Lin Li, Tian Shulan, Kaeppler Shawn, Liu Zongrang, An Yong-Qiang Charles
USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Sciences Center, Saint Louis, Missouri, United States of America ; Department of Agronomy, University of Wisconsin, Wisconsin, United States of America.
USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Sciences Center, Saint Louis, Missouri, United States of America ; Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin, United States of America.
PLoS One. 2014 Feb 18;9(2):e87261. doi: 10.1371/journal.pone.0087261. eCollection 2014.
Germination is a biological process important to plant development and agricultural production. Barley and rice diverged 50 million years ago, but share a similar germination process. To gain insight into the conservation of their underlying gene regulatory programs, we compared transcriptomes of barley and rice at start, middle and end points of germination, and revealed that germination regulated barley and rice genes (BRs) diverged significantly in expression patterns and/or protein sequences. However, BRs with higher protein sequence similarity tended to have more conserved expression patterns. We identified and characterized 316 sets of conserved barley and rice genes (cBRs) with high similarity in both protein sequences and expression patterns, and provided a comprehensive depiction of the transcriptional regulatory program conserved in barley and rice germination at gene, pathway and systems levels. The cBRs encoded proteins involved in a variety of biological pathways and had a wide range of expression patterns. The cBRs encoding key regulatory components in signaling pathways often had diverse expression patterns. Early germination up-regulation of cell wall metabolic pathway and peroxidases, and late germination up-regulation of chromatin structure and remodeling pathways were conserved in both barley and rice. Protein sequence and expression pattern of a gene change quickly if it is not subjected to a functional constraint. Preserving germination-regulated expression patterns and protein sequences of those cBRs for 50 million years strongly suggests that the cBRs are functionally significant and equivalent in germination, and contribute to the ancient characteristics of germination preserved in barley and rice. The functional significance and equivalence of the cBR genes predicted here can serve as a foundation to further characterize their biological functions and facilitate bridging rice and barley germination research with greater confidence.
种子萌发是对植物发育和农业生产至关重要的生物学过程。大麦和水稻在5000万年前分化，但具有相似的萌发过程。为深入了解其潜在基因调控程序的保守性，我们比较了大麦和水稻在萌发起始、中期和末期的转录组，发现萌发调控的大麦和水稻基因（BRs）在表达模式和/或蛋白质序列上有显著差异。然而，蛋白质序列相似性较高的BRs往往具有更保守的表达模式。我们鉴定并表征了316组在蛋白质序列和表达模式上具有高度相似性的大麦和水稻保守基因（cBRs），并在基因、途径和系统水平上全面描绘了大麦和水稻萌发过程中保守的转录调控程序。cBRs编码参与多种生物学途径的蛋白质，具有广泛的表达模式。编码信号通路中关键调控成分的cBRs通常具有多样的表达模式。细胞壁代谢途径和过氧化物酶在萌发早期的上调以及染色质结构和重塑途径在萌发后期的上调在大麦和水稻中均保守。如果一个基因没有受到功能限制，其蛋白质序列和表达模式会迅速改变。这些cBRs的萌发调控表达模式和蛋白质序列在5000万年中得以保留，强烈表明cBRs在萌发中具有功能重要性且等同，并促成了大麦和水稻中保留的古老萌发特征。这里预测的cBR基因的功能重要性和等同性可作为进一步表征其生物学功能的基础，并有助于更有信心地衔接水稻和大麦的萌发研究。
