Roulin Anne, Auer Paul L, Libault Marc, Schlueter Jessica, Farmer Andrew, May Greg, Stacey Gary, Doerge Rebecca W, Jackson Scott A
Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
Zoologisches Institut, Universität Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
Plant J. 2013 Jan;73(1):143-53. doi: 10.1111/tpj.12026. Epub 2012 Oct 22.
Polyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result in extensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally and evolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 million years ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutes a good model to study the impact of whole-genome duplication on gene expression. Using RNA-seq, we tested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested, approximately 50% of paralogs were differentially expressed and thus had undergone expression sub-functionalization. Based on gene ontology and expression data, our analysis also revealed that only a small proportion of the duplicated genes have been neo-functionalized or non-functionalized. In addition, duplicated genes were often found in collinear blocks, and several blocks of duplicated genes were co-regulated, suggesting some type of epigenetic or positional regulation. We also found that transcription factors and ribosomal protein genes were differentially expressed in many tissues, suggesting that the main consequence of polyploidy in soybean may be at the regulatory level.
多倍体在动物中通常无法被耐受，但在植物基因组中却广泛存在，并且可能导致大量的基因冗余。无论是在功能上还是进化方面，人们对重复基因的命运了解甚少。大豆（Glycine max L.）经历了两次独立的多倍体事件（分别在1300万年前和5900万年前），导致其75%的基因以多拷贝形式存在。因此，大豆构成了一个研究全基因组复制对基因表达影响的良好模型。我们利用RNA测序技术，测试了一组约18000个重复基因的功能命运。在测试的七个组织中，约50%的旁系同源基因存在差异表达，因此经历了表达亚功能化。基于基因本体和表达数据，我们的分析还表明，只有一小部分重复基因发生了新功能化或非功能化。此外，重复基因常常出现在共线区域，并且有几个重复基因区域受到共同调控，这表明存在某种类型的表观遗传或位置调控。我们还发现转录因子和核糖体蛋白基因在许多组织中存在差异表达，这表明大豆多倍体的主要后果可能体现在调控层面。
