Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA.
Plant J. 2012 Aug;71(3):492-502. doi: 10.1111/j.1365-313X.2012.05005.x. Epub 2012 Jun 5.
The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. More generally, we show that evolution of gene expression profiles and coding sequences in the grasses may be linked. Genes that are highly and broadly expressed tend to be conserved at the coding sequence level while genes with narrow expression patterns show accelerated rates of sequence evolution. We further show that orthologs in syntenic genomic blocks are more likely to share correlated expression patterns compared with non-syntenic orthologs. These findings are important for agricultural improvement because sequence information is transferred from model species, such as Brachypodium, rice, and sorghum to crop plants without sequenced genomes.
禾本科植物，又称草类，包括农业上重要的谷类作物，如水稻、玉米、高粱和小麦。以前的比较研究表明，草类之间有很大一部分基因内容是共享的；然而，同源基因的功能保守性尚未得到探索。为了了解生殖组织中基因表达的全基因组进化模式，我们采用基于序列的方法比较了代表禾本科三个亚科的物种中的类似转录组，包括禾本科（Brachypodium distachyon）、黍亚科（高粱）和画眉草亚科（水稻）。我们的转录组分析表明，只有一部分同源基因表现出保守的表达模式。大量保守的同源基因包括在生理上相似的组织（如叶片、花药、雌蕊和胚胎）中上调的基因，而在种子中高度表达的同源基因表现出最分化的表达模式。更一般地说，我们表明草类中基因表达谱和编码序列的进化可能是相关的。高度广泛表达的基因往往在编码序列水平上保守，而表达模式狭窄的基因则表现出加速的序列进化速度。我们进一步表明，在同线性基因组块中的同源基因比非同线性同源基因更有可能共享相关的表达模式。这些发现对于农业改良很重要，因为序列信息是从模式物种（如拟南芥、水稻和高粱）转移到没有测序基因组的作物植物的。
