Genome-wide characterization and evolution analysis of long terminal repeat retroelements in moso bamboo (Phyllostachys edulis)
Genome-wide characterization and evolution analysis of long terminal repeat retroelements in moso bamboo (Phyllostachys edulis)
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毛竹（Phyllostachys edulis）长末端重复逆转录因子的全基因组表征和进化分析
DOI：
10.1007/s11295-017-1114-3
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发表时间：
2017-03
影响因子：
2.4
通讯作者：
朱怡航
中科院分区：
文献类型：
--
作者：
周明兵;胡冰杰;朱怡航
近乎完整的毛竹基因组序列的获得，使得在整个基因组水平上详细地发现竹科和其他禾本科植物之间的转座元件(TES)并进行跨物种比较成为可能。长末端重复序列逆转录元件是大多数植物基因组中最大的单一组分，可以以各种方式对基因组产生重大影响。通过结构分析和同源性分析相结合的方法，我们初步研究了包含2,004,644个LTR反转录元件序列的982个LTR反转录元件家族，它们占毛竹基因组的40%以上。进一步的分析表明，毛竹中LTRs与完整元素的比值(S/i)很低(约0.28：1)，这表明毛竹中的LtR逆转录元件可能经历了相对较低的不均匀重组和非法重组。系统发育分析显示，在优子叶植物和单子叶植物物种分化之前，存在4个类型1拷贝和5个类型3吉卜赛进化谱系，但它们的繁殖规模和时间框架在不同家族和谱系之间存在显著差异。插入时间估计表明，LTR逆转录元件被扩增的时间约为0~300万年，并且比水稻和拟南芥具有更长的活动期。这些发现表明，在毛竹进化过程中，LTR反转录元件的扩张可能是宿主基因组大小的原因。
The availability of nearly complete moso bamboo genome sequences permits the detailed discovery and cross-species comparison of transposable elements (TEs) between Bambusoideae and other Poaceae species at the whole genome level. Long terminal repeat retroelements (LTR-retroelements) are the single largest components of most plant genomes and can substantially impact the genome in various ways. Through a combination of structure- and homology-based approaches, we initially investigated 982 LTR-retroelement families comprising 2,004,644 LTR-retroelement sequences, which accounted for more than 40% of the moso bamboo genome. Further analysis revealed that the ratio of solo LTRs to intact elements (S/I) in moso bamboo is significantly low (approximately 0.28:1), indicating that bamboo LTR-retroelements might have undergone relatively low frequencies of unequal recombination and illegitimate recombination. Phylogenetic analysis revealed fourTy1-copiaand fiveTy3-gypsyevolutionary lineages that were present before the divergence of eudicot and monocot species, but the scales and timeframes within which they proliferated significantly varied across families and lineages. Insertion time estimates showed that LTR-retroelements were amplified for approximately 0~3 million years and had longer periods of activity than those of rice andArabidopsis. These findings suggest that the expansion of LTR-retroelements might be responsible for host large genome size during moso bamboo evolution.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
4.4
作者：
Wang H;Liu JS
通讯作者：
Liu JS
DOI：
--
发表时间：
2004
影响因子：
11.1
作者：
Jonathan Blumenthal Ma
通讯作者：
Jonathan Blumenthal Ma
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
1.5
作者：
V. Steinbauerová;P. Neumann;P. Novák;J. Macas
通讯作者：
V. Steinbauerová;P. Neumann;P. Novák;J. Macas