - Paszkowski2015 ER - TY - JOUR AU - Grandbastien, M. -. A. PY - 1998 DA - 1998// TI - Activation of plant retrotransposons under stress conditions JO - Trends Plant Sci VL - 3 UR - https://doi.org/10.1016/S1360-1385(98)01232-1 DO - 10.1016/S1360-1385(98)01232-1 ID - Grandbastien1998 ER - TY - JOUR AU - Duan, K. AU - Ding, X. AU - Zhang, Q. AU - Zhu, H. AU - Pan, A. AU - Huang, J. PY - 2008 DA - 2008// TI - AtCopeg1, the unique gene originated from AtCopia95 retrotransposon family, is sensitive to external hormones and abiotic stresses JO - Plant Cell Rep VL - 27 UR - https://doi.org/10.1007/s00299-008-0520-2 DO - 10.1007/s00299-008-0520-2 ID - Duan2008 ER - TY - JOUR AU - Manninen, O. AU - Kalendar, R. AU - Robinson, J. AU - Schulman, A. PY - 2000 DA - 2000// TI - Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley JO - Mol Gen Genet VL - 264 UR - https://doi.org/10.1007/s004380000326 DO - 10.1007/s004380000326 ID - Manninen2000 ER - TY - JOUR AU - Ito, H. AU - Gaubert, H. AU - Bucher, E. AU - Mirouze, M. AU - Vaillant, I. AU - Paszkowski, J. PY - 2011 DA - 2011// TI - An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress JO - Nature VL - 472 UR - https://doi.org/10.1038/nature09861 DO - 10.1038/nature09861 ID - Ito2011 ER - TY - JOUR AU - Ito, H. AU - Yoshida, T. AU - Tsukahara, S. AU - Kawabe, A. PY - 2013 DA - 2013// TI - Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae JO - Gene VL - 518 UR - https://doi.org/10.1016/j.gene.2013.01.034 DO - 10.1016/j.gene.2013.01.034 ID - Ito2013 ER - TY - JOUR AU - Jiang, N. AU - Bao, Z. AU - Zhang, X. AU - Hirochika, H. AU - Eddy, S. R. AU - McCouch, S. R. PY - 2003 DA - 2003// TI - An active DNA transposon family in rice JO - Nature VL - 421 UR - https://doi.org/10.1038/nature01214 DO - 10.1038/nature01214 ID - Jiang2003 ER - TY - JOUR AU - Butelli, E. AU - Licciardello, C. AU - Zhang, Y. AU - Liu, J. AU - Mackay, S. AU - Bailey, P. PY - 2012 DA - 2012// TI - Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges JO - Plant Cell VL - 24 UR - https://doi.org/10.1105/tpc.111.095232 DO - 10.1105/tpc.111.095232 ID - Butelli2012 ER - TY - JOUR AU - Rocheta, M. AU - Carvalho, L. AU - Viegas, W. AU - Morais-Cecílio, L. PY - 2012 DA - 2012// TI - Corky, a gypsy-like retrotransposon is differentially transcribed in Quercus Suber tissues JO - BMC Res Notes VL - 5 UR - https://doi.org/10.1186/1756-0500-5-432 DO - 10.1186/1756-0500-5-432 ID - Rocheta2012 ER - TY - JOUR AU - Felice, B. AU - Wilson, R. R. AU - Argenziano, C. AU - Kafantaris, I. AU - Conicella, C. PY - 2008 DA - 2008// TI - A transcriptionally active copia-like retroelement in Citrus limon JO - Cell Mol Biol Lett VL - 14 ID - Felice2008 ER - TY - JOUR AU - Kimura, Y. AU - Tosa, Y. AU - Shimada, S. AU - Sogo, R. AU - Kusaba, M. AU - Sunaga, T. PY - 2001 DA - 2001// TI - OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses JO - Plant Cell Physiol VL - 42 UR - https://doi.org/10.1093/pcp/pce171 DO - 10.1093/pcp/pce171 ID - Kimura2001 ER - TY - JOUR AU - Mhiri, C. AU - Morel, J. -. B. AU - Vernhettes, S. AU - Casacuberta, J. M. AU - Lucas, H. AU - Grandbastien, M. -. A. PY - 1997 DA - 1997// TI - The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress JO - Plant Mol Biol VL - 33 UR - https://doi.org/10.1023/A:1005727132202 DO - 10.1023/A:1005727132202 ID - Mhiri1997 ER - TY - JOUR AU - Jiang, S. AU - Cai, D. AU - Sun, Y. AU - Teng, Y. PY - 2016 DA - 2016// TI - Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome JO - Mob DNA VL - 7 UR - https://doi.org/10.1186/s13100-016-0058-8 DO - 10.1186/s13100-016-0058-8 ID - Jiang2016 ER - TY - STD TI - Rosaceae KC. In:Kubitzki K. (eds) Flowering Plants · Dicotyledons. The Families and Genera of Vascular Plants. Berlin, Heidelberg: Springer; 2004. p. 343–86. ID - ref34 ER - TY - JOUR AU - Zhang, Q. AU - Chen, W. AU - Sun, L. AU - Zhao, F. AU - Huang, B. AU - Yang, W. PY - 2012 DA - 2012// TI - The genome of Prunus mume JO - Nat Commun VL - 3 UR - https://doi.org/10.1038/ncomms2290 DO - 10.1038/ncomms2290 ID - Zhang2012 ER - TY - JOUR AU - Shulaev, V. AU - Sargent, D. J. AU - Crowhurst, R. N. AU - Mockler, T. C. AU - Folkerts, O. AU - Delcher, A. L. PY - 2011 DA - 2011// TI - The genome of woodland strawberry (Fragaria vesca) JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.740 DO - 10.1038/ng.740 ID - Shulaev2011 ER - TY - STD TI - Potter D, Eriksson T, Evans RC, Oh S, Smedmark J, Morgan DR, et al. Phylogeny and classification of Rosaceae. Plant Syst Evol. 2007;266(1-2):5–43. ID - ref37 ER - TY - STD TI - Yin H, Du J, Wu J, Wei S, Xu Y, Tao S, et al. Genome-wide annotation and comparative analysis of long terminal repeat Retrotransposons between pear species of P. bretschneideri and P. Communis. Sci Rep. 2015;5 ID - ref38 ER - TY - JOUR AU - McCarthy, E. M. AU - JF, M. D. PY - 2003 DA - 2003// TI - LTR_STRUC: a novel search and identification program for LTR retrotransposons JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btf878 DO - 10.1093/bioinformatics/btf878 ID - McCarthy2003 ER - TY - JOUR AU - Wicker, T. AU - Sabot, F. AU - Hua-Van, A. AU - Bennetzen, J. L. AU - Capy, P. AU - Chalhoub, B. PY - 2007 DA - 2007// TI - A unified classification system for eukaryotic transposable elements JO - Nat Rev Genet VL - 8 UR - https://doi.org/10.1038/nrg2165 DO - 10.1038/nrg2165 ID - Wicker2007 ER - TY - JOUR AU - SanMiguel, P. AU - Gaut, B. S. AU - Tikhonov, A. AU - Nakajima, Y. AU - Bennetzen, J. L. PY - 1998 DA - 1998// TI - The paleontology of intergene retrotransposons of maize JO - Nat Genet VL - 20 UR - https://doi.org/10.1038/1695 DO - 10.1038/1695 ID - SanMiguel1998 ER - TY - JOUR AU - Du, J. AU - Tian, Z. AU - Hans, C. S. AU - Laten, H. M. AU - Cannon, S. B. AU - Jackson, S. A. PY - 2010 DA - 2010// TI - Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison JO - Plant J VL - 63 UR - https://doi.org/10.1111/j.1365-313X.2010.04263.x DO - 10.1111/j.1365-313X.2010.04263.x ID - Du2010 ER - TY - JOUR AU - Zhao, M. AU - Ma, J. PY - 2013 DA - 2013// TI - Co-evolution of plant LTR-retrotransposons and their host genomes JO - Protein Cell VL - 4 UR - https://doi.org/10.1007/s13238-013-3037-6 DO - 10.1007/s13238-013-3037-6 ID - Zhao2013 ER - TY - JOUR AU - Ma, J. AU - Bennetzen, J. L. PY - 2006 DA - 2006// TI - Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice JO - P Natl Acad Sci USA. VL - 103 UR - https://doi.org/10.1073/pnas.0509810102 DO - 10.1073/pnas.0509810102 ID - Ma2006 ER - TY - JOUR AU - Wessler, S. R. PY - 1996 DA - 1996// TI - Plant retrotransposons: turned on by stress JO - Curr Biol VL - 6 UR - https://doi.org/10.1016/S0960-9822(02)00638-3 DO - 10.1016/S0960-9822(02)00638-3 ID - Wessler1996 ER - TY - JOUR AU - Hobaika, Z. AU - Zargarian, L. AU - Boulard, Y. AU - Maroun, R. G. AU - Mauffret, O. AU - Fermandjian, S. PY - 2009 DA - 2009// TI - Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase α4 helix JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp824 DO - 10.1093/nar/gkp824 ID - Hobaika2009 ER - TY - JOUR AU - Zhou, H. AU - Rainey, G. J. AU - Wong, S. -. K. AU - Coffin, J. M. PY - 2001 DA - 2001// TI - Substrate sequence selection by retroviral integrase JO - J Virol VL - 75 UR - https://doi.org/10.1128/JVI.75.3.1359-1370.2001 DO - 10.1128/JVI.75.3.1359-1370.2001 ID - Zhou2001 ER - TY - JOUR AU - Schaack, S. AU - Gilbert, C. AU - Feschotte, C. PY - 2010 DA - 2010// TI - Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution JO - Trends Ecol Evol VL - 25 UR - https://doi.org/10.1016/j.tree.2010.06.001 DO - 10.1016/j.tree.2010.06.001 ID - Schaack2010 ER - TY - STD TI - El Baidouri M, Panaud O. Horizontal transfers and the new model of TE-driven genome evolution in eukaryotes. In:Pontarotti P. (eds) Evolutionary biology: biodiversification from genotype to phenotype: Springer Cham. 2015. p. 77–92. ID - ref49 ER - TY - JOUR AU - Walsh, A. M. AU - Kortschak, R. D. AU - Gardner, M. G. AU - Bertozzi, T. AU - Adelson, D. L. PY - 2013 DA - 2013// TI - Widespread horizontal transfer of retrotransposons JO - P Natl Acad Sci USA. VL - 110 UR - https://doi.org/10.1073/pnas.1205856110 DO - 10.1073/pnas.1205856110 ID - Walsh2013 ER - TY - JOUR AU - Wallau, G. L. AU - Ortiz, M. F. AU - Loreto, E. L. S. PY - 2012 DA - 2012// TI - Horizontal transposon transfer in eukarya: detection, bias, and perspectives JO - Genome Biol Evol VL - 4 UR - https://doi.org/10.1093/gbe/evs055 DO - 10.1093/gbe/evs055 ID - Wallau2012 ER - TY - JOUR AU - Fawcett, J. A. AU - Innan, H. PY - 2016 DA - 2016// TI - High similarity between distantly related species of a plant SINE family is consistent with a scenario of vertical transmission without horizontal transfers JO - Mol Biol Evol VL - 33 UR - https://doi.org/10.1093/molbev/msw130 DO - 10.1093/molbev/msw130 ID - Fawcett2016 ER - TY - STD TI - Gilbert C, Chateigner A, Ernenwein L, Barbe V, Bézier A, Herniou EA, et al. Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons. Nat Commun. 2014;5 ID - ref53 ER - TY - JOUR AU - Gilbert, C. AU - Schaack, S. AU - Pace, I. I. J. K. AU - Brindley, P. J. AU - Feschotte, C. PY - 2010 DA - 2010// TI - A role for host-parasite interactions in the horizontal transfer of transposons across phyla JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08939 DO - 10.1038/nature08939 ID - Gilbert2010 ER - TY - JOUR AU - Won, H. AU - Renner, S. S. PY - 2003 DA - 2003// TI - Horizontal gene transfer from flowering plants to Gnetum JO - P Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.1833775100 DO - 10.1073/pnas.1833775100 ID - Won2003 ER - TY - JOUR AU - Dupuy, C. AU - Periquet, G. AU - Serbielle, C. AU - Bézier, A. AU - Louis, F. AU - Drezen, J. -. M. PY - 2011 DA - 2011// TI - Transfer of a chromosomal maverick to endogenous bracovirus in a parasitoid wasp JO - Genetica VL - 139 UR - https://doi.org/10.1007/s10709-011-9569-x DO - 10.1007/s10709-011-9569-x ID - Dupuy2011 ER - TY - JOUR AU - Neumann, P. AU - Požárková, D. AU - Macas, J. PY - 2003 DA - 2003// TI - Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced JO - Plant Mol Biol VL - 53 UR - https://doi.org/10.1023/B:PLAN.0000006945.77043.ce DO - 10.1023/B:PLAN.0000006945.77043.ce ID - Neumann2003 ER - TY - JOUR AU - Gómez, E. AU - Schulman, A. H. AU - Martínez-Izquierdo, J. A. AU - Vicient, C. M. PY - 2006 DA - 2006// TI - Integrase diversity and transcription of the maize retrotransposon Grande JO - Genome VL - 49 UR - https://doi.org/10.1139/g05-129 DO - 10.1139/g05-129 ID - Gómez2006 ER - TY - JOUR AU - Marcon, H. S. AU - Domingues, D. S. AU - Silva, J. C. AU - Borges, R. J. AU - Matioli, F. F. AU - de Mattos Fontes, M. R. PY - 2015 DA - 2015// TI - Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic JO - BMC Plant Biol VL - 15 UR - https://doi.org/10.1186/s12870-015-0550-1 DO - 10.1186/s12870-015-0550-1 ID - Marcon2015 ER - TY - STD TI - Huang J, Wang Y, Liu W, Shen X, Fan Q, Jian S, et al. EARE-1, a transcriptionally active Ty1/copia-like retrotransposon has colonized the genome of Excoecaria agallocha through horizontal transfer. Front Plant Sci. 2017;8 ID - ref60 ER - TY - JOUR AU - Pietzenuk, B. AU - Markus, C. AU - Gaubert, H. AU - Bagwan, N. AU - Merotto, A. AU - Bucher, E. PY - 2016 DA - 2016// TI - Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-1072-3 DO - 10.1186/s13059-016-1072-3 ID - Pietzenuk2016 ER - TY - BOOK AU - McClintock, B. PY - 1993 DA - 1993// TI - The significance of responses of the genome to challenge PB - World Scientific Pub. Co CY - Singapore ID - McClintock1993 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Jukes, T. H. AU - Cantor, C. R. PY - 1969 DA - 1969// TI - Evolution of protein molecules JO - Mamm Protein Metab VL - 3 ID - Jukes1969 ER - TY - JOUR AU - Katoh, K. AU - Standley, D. M. PY - 2013 DA - 2013// TI - MAFFT multiple sequence alignment software version 7: improvements in performance and usability JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst010 DO - 10.1093/molbev/mst010 ID - Katoh2013 ER - TY - JOUR AU - Tamura, K. AU - Peterson, D. AU - Peterson, N. AU - Stecher, G. AU - Nei, M. AU - Kumar, S. PY - 2011 DA - 2011// TI - MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr121 DO - 10.1093/molbev/msr121 ID - Tamura2011 ER - TY - JOUR AU - Li, L. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2003 DA - 2003// TI - OrthoMCL: identification of ortholog groups for eukaryotic genomes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1224503 DO - 10.1101/gr.1224503 ID - Li2003 ER - TY - JOUR AU - Yang, Z. PY - 1997 DA - 1997// TI - PAML: a program package for phylogenetic analysis by maximum likelihood JO - Bioinformatics VL - 13 UR - https://doi.org/10.1093/bioinformatics/13.5.555 DO - 10.1093/bioinformatics/13.5.555 ID - Yang1997 ER - TY - JOUR AU - Kim, D. AU - Langmead, B. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - HISAT: a fast spliced aligner with low memory requirements JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3317 DO - 10.1038/nmeth.3317 ID - Kim2015 ER - TY - JOUR AU - Livak, K. J. AU - Schmittgen, T. D. PY - 2001 DA - 2001// TI - Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method JO - Methods VL - 25 UR - https://doi.org/10.1006/meth.2001.1262 DO - 10.1006/meth.2001.1262 ID - Livak2001 ER -