Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes.
Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes.
复制标题
DOI：
10.1186/1471-2164-14-71
复制
发表时间：
2013-01-31
期刊：
影响因子：
4.4
通讯作者：
Wessler SR
中科院分区：
文献类型：
--
作者：
Han Y;Qin S;Wessler SR
2 类转座元件 (TE) 是植物基因内部和周围的主要元件，它们在其中产生显着的等位基因多样性。利用四种草的完整序列，我们对 2 类 TE 进行了新颖的比较分析。为了确保比较分析的一致性，我们重新注释了二穗短柄草、水稻、高粱和玉米中的 2 类 TE，并将它们分配给植物基因组中发现的五个剪切粘贴超家族之一（Tc1/mariner、PIF/Harbinger、hAT、Mutator、CACTA）。我们重点关注非编码元件，因为它们丰富，并比较了超家族的拷贝数、大小和基因组分布以及与附近基因表达水平的相关性。我们的比较揭示了独特和保守的特征。首先，每个超家族中元件的平均长度或大小分布在很大程度上是保守的，最短的总是 Tc1/mariner 元件，其次是 PIF/Harbinger、hAT、Mutator 和 CACTA。该顺序也适用于非编码元件与编码元件的拷贝数之比。其次，除了 CACTA 之外，非编码 TE 在基因内部和侧翼富集，表现出保守的分布模式，在启动子区域具有最高峰值。最后，我们对微阵列数据的分析表明，与 Tc1/mariner 和 PIF/Harbinger 非编码元件相关的基因比没有 2 类 TE 的基因具有显着更高的表达水平。相反，具有 CACTA 元件的基因的表达显着低于不具有 2 类 TE 的基因。我们已经在这四种草基因组中实现了迄今为止最全面的 2 类 TE 注释。通过对这个强大数据集的比较分析，确定了每个超家族的几个先前未知的特征，这些特征涉及拷贝数、元件大小、基因组分布以及与附近基因表达水平的相关性。这些结果强调了在评估 TE 超家族对基因和基因组进化的影响时区分它们的重要性。
Class 2 transposable elements (TEs) are the predominant elements in and around plant genes where they generate significant allelic diversity. Using the complete sequences of four grasses, we have performed a novel comparative analysis of class 2 TEs. To ensure consistent comparative analyses, we re-annotated class 2 TEs in Brachypodium distachyon, Oryza sativa (rice), Sorghum bicolor and Zea mays and assigned them to one of the five cut-and-paste superfamilies found in plant genomes (Tc1/mariner, PIF/Harbinger, hAT, Mutator, CACTA). We have focused on noncoding elements because of their abundance, and compared superfamily copy number, size and genomic distribution as well as correlation with the level of nearby gene expression. Our comparison revealed both unique and conserved features. First, the average length or size distribution of elements in each superfamily is largely conserved, with the shortest always being Tc1/mariner elements, followed by PIF/Harbinger, hAT, Mutator and CACTA. This order also holds for the ratio of the copy numbers of noncoding to coding elements. Second, with the exception of CACTAs, noncoding TEs are enriched within and flanking genes, where they display conserved distribution patterns, having the highest peak in the promoter region. Finally, our analysis of microarray data revealed that genes associated with Tc1/mariner and PIF/Harbinger noncoding elements have significantly higher expression levels than genes without class 2 TEs. In contrast, genes with CACTA elements have significantly lower expression than genes without class 2 TEs. We have achieved the most comprehensive annotation of class 2 TEs to date in these four grass genomes. Comparative analysis of this robust dataset led to the identification of several previously unknown features of each superfamily related to copy number, element size, genomic distribution and correlation with the expression levels of nearby genes. These results highlight the importance of distinguishing TE superfamilies when assessing their impact on gene and genome evolution.
登录
查看更多内容
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
64.8
作者：
Vogel, John P.;Garvin, David F.;Baxter, Ivan
通讯作者：
Baxter, Ivan
影响因子：
4
作者：
WESSLER, SR;BUREAU, TE;WHITE, SE
通讯作者：
WHITE, SE
DOI：
10.1073/pnas.1018222108
发表时间：
2011-02-08
影响因子：
11.1
作者：
Hollister, Jesse D.;Smith, Lisa M.;Gaut, Brandon S.
通讯作者：
Gaut, Brandon S.