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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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图 1 LTR反转录转座子全长与LTR序列长度的相关性
Figure 1 Correlation of length between LTR and LTR retrotransposons
图 2 毛竹LTR反转录转座子各个谱系的插入时间
Figure 2 Insertion time distribution of different lineages of moso bamboo LTR retrotransposons
图 3 毛竹LTR反转录转座超家族的插入时间
Figure 3 Insertion times of superfumily of moso bamboo LTR retrotransposons
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 
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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
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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
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