[1] 殷豪. 梨基因组 LTR 反转座子注释及进化分析研究[D]. 南京: 南京农业大学, 2014.

YIN Hao. Genome-wide Annotation and Evolutionary Analysis of Long Terminal Repeat Retrotransposons in Pear (Pyrus bretschneideri Rehd.)[D]. Nanjing: Nanjing Agricultural University, 2014.
[2] NIE Qiong, QIAO Guang, PENG Lei, et al. Transcriptional activation of long terminal repeat retrotransposon sequences in the genome of pitaya under abiotic stress [J]. Plant Physiol Biochem, 2019, 135: 460 − 468.
[3] 蒋爽. 基于反转录转座子标记的梨属植物亲缘关系研究[D]. 杭州: 浙江大学, 2015.

JIANG Shuang. Studies on Genetic Relationships of Pyrus Species and Cultivars based on Retrotransposons Markers[D]. Hangzhou: Zhejiang University, 2015.
[4] 汪浩. 植物基因组 LTR 反转录转座子注释和比较研究[D]. 上海: 复旦大学, 2008.

WANG Hao. Annotation and Comparative Study of LTR Retrotransposons in Plant Genomes[D]. Shanghai: Fudan University, 2008.
[5] KOBAYASHI S, GOTO-YAMAMOTO N, HIROCHIKA H. Retrotransposon-induced mutations in grape skin color[J]. Science, 2004, 304(5673): 982. doi: 10.1126/science.1095011.
[6] ZHOU Mingbing, LIANG Linlin, HANNINEN H. A transposition-active Phyllostachys edulis long terminal repeat (LTR) retrotransposon [J]. J Plant Res, 2018, 131(2): 203 − 210.
[7] JIANG Shuag, TENG Yuanwen, ZONG Yu, et al. Review of LTR retrotransposons in plants [J]. Acta Bot Boreali-Occident Sin, 2013, 33(11): 2354 − 2360.
[8] 张赞一. 毛竹 LTR 反转录转座子-PHRE6 的克隆与转座活性鉴定以及转座监测系统的构建[D]. 杭州: 浙江农林大学, 2018.

ZHANG Zanyi. Phyllostachys edulis LTR Transposon-cloning and Transposition Activity Identification of PHRE6 and Construction of Transposition Monitoring System[D]. Hangzhou: Zhejiang A&F University, 2018.
[9] 吴骏澜. 长末端重复序列反转录转座子分析流程构建及应用[D]. 合肥: 安徽农业大学, 2017.

WU Julan. Construction and Application of Identification and Analysis Process of Full-length LTR-retrotransposons[D]. Hefei: Anhui Agricultural University, 2017.
[10] ROY N S, CHOI J Y, LEE S I, et al. Marker utility of transposable elements for plant genetics, breeding, and ecology: a review [J]. Genes Genomics, 2015, 37(2): 141 − 151.
[11] 周鹏. 梨 Ty1-copia 反转录转座子的分子特性研究[D]. 杨凌: 西北农林科技大学, 2013.

ZHOU PENG. Molecular Character of Novel Ty1-copia Retrotransposons in Pear[D]. Yangling: Northwest A&F University, 2013.
[12] 马赑. 桑树全基因组转座子的鉴定及特征分析[D]. 重庆: 西南大学, 2014.

MA Bi. Genome-wide Identification and Characterization of Transposable Elements in Mulberry (Morus notabilis)[D]. Chongqing: Southwest University, 2014.
[13] 侯菲. 蔷薇目 7 个物种间 LTR 反转录转座子水平转移的鉴定以及转座活性分析[D]. 重庆: 西南大学, 2018.

HOU Fei. Horizontal Transfers and Activity Analysis of LTR Retrotransposons in Seven Rosales Species[D]. Chongqing: Southwest University, 2018.
[14] FINATTO T, de OLIVEIRA A C, CHAPARRO C, et al. Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice [J]. Rice, 2015, 8: 13. doi: 10.1186/s12284-015-0045-6.
[15] GALINDO-GONZALEZ L, MHIRI C, DEYHOLOS M K, et al. LTR-retrotransposons in plants: engines of evolution [J]. Gene, 2017, 626: 14 − 25.
[16] WICKER T, SABOT F, HUA-VAN A, et al. A unified classification system for eukaryotic transposable elements [J]. Nat Rev Genet, 2007, 8(12): 973 − 982.
[17] SHINGOTE P R, MITHRA S V A, SHARMA P, et al. LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane [J]. Mol Breed, 2019, 39(2): 25.
[18] SAZE H, KAKUTANI T. Differentiation of epigenetic modifications between transposons and genes [J]. Curr Opin Plant Biol, 2011, 14(1): 81 − 87.
[19] DU Jianchang, TIAN Zhixi, BOWEN N J, et al. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean [J]. Plant Cell, 2010, 22(1): 48 − 61.
[20] LLORENS C, MUNOZ-POMER A, BERNAD L, et al. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees [J]. Biol Dir, 2009, 4(12): 41 − 72.
[21] 虞洪杰. 植物 LTR 反转录转座子的预测和注释及邻聚法构建系统进化树研究[D]. 杭州: 浙江大学, 2011.

YU Hongjie. Prediction and Annotation of LTR Retrotranspons in Plant and a New Method to Construct Phylogeneic Trees[D]. Hangzhou: Zhejiang University, 2011.
[22] XU Ling, ZHANG Yue, SU Yuan, et al. Structure and evolution of full-length LTR retrotransposons in rice genome [J]. Plant Syst Evol, 2010, 287(1/2): 19 − 28.
[23] WANG Qinghua, DOONER H K. Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses [J]. Plant J, 2012, 72(2): 212 − 221.
[24] LAVERGNE S, MUENKE N J, MOLOFSKY J. Genome size reduction can trigger rapid phenotypic evolution in invasive plants [J]. Ann Bot, 2010, 105(1): 109 − 116.
[25] ELLINGHAUS D, KURTZ S, WILLHOEFT U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons[J]. BMC Bioinf, 2008, 9(1). doi: 10.1186/1471-2105-9-18.
[26] WANG Hao, LIU Jinsong. LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice [J]. BMC Genomics, 2008, 9(1). doi: 10.1186/1471-2164-9-382.
[27] LERAT E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs [J]. Heredity, 2010, 104(6): 520 − 533.
[28] SU Shuai, CUI Ning, SUN Aijun, et al. Sequence analysis of the whole genome of a recombinant Marek’s disease virus strain, GX0101, with a reticuloendotheliosis virus LTR insert [J]. Arch Virol, 2013, 158(9): 2007 − 2014.
[29] LIAN Shuaibin, CHEN Xinwu, WANG Peng, et al. A complete and accurate Ab initio repeat finding algorithm [J]. Interdisciplinary Sci Comput Life Sci, 2016, 8(1): 75 − 83.
[30] OU Shujun, JIANG Ning. LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons[J]. Mobile DNA, 2019, 10(6403). doi: 10.11011722736.
[31] BEDELL J A, KORF I, GISH W, et al. MaskerAid: a performance enhancement to RepeatMaskerf [J]. Broinformatics, 2000, 16(11): 1040 − 1041.
[32] 周敏. 竹子 LINEs, Ty3-gypsy 类转座子的克隆、鉴定及特性分析[D]. 杭州: 浙江农林大学, 2014.

ZHOU Min. Cloning, Identification and Analysis Characteristics of LINEs and Ty3-gypsy Retrotransposons from Bamboo[D]. Hangzhou: Zhejiang A&F University, 2014.
[33] PENG Zhenhua, LU Yuying, LI Lubin, et al. The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla) [J]. Nat Genet, 2013, 45(4): 456 − 461.
[34] ZHAO Hansheng, GAO Zhimin, WANG Le, et al. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)[J]. GigaScience, 2018, 7(10): giy115. doi: 10.1093/gigascience/giy115.
[35] MONAT C, TANDO N, TRANCHANT-DUBREUIL C, et al. LTRclassifier: a website for fast structural LTR retrotransposons classification in plants[J]. Mobile Genet Elem, 2016, 6(6). doi: 10.1080/2159256X.2016.1241050.
[36] BERNARD H R, WUTICH A, RYAN G W. Analyzing Qualitative Data: Systematic Approaches[M]. New York: SAGE Publications, 2016.
[37] MA Jianxin, BENNETZEN J L. Rapid recent growth and divergence of rice nuclear genomes [J]. Proc Nat Acad Sci, 2004, 101(34): 12404 − 12410.
[38] EDGAR R C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity [J]. BMC Bioinf, 2004, 5(1): 113. doi: 10.1186/1471-2105-5-113.
[39] KIMURA M, OHTA T. On the stochastic model for estimation of mutational distance between homologous proteins [J]. J Mol Evol, 1972, 2(1): 87 − 90.
[40] PATERSON A H, BOWERS J E, BRUGGMANN R, et al. The Sorghum bicolor genome and the diversification of grasses [J]. Nature, 2009, 457(7229): 551 − 556.
[41] WANG Hao, XU Zhao, YU Hongjie. LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice [J]. BMC Genomics, 2008, 9(1): 1 − 13.
[42] HAVECKER E R, GAO Xiang, VOYTAS D F. The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain 8 [J]. Plant Physiol, 2005, 139(2): 857 − 868.
[43] CHADHA S, SHARMA M. Genetic differentiation and phylogenetic potential of Ty3/Gypsy LTR retrotransposon markers in soil and plant pathogenic fungi [J]. J Basic Microbiol, 2020, 60(6): 508 − 516.
[44] BENNETZEN J L. Transposable element contributions to plant gene and genome evolution [J]. Plant Mol Biol, 2000, 42(1): 251 − 269.
[45] PICAULT N, CHAPARRO C, PIEGU B, et al. Identification of an active LTR retrotransposon in rice [J]. Plant J, 2009, 58(5): 754 − 765.
[46] HU Bingjie, ZHOU Mingbing, ZHU Yihang. Genome-wide characterization and evolution analysis of long terminal repeat retroelements in moso bamboo (Phyllostachys edulis)[J]. Tree Genet Genomes, 2017, 13(2): 43. doi: 10.1007/s11295-017-1114-3.
[47] PENG Yu, ZHANG Yingying, GUI Yijie, et al. Elimination of a retrotransposon for quenching genome instability in modern rice [J]. Mol Plant, 2019, 12(10): 1395 − 1407.
[48] WAGNER A. Distribution of transcription factor binding sites in the yeast genome suggests abundance of coordinately regulated genes [J]. Genomics, 1998, 50(2): 293 − 295.
[49] LOCKTON S, GAUT B S. The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana [J]. J Mol Evol, 2009, 68(1): 80 − 89.
[50] FESCHOTTE C, JIANG N, WESSLER S R. Plant transposable elements: where genetics meets genomics [J]. Nat Rev Genet, 2002, 3(5): 329 − 341.
[51] KASHKUSH K, FELDMAN M, LEVY A A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat [J]. Nat Genet, 2003, 33(1): 102 − 106.
[52] HE Ningjia, ZHANG Chi, QI Xiwu, et al. Draft genome sequence of the mulberry tree Morus notabilis [J]. Nat Commun, 2013, 4(1): 1 − 9.