Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula
Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula
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DOI：
10.1016/j.gene.2009.06.004
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发表时间：
2009-12-15
期刊：
影响因子：
3.5
通讯作者：
Gambin, Anna
中科院分区：
文献类型：
--
作者：
Grzebelus, Dariusz;Gladysz, Miroslawa;Gambin, Anna
微型逆重复转座因子（MITEs）是一种小而高拷贝数的转座子，与一些II类自主元件相关并被其调动。新的螨虫家族可以通过基于计算机的测序基因组挖掘来鉴定。我们描述了四个与在Medicago， truncatula基因组中重新发现的MtPH转座子相关的MITE家族，以及一个先前描述的MITRAV家族。不同的家族内序列多样性和插入多态性水平表明它们在不同的进化时期活跃。MetMIT1和MITRAV家族序列一致，在26个生态型中产生高度多态性的插入位点。一个插入的子集只存在于A17 ‘Jemalong’的参考基因组中，这表明这两个家族可能在驯化过程中很活跃。相比之下，MetMIT2家族的所有插入都是固定的，这表明它在M. truncatula物种形成后没有活性。MetMIT1元件被划分为3个簇，即(I)相对异质的拷贝固定在M. truncatula基因组中，（II）均匀但也大部分固定，（III）在所调查的材料中均匀且多态。它可能反映了MetMIT1家族的进化史，显示出多次活动的爆发。许多MetMIT1和MITRAV插入出现在ORE上游或下游1kb范围内，在编码区近端的插入比例很高，这是A17 ‘Jemalong’所特有的。(c) 2009 Elsevier B.V.版权所有
Miniature inverted-repeat transposable elements (MITEs) are small and high copy number transposons, related to and mobilized by some class II autonomous elements. New MITE families can be identified by computer-based mining of sequenced genomes. We describe four MITE families related to MtPH transposons mined de novo in the genome of Medicago, truncatula, together with one previously described family MITRAV. Different levels of their intra-family sequence diversity and insertion polymorphism indicate that they were active at different evolutionary periods. MetMIT1 and MITRAV families were uniform in sequence and produced highly polymorphic insertion sites in 26 ecotypes representing a M. truncatula core collection. A subset of insertions was present only in the reference genome of A17 'Jemalong', suggesting that the two families might have been active in the course of domestication. In contrast, all investigated insertions of the MetMIT2 family were fixed, showing that it was not active after M. truncatula speciation. MetMIT1 elements were divided into three clusters, i.e. (I) relatively heterogenous copies fixed in the genome of M. truncatula, (II) uniform but also mostly fixed, and (III) uniform and polymorphic among the investigated accessions. it might reflect the evolutionary history of the MetMIT1 family, showing multiple bursts of activity. A number of MetMIT1 and MITRAV insertions were present within 1 kb upstream or downstream the ORE A high proportion of insertions proximal to coding regions was unique to A17 'Jemalong'. (c) 2009 Elsevier B.V. All rights reserved.