LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice.
LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice.
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DOI：
10.1186/1471-2164-9-382
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发表时间：
2008-08-10
期刊：
影响因子：
4.4
通讯作者：
Liu JS
中科院分区：
文献类型：
--
作者：
Wang H;Liu JS
长末端重复逆转录转座子（LTR 元件）是普遍存在的真核 TE，通过 RNA 中间体进行转座。 LTR 元件在许多植物基因组中占很大比例，已被确定为植物基因组大小、结构和功能进化的主要力量之一。模型豆科植物蒺藜苜蓿 (Medicago truncatula, Mt) 超过 40% 的基因组序列的可访问性使得对其 LTR 元件的全面研究成为可能。我们使用新开发的工具LTR_FINDER来识别Mt基因组中的LTR反转录转座子，并检测到526个全长元件以及与其相关的大量拷贝。这些元件约占目前可用基因组序列的 9.6%。分为85个科，其中64个科为首次报道。大多数 LTR 反转录转座子属于 Copia 或 Gypsy 超家族，其他转座子根据长度分为 TRIM 或 LARD。我们发现Copia类家族的拷贝数是Gypsy类家族的3倍，但后者对基因组的贡献更大。对LTR家族的PBS和蛋白质编码结构域结构的分析表明，它们往往仅使用4-5种类型的tRNA，并且许多家族除了已知的TE结构域外还具有相当保守的ORF。对于几个重要的家族，我们详细描述了它们的丰度、保守性、插入时间和结构。我们研究了元件的扩增-缺失模式，发现可检测到的全长元件相对年轻，并且大多数是在最后 0.52 MY 内插入的。我们还估计，超过一千万个碱基对的 Mt 基因组序列已通过 LTR 元件的删除而被去除，并且 Mt 中全长结构的去除速度比水稻更快。该报告是对 Mt 基因组中 LTR 反转录转座子的首次全面描述和分析。许多重要的新型 LTR 家族被发现并阐明了它们的进化。我们的结果可能概述了模型豆科植物的 LTR 反转录转座子景观。
Long terminal repeat retrotransposons (LTR elements) are ubiquitous Eukaryotic TEs that transpose through RNA intermediates. Accounting for significant proportion of many plant genomes, LTR elements have been well established as one of the major forces underlying the evolution of plant genome size, structure and function. The accessibility of more than 40% of genomic sequences of the model legume Medicago truncatula (Mt) has made the comprehensive study of its LTR elements possible. We use a newly developed tool LTR_FINDER to identify LTR retrotransposons in the Mt genome and detect 526 full-length elements as well as a great number of copies related to them. These elements constitute about 9.6% of currently available genomic sequences. They are classified into 85 families of which 64 are reported for the first time. The majority of the LTR retrotransposons belong to either Copia or Gypsy superfamily and the others are categorized as TRIMs or LARDs by their length. We find that the copy-number of Copia-like families is 3 times more than that of Gypsy-like ones but the latter contribute more to the genome. The analysis of PBS and protein-coding domain structure of the LTR families reveals that they tend to use only 4–5 types of tRNAs and many families have quite conservative ORFs besides known TE domains. For several important families, we describe in detail their abundance, conservation, insertion time and structure. We investigate the amplification-deletion pattern of the elements and find that the detectable full-length elements are relatively young and most of them were inserted within the last 0.52 MY. We also estimate that more than ten million bp of the Mt genomic sequences have been removed by the deletion of LTR elements and the removal of the full-length structures in Mt has been more rapid than in rice. This report is the first comprehensive description and analysis of LTR retrotransposons in the Mt genome. Many important novel LTR families were discovered and their evolution is elucidated. Our results may outline the LTR retrotransposon landscape of the model legume.
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
DOI：
10.1098/rstb.1986.0004
发表时间：
1986-01-29
影响因子：
6.3
作者：
FLAVELL, RB
通讯作者：
FLAVELL, RB
影响因子：
1.5
作者：
Kapitonov, VV;Jurka, J
通讯作者：
Jurka, J
影响因子：
7
作者：
Kim, JM;Vanguri, S;Voytas, DF
通讯作者：
Voytas, DF
影响因子：
7.4
作者：
Graham, PH;Vance, CP
通讯作者：
Vance, CP