[1] Slotkin RK, Nuthikattu S, Jiang N. The impact of trans-posable elements on gene and genome evolution // Plant genome diversity. Wien: Springer, 2012.[2] 陈建军, 王瑛. 植物基因组大小进化的研究进展. 遗传, 2009, 31(5): 464-470.[3] Shepherd NS, Schwarz-Sommer Z, VelSpalve JB, Gupta M, Wienand U, Saedler H. Similarity of the Cin1 repetitive family of Zea mays to eukaryotic trans-posable elements. Nature, 1984, 307(5947): 185-187.[4] 郭玉双, 陈静, 张建华, 李祥羽, 胡重怡, 任学良. 植物LTR类反转录转座子在植物基因组学研究中的应用. 黑龙江农业科学, 2011, (11): 139-142.[5] 陈志伟, 吴为人. 植物中的反转录转座子及其应用. 遗传, 2004, 26(1): 122-126.[6] Sabot F, Schulman AH. Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome. Heredity, 2006, 97(6): 381-388.[7] 王石平, 张启发. 高等植物基因组中的反转录转座子. 植物学报, 1998, 40(4): 291-297.[8] 程旭东, 凌宏清. 植物基因组中的非LTR反转录转座子SINEs和LINEs. 遗传, 2006, 28(6): 731-736.[9] Kumar A, Jeffrey B. Plant retrotransposons. Annu Rev Genet, 1999, 33(1): 479-532.[10] 石凤敏, 云锦凤, 赵彦, 张瑞霞. 蒙古冰草基因组类反转录转座子基因同源序列的克隆与序列分析. 华北农学报, 2010, 25(6): 52-56.[11] Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, Mcginnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Res, 2008, 36(2): W5-W9.[12] Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science, 1985, 227(4693): 1435-1441.[13] 唐益苗, 马有志, 李连城, 辛志勇. 小麦反转录转座子家族鉴定及其转录活性分析. 科学通报, 2005, 50(6): 546-551.[14] Matsuoka Y, Tsunewaki K. Wheat retrotransposon fami-lies identified by reverse transcriptase domain analysis. Mol Biol Evol, 1996, 13(10): 1384-1392.[15] Rocheta M, Cordeiro J, Oliveira M, Miguel C. PpRT1: the first complete gypsy-like retrotransposon isolated in Pinus pinaster. Planta, 2007, 225(3): 551-562.[16] 何予卿, 孙梅, 朱英国, 张利达. Copia类型反转录转座子在籽粒苋中的表现. 遗传学报, 2002, (5): 461-466.[17] Kim H, Terakami S, Nishitani C, Kurita K, Kanamori H, Katayose Y, Yutaka S, Saito T, Yamamoto T. Develop-ment of cultivar-specific DNA markers based on retro-transposon-based insertional polymorphism in Japanese pear. Breed Sci, 2012, 62(1): 53-62.[18] Zhao GL, Dai HY, Chang LL, Ma Y, Sun HY, He P, Zhang ZH. Isolation of two novel complete Ty1-copiaretrotransposons from apple and dem-onstration of use of derived S-SAP markers for distin-guishing bud sports of Malusdomestica cv. Fuji. Tree Genet Genomes, 2010, 6(1): 149-159.[19] Pelsy F, Merdinoglu D. Complete sequence of Tvv1, a family of Ty 1 copia-like retro-transposons of Vitisvinifera L., reconstituted by chromosome walking. Theor Appl Genet, 2002, 105(4): 614-621.[20] 杜晓云, 张青林, 罗正荣. 罗田甜柿Ty1-copia类逆转座子RNaseH-LTR序列的分离和特性分析. 园艺学报, 2008, 35(4): 501-508.[21] Kalendar R, Antonius K, Smykal P, Schulman AH. iPBS: a universal method for DNA fingerprinting and retro-transposon isolation. Theor Appl Genet, 2010, 121(8): 1419-1430.[22] Woodrow P, Pontecorvo G, Fantaccione S, Fuggi A, Kafantaris I, Parisi D, Carillo P. Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses. Theor Appl Genet, 2010, 121(2): 311-322.[23] Schulman AH, Flavell AJ, Ellis THN. The application of LTR retrotransposons as molecular markers in plants. Methods Mol Biol, 2004, 260: 145-173.[24] 单晓辉, 李毅丹, 李彦舫, 原亚萍. 利用AFLP和SSAP研究短芒大麦突变系种群遗传多样性. 生态学杂志, 2012, 31(4): 830-836.[25] Maka?owski W, Pande A, Gotea V, Maka?owska I. Trans-posable elements and their identification // Methods in Molecular Biology. NJ: Humana Press, 2012.[26] Bergman CM, Quesneville H. Discovering and detecting transposable elements in genome sequences. Brief Bioinform, 2007, 8(6): 382-392.[27] Mccarthy EM, Mcdonald JF. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics, 2003, 19(3): 362-367.[28] Domingues DS, Cruz GMQ, Metcalfe CJ, Nogueira FTS, Vicentini R, de Alves CS, van Sluys M. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics, 2012, 13(1): 137.[29] Kalyanaraman A, Aluru S. Efficient algorithms and soft-ware for detection of full-length LTR retrotransposons. J Bioinform Comput Biol, 2006, 4(2): 56-64.[30] Rho M, Schaack S, Gao X, Kim S, Lynch M, Tang HX. LTR retroelements in the genome of Daphnia pulex. BMC Genomics, 2010, 11(1): 425.[31] 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.[32] Morgante M, Policriti A, Vitacolonna N, Zuccolo A. Structured motifs search. J Comput Biol, 2005, 12(8): 1065-1082.[33] Lerat E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity, 2010, 104(6): 520-533.[34] Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nu-cleic Acids Res, 2007, 35(2): W265-W268.[35] Gao DY, Chen JF, Chen MS, Meyers BC, Jackson S. A highly conserved, small LTR retrotransposon that prefer-entially targets genes in grass genomes. PloS One, 2012, 7(2): e32010.[36] 汪浩. 植物基因组LTR反转录转座子注释和比较研究[学位论文]. 复旦大学, 2008.[37] Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable elements and genome organization: a com-prehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome se-quence. Genome Res, 1998, 8(5): 464-478.[38] Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res, 2001, 29(22): 4633-4642.[39] Edgar RC, Myers. PILER: identification and classification of genomic repeats. Bioinformatics, 2005, 21(1): i152-i158.[40] Bao ZR, Eddy SE. Automated de novo identification of repeat sequence families in sequenced genomes. Ge-nome Res, 2002, 12(8): 1269-1276.[41] Nagarajan N, Navajas-Pérez R, Pop M, Alam M, Ming R, Paterson AH, Salzberg SL. Genome-wide analysis of re-petitive elements in Papaya. Tropical Plant Biol, 2008, 1(3-4): 191-201.[42] Steinbiss S, Willhoeft U, Gremme G, Kurtz S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res, 2009, 37(21): 7002-7013.[43] Wang H, Xu Z, Yu HJ. LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice. BMC Genomics, 2008, 9(1): 565.[44] Mccarthy EM, Liu JD, Gao LZ, Mcdonald JF. Long ter-minal repeat retrotransposons of Oryza sativa. Genome Biol, 2002, 3(10): 1-11.[45] Smit AFA, Hubley R, Green P. RepeatMasker at http:// repeatmasker.Org.[46] Kramerov DA, Vassetzky NS. Short retroposons in eu-karyotic genomes. Int Rev Cytol, 2005, 247: 165-221.[47] Abrusán GR, Grundmann N, Demester L, Makalowski W. TEclass-a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics, 2009, 25(10): 1329-1330.[48] Feschotte C, Keswani U, Ranganathan N, Guibotsy ML, Levine D. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. Genome Biol Evol, 2010, 1: 205-220.[49] Kronmiller BA, Wise RP. TEnest: automated chronological annotation and visualization of nested plant transpos-able elements. Plant Physiol, 2008, 146(1): 45-59.[50] Cossu RM, Buti M, Giordani T, Natali L, Cavallini A. A computational study of the dynamics of LTR retrotrans-posons in the Populustrichocarpa genome. Tree Genet Genomes, 2012, 8(1): 61-75.[51] Lavrentieva I, Broude NE, Lebedev Y, Gottesman II, Lukyanov SA, Smith CL, Sverdlov ED. High polymor-phism level of genomic sequences flanking insertion sites of human endogenous retroviral long terminal repeats. FEBS Lett, 1999, 443(3): 341-347. |