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毛竹长末端重复序列反转录转座子的全基因组特征及进化分析
doi: 10.11833/j.issn.2095-0756.20200458
Genome-wide characteristics and evolution analysis of long terminal repeat retrotransposons in Phyllostachys edulis
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摘要:
目的 研究毛竹Phyllostachys edulis基因组中的长末端重复序列反转录转座子(long terminal repeat retrotransposons, LTR-REs)的特征,为今后利用LTR反转录转座子对毛竹基因组的功能和对竹种资源遗传多样性的研究奠定基础。 方法 通过生物信息学方法,利用LTRharvest和RepeatMakser软件对第2版毛竹基因组中的LTR反转录转座子进行全面注释与分类,并对得到的LTR反转录转座子的分布特征、进化特性和插入时间进行分析。 结果 在毛竹基因组中共注释得到1 014 565个LTR反转录转座子,1 562个家族,占毛竹基因组的54.97%。其中solo LTR反转录转座子与完整LTR反转录转座子(S/F)的比例较高(约1.77∶1.00),表明在毛竹LTR反转录转座子中可能发生了相对较高频率的非法重组和不平衡重组。毛竹LTR反转录转座子分为Ty1-copia和Ty3-gypsy超家族,Tork、Reftrofit、Sire、Oryco、Del、Reina、Crm、Tat、Galadriel、Athila等10个谱系。毛竹LTR反转录转座子的Ty1-copia和Ty3-gypsy超家族对PBS位点的偏好性呈相反趋势,较长的LTR反转录转座子具有更长的LTR序列,结构也更加完整。毛竹LTR反转录转座子的插入时间主要集中在0~2.0 Ma,且还处于不断缓慢增长的状态。 结论 第2版毛竹基因组的高质量组装,能更好地注释和分析毛竹基因组中的LTR反转录转座子。基于结构预测的LTRharvest法,能更精准地预测毛竹LTR反转录转座子。不同谱系的毛竹LTR反转录转座子在进化过程中具有不同的分化和扩增活性。毛竹LTR反转录转座子总体上处于不断扩增状态,这是导致毛竹基因组较大的主要原因之一。图3表3参52 Abstract:Objective This study aims to analyze the characteristics of long terminal repeat retrotransposons (LTR-REs) in moso bamboo genome, so as to promote the research on the function of LTR-REs in moso bamboo genome and the genetic diversity of bamboo resources. Method Based on bioinformatics methods, LTR retrotransposons in the second edition of moso bamboo genome were annotated and classified by LTRharvest and RepeatMakser software, and the distribution characteristics, evolution characteristics and insertion time of the obtained LTR retrotransposons were analyzed. Result A total of 1 014 565 LTR retrotransposons and 1 562 families were identified, accounting for 54.97% of moso bamboo genome. Among them, the ratio of solo LTR retrotransposons to intact LTR retrotransposons (S/F) was relatively high (about 1.77∶1.00), indicating that a higher frequency of illegitimate recombination and unbalanced recombination might have occurred in the LTR-REs of moso bamboo genome. LTR retrotransposons were divided into Ty1-copia and Ty3-gypsy superfamilies, and ten lineages included Tork, Reftrofit, Sire, Oryco, Del, Reina, Crm, Tat, Galadriel, and Athila. The preference of Ty1-copia and Ty3-gypsy superfamiles for PBS sites showed an opposite tendency. The longer LTR retrotransposons had longer LTR sequences and more complete structures. The insertion time of LTR retrotransposon in moso bamboo was mainly concentrated in the 0−2.0 Ma region, and it was still in a state of slow growth. Conclusion The high-quality assembly of the second edition of moso bamboo genome can better annotate and analyze the LTR retrotransposons in moso bamboo genome. The LTR harvest method based on structure prediction can more accurately predict the LTR retrotransposons of moso bamboo. The LTR retrotransposons of different lineages have different differentiation and amplification activities during evolution. LTR retrotransposons are generally in a state of continuous amplification, which is one of the reasons for the large genome of moso bamboo. [Ch, 3 fig. 3 tab. 52 ref.] -
Key words:
- LTR retrotransposons /
- Phyllostachys edulis /
- genome /
- evolution
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表 1 毛竹LTR反转录转座子超家族分类
Table 1. Classification of LTR retrotransposons superfamily of moso bamboo genome
超家族 谱系 家族a 结构 数量/个 全长/bp 百分比b/% Ty1-copia Tork 236 GAG-PR-INT-RT-RH 145 708 124 219 995 6.51 Retrofit 342 GAG-PR-INT-RT-RH 41 965 43 615 815 2.29 Sire 136 GAG-PR-INT-RT-RH-ENV 223 386 210 097 734 11.01 Oryco 105 GAG-PR-INT-RT-RH 22 078 22 854 591 1.20 合计 819 433 137 400 788 135 21.01 Ty3-gypsy Del 207 GAG-PR-RT-RH-INT-CHR 295 222 334 005 916 17.51 Reina 249 GAG-PR-RT-RH-INT-CHR 27 803 39 235 939 2.06 Crm 47 GAG-PR-RT-RH-INT 40 781 44 298 955 2.32 Tat 238 GAG-PR-RT-RH-INT 217 288 230 055 053 12.06 Galadriel 1 GAG-PR-RT-RH-INT-CHR 23 51 248 0.00 Athila 1 GAG-PR-RT-RH-INT-ENV 311 257 970 0.01 合计 743 581 428 647 905 081 33.96 总计 1 562 1 014 565 1 048 693 216 54.97 说明:a表示每个谱系的数量;b表示在毛竹基因组中LTR反转录转座子所占的比例 表 2 毛竹LTR反转录转座子谱系特征
Table 2. Structure of LTR retrotransposon family of moso bamboo
谱系 家族a 百分比c/% 全长LTRd Solo LTRe 全长LTR/Solo LTR 全长 LTR+Solo LTR 百分比f/% Tork 236 28.82 1 169 1 492 1.28 2 661 28.76 Retrofit 342 41.76 302 1 158 3.83 1 460 15.78 Sire 136 16.61 464 3 139 6.77 3 603 38.95 Oryco 105 12.82 521 1 006 1.93 1 527 16.51 Ty1-copia 819 100.00 2 456 6 795 2.77 9 251 100.00 Del 207 27.86 2 102 2 992 1.42 5 094 41.97 Reina 249 33.51 495 1 245 2.52 1 740 14.34 Crm 47 6.33 510 1 352 2.65 1 862 15.34 Tat 238 32.03 2 168 1 251 0.58 3 419 28.17 Galadriel 1 0.13 0 7 0 7 0.06 Athila 1 0.13 0 14 0 14 0.12 Ty3-gypsy 743 100.00 5 275 6 861 1.30 12 136 100.00 总计 1 562 100.00 7 731 13 656 1.77 21 387 100.00 说明:a表示每个谱系的数量;c表示每个谱系在超家族中所占的比例;d表示结构完整的LTR反转录转座子(full-length LTR),包含 两端LTR序列和完整的编码结构域[44];e表示仅含有两端LTR序列,编码结构域有缺失的LTR反转录转座子(solo LTR)[44];f表 示每个谱系中full-length LTR和solo LTR在超家族中所占的比例 表 3 LTR反转录转座子PBS使用统计
Table 3. Usage status of PBS in LTR retrotransposons
tRNA 数量/个 百分比/% Ty1-copia
使用比例/%Ty3-gypsy
使用比例/%MetCAT24 1 383 4.05 1.70 0.83 LysTTT 486 1.42 0.00 1.10 LysTTT10 285 0.83 0.31 0.03 LeuAAG21 131 0.38 0.00 0.15 LysTTT3 111 0.32 0.16 0.01 LeuTAG9 66 0.19 0.07 0.01 -
[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. doi: 10.1016/j.plaphy.2018.11.014 [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. doi: 10.1007/s10265-017-0983-8 [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. doi: 10.1007/s13258-014-0252-3 [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, OLIVEIRA A C D, CHAPARRO C, et al. Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice [J]. Rice, 2015, 8(1): 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. doi: 10.1016/j.gene.2017.04.051 [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. doi: 10.1038/nrg2165 [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. doi: 10.1007/s11032-019-0931-5 [18] SAZE H, KAKUTANI T. Differentiation of epigenetic modifications between transposons and genes [J]. Curr Opin Plant Biol, 2011, 14(1): 81 − 87. doi: 10.1016/j.pbi.2010.08.017 [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. doi: 10.1105/tpc.109.068775 [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. doi: 10.1007/s00606-010-0285-2 [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. doi: 10.1111/j.1365-313X.2012.05059.x [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. doi: 10.1093/aob/mcp271 [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]. Hered, 2010, 104(6): 520 − 533. doi: 10.1038/hdy.2009.165 [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. doi: 10.1007/s00705-013-1671-1 [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. doi: 10.1007/s12539-015-0119-6 [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: 10.10.11011722736. [31] BEDELL J A, KORF I, GISH W, et al. MaskerAid: a performance enhancement to RepeatMaskerf [J]. Broinformatics, 2000, 16(11): 1040 − 1041. doi: 10.1093/bioinformatics/16.11.1040 [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. doi: 10.1038/ng.2569 [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 Elements, 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. doi: 10.1073/pnas.0403715101 [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. doi: 10.1007/BF01653945 [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. doi: 10.1186/1471-2164-9-1 [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. doi: 10.1104/pp.105.065680 [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. doi: 10.1002/jobm.201900487 [44] BENNETZEN J L. Transposable element contributions to plant gene and genome evolution [J]. Plant Mol Biol, 2000, 42(1): 251 − 269. doi: 10.1023/A:1006344508454 [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. doi: 10.1111/j.1365-313X.2009.03813.x [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. doi: 10.1016/j.molp.2019.06.004 [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. doi: 10.1006/geno.1998.5303 [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. doi: 10.1007/s00239-008-9190-5 [50] FESCHOTTE C, JIANG N, WESSLER S R. Plant transposable elements: where genetics meets genomics [J]. Nat Rev Genet, 2002, 3(5): 329 − 341. doi: 10.1038/nrg793 [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. doi: 10.1038/ng1063 [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. -
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