Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
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DOI：
10.1101/gr.4708406
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发表时间：
2006-07-01
期刊：
影响因子：
7
通讯作者：
Freeling, Michael
中科院分区：
文献类型：
--
作者：
Thomas, Brian C.;Pedersen, Brent;Freeling, Michael
大约90%的拟南芥的独特基因内容是在最近的全基因组复制过程中形成的同线块中发现的。在这些区块中，28.6%的基因有一个保留的对;其余的基因已经从其中一个同源物中丢失。我们通过将局部重复压缩到一个基因，去除转座子，并仅包括保留对定义的块内的基因来创建最小化的基因组。我们使用保留和非保留基因的移动平均值来找到保留的集群，然后确定以高于预期的频率出现在集群中的基因类型。几乎所有染色体片段都存在显著的保留簇。详细比对显示，对于85%的基因组，一个同源物优先（1.6x）靶向分级分离。这种同源分馏偏差表明一种表观遗传机制。我们发现保留岛包含“连接基因”，这些基因被基因平衡假设预测为抵抗移除，因为它们编码的产物以剂量敏感的方式与其他产物相互作用，形成依赖网络。在簇中过度表达的基因家族包括蛋白酶体/蛋白质修饰复合物、信号转导机制、核糖体和转录因子复合物的编码组分。多倍体或片段复制后的基因对分离留下了富含“连接”基因的基因组。这些重复基因簇可能有助于解释共调节染色体区域和新功能模块的进化起源。
Approximately 90% of Arabidopsis' unique gene content is found in syntenic blocks that were formed during the most recent whole-genome duplication. Within these blocks, 28.6% of the genes have a retained pair; the remaining genes have been lost from one of the homeologs. We create a minimized genome by condensing local duplications to one gene, removing transposons, and including only genes within blocks defined by retained pairs. We use a moving average of retained and non-retained genes to find clusters of retention and then identify the types of genes that appear in clusters at frequencies above expectations. Significant clusters of retention exist for almost all chromosomal segments. Detailed alignments show that, for 85% of the genome, one homeolog was preferentially (1.6 x) targeted for fractionation. This homeolog fractionation bias suggests an epigenetic mechanism. We find that islands of retention contain "connected genes," those genes predicted-by the gene balance hypothesis-to be resistant to removal because the products they encode interact with other products in a dose-sensitive manner, creating a web of dependency. Gene families that are overrepresented in clusters include those encoding components of the proteasome/protein modification complexes, signal transduction machinery, ribosomes, and transcription factor complexes. Gene pair fractionation following polyploidy or segmental duplication leaves a genome enriched for "connected" genes. These clusters of duplicate genes may help explain the evolutionary origin of coregulated chromosomal regions and new functional modules.