Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.
Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.
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DOI：
10.1371/journal.pgen.1000732
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发表时间：
2009-11
期刊：
影响因子：
4.5
通讯作者：
Bennetzen JL
中科院分区：
文献类型：
--
作者：
Baucom RS;Estill JC;Chaparro C;Upshaw N;Jogi A;Deragon JM;Westerman RP;Sanmiguel PJ;Bennetzen JL
最近对玉米基因组的全面序列分析现在允许在这个复杂的核环境中详细发现和描述所有转座因子（te）。反复优化的结构和同源性标准用于计算机辅助搜索逆转录元件，通过RNA中间体的逆转录进行转座的te，并通过人工检查验证最终结果。在玉米自交系B73中发现逆转录因子占据了核基因组的大部分（约75%）。在长末端重复（LTR）逆转录转座子类逆转录元件中发现了前所未有的遗传多样性，>400个家族（>350个新发现）贡献了> 31000个完整元件。另外两类逆转录因子，SINEs（4个家族）和LINEs（至少30个家族），分别贡献了1,991和~ 35,000个拷贝，占B73核基因组的1%。对于完全完整的元件，玉米中所有逆转录元件家族的中位数拷贝数为2，这是因为>250 LTR逆转录转座子家族只包含一两个在B73草案序列中可以检测到的完整成员。大多数被研究的逆转录因子家族在玉米基因组中表现出非随机分布，LINEs、sin和许多低拷贝数LTR逆转录转座子表现出在基因丰富区域积累的倾向。相反，大多数（但不是全部）中拷贝数和高拷贝数的LTR反转录转座子被发现优先积聚在基因缺乏的区域，如周中心异染色质，而少数高拷贝数的家族则表现出相反的偏好。LTR反转录转座子密度最高的基因组区域包含的LTR反转录转座子多样性最低。这些结果表明，玉米基因组为各种各样的逆转录因子的生存和繁殖提供了大量不同的生态位，这些逆转录因子已经进化到以不同的方式占据和利用这种基因组多样性。尽管te是所有已研究植物基因组的主要组成部分，并且是几乎所有已研究的真核生物基因组结构和进化的最重要贡献者，但它们的性质和存在原因在任何真核生物基因组中都没有得到很好的理解。为了全面研究TE对基因和基因组的结构、功能和进化的贡献，我们首先确定了玉米中的所有TE，然后调查了它们在传播过程中是否存在非随机模式。我们利用同源性和TE结构标准发现了最近测序的玉米自交系B73基因组中的所有逆转录因子。我们发现，在玉米中，逆转录因子的多样性令人难以置信，有数百个家族在玉米染色体上表现出不同的插入和/或保留特异性。这些元素族中的大多数以低拷贝数出现，并且在以前依赖于高拷贝数标准的搜索中被遗漏了。不同的元件家族在染色体上的积累表现出非常不同的倾向，表明它们可以检测和利用许多不同的染色质环境。
Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ∼35,000 copies, respectively, or a combined ∼1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity. Although TEs are a major component of all studied plant genomes, and are the most significant contributors to genome structure and evolution in almost all eukaryotes that have been investigated, their properties and reasons for existence are not well understood in any eukaryotic genome. In order to begin a comprehensive study of TE contributions to the structure, function, and evolution of both genes and genomes, we first identified all of the TEs in maize and then investigated whether there were non-random patterns in their dispersal. We used homology and TE structure criteria in an effort to discover all of the retroelements in the recently sequenced genome from maize inbred B73. We found that the retroelements are incredibly diverse in maize, with many hundreds of families that show different insertion and/or retention specificities across the maize chromosomes. Most of these element families are present in low copy numbers and had been missed by previous searches that relied on a high-copy-number criterion. Different element families exhibited very different biases for accumulation across the chromosomes, indicating that they can detect and utilize many different chromatin environments.
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DOI：
10.1073/pnas.132259199
发表时间：
2002-07-09
影响因子：
11.1
作者：
Fu, HH;Dooner, HK
通讯作者：
Dooner, HK
影响因子：
6.5
作者：
Deragon, Jean-Marc;Zhang, Xiaoyu
通讯作者：
Zhang, Xiaoyu
影响因子：
2.3
作者：
Fengler, Kevin;Allen, Stephen M.;Rafalski, Antoni
通讯作者：
Rafalski, Antoni
影响因子：
64.8
作者：
GRANDBASTIEN, MA;SPIELMANN, A;CABOCHE, M
通讯作者：
CABOCHE, M
影响因子：
5.1
作者：
Estill, James C.;Bennetzen, Jeffrey L.
通讯作者：
Bennetzen, Jeffrey L.