Cross species selection scans identify components of C4 photosynthesis in the grasses.
Cross species selection scans identify components of C4 photosynthesis in the grasses.
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DOI：
10.1093/jxb/erw256
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发表时间：
2017-01
影响因子：
6.9
通讯作者：
Brutnell TP
中科院分区：
文献类型：
--
作者：
Huang P;Studer AJ;Schnable JC;Kellogg EA;Brutnell TP
一种新的全基因组扫描方法，使用信号的积极选择确定C4候选基因的草独立的先验知识的C4生物化学。C4光合作用可能是趋同适应性进化的最好例子之一，仅禾本科就有超过25个独立的起源。高质量的草基因组序列的可用性提供了新的机会，探索这种复杂的性状使用进化生物学为基础的方法的机制。在这项研究中，我们在C4谱系中进行了全基因组跨物种选择扫描，以促进C4基因的发现。这项研究是由禾本科植物基因组和最近测序的C3 panicoid草，Dichanthropus oligosanthes的基因组的高度保守的共线性。与以前的研究相比，这种方法不依赖于任何有助于与C4光合作用相关的生物化学或解剖学创新的基因的先验知识。我们确定了88个候选基因，其中包括C4途径的已知和潜在的新成分。这套包括碳穿梭酶丙酮酸，磷酸二激酶，磷酸烯醇丙酮酸羧化酶和NADP苹果酸酶，以及几个预测的转运蛋白，可能发挥重要作用，促进束鞘和叶肉细胞之间的代谢物通量。重要的是，这种方法展示了基本分子进化原理的应用，以剖析植物复杂的光合适应的遗传基础。此外，我们展示了选择扫描的输出如何与表达数据相结合，以提供额外的力量来优先考虑候选基因列表，并为途径工程提供新的机会。
A new genome wide scan method using signals of positive selection identifies C4 candidate genes in the grasses independent of a priori knowledge of C4 biochemistry. C4 photosynthesis is perhaps one of the best examples of convergent adaptive evolution with over 25 independent origins in the grasses (Poaceae) alone. The availability of high quality grass genome sequences presents new opportunities to explore the mechanisms underlying this complex trait using evolutionary biology-based approaches. In this study, we performed genome-wide cross-species selection scans in C4 lineages to facilitate discovery of C4 genes. The study was enabled by the well conserved collinearity of grass genomes and the recently sequenced genome of a C3 panicoid grass, Dichanthelium oligosanthes. This method, in contrast to previous studies, does not rely on any a priori knowledge of the genes that contribute to biochemical or anatomical innovations associated with C4 photosynthesis. We identified a list of 88 candidate genes that include both known and potentially novel components of the C4 pathway. This set includes the carbon shuttle enzymes pyruvate, phosphate dikinase, phosphoenolpyruvate carboxylase and NADP malic enzyme as well as several predicted transporter proteins that likely play an essential role in promoting the flux of metabolites between the bundle sheath and mesophyll cells. Importantly, this approach demonstrates the application of fundamental molecular evolution principles to dissect the genetic basis of a complex photosynthetic adaptation in plants. Furthermore, we demonstrate how the output of the selection scans can be combined with expression data to provide additional power to prioritize candidate gene lists and suggest novel opportunities for pathway engineering.