Leveraging the genome sequences of two Arabidopsis relatives for evolutionary and ecological genomics

DNA序列的变化是如何导致新的适应性和新物种形成的问题是进化生物学的核心，从自然变化中发展出来的方法对于研究作物驯化过程中的进化变化也很重要。比较亲缘物种的基因组DNA并不能确定选择了哪些序列差异。统计种群遗传方法利用物种之间和物种内部的序列差异可以精确定位可能导致适应性变化的DNA区域。然而，这些技术只有在要比较的基因组序列既不太相似也不太不同的情况下才有效，而且在动物或植物王国中，甚至在真菌中，适合分析的基因组序列很少。即将完成的两种芸苔科拟南芥和风帆芥的基因组序列，以及拟南芥的可用基因组序列，为研究处于中间进化距离的植物物种提供了机会，这对于进化过程的计算研究是理想的；这三个物种也适合进行功能研究。我们将利用这一资源，在全基因组范围内研究序列进化，并研究开花时间和自交不亲和（SI）这两个特征明确且与生态相关的性状的进化分子基础。我们将首先生成所有三个物种的序列比对，并编译所有的同源基因，即来自物种共同祖先的同一基因。由于已知这三个物种的遗传图谱非常相似，因此可以确定大的同源基因组延伸。这些比对将使我们能够立即发现在单个物种中存在/缺失的特别有趣的基因类别，从而研究基因组进化。接下来，我们将估计同义序列变化（不改变编码蛋白质的氨基酸序列）和每个物种对中存在的基因对之间的非同义变化的比率。比较所有基因的这些比率可以回答几个重要的问题，包括非同义取代的比率在基因或区域之间是否相似，如果不是，变异是否在大的基因组区域之间是系统的。具有适应性进化和/或促成物种形成的候选基因将是非同义替换率异常高的基因，相对于群体内的多态性水平（我们将从大量的位点组中估计作为“对照”）。其他有趣的候选基因可以从自然种群之间异常高或低的分化中识别出来。序列分析将为开花时间和SI两个适应性性状的功能研究提供基础。影响开花时间的基因将通过两种互补的方法进行鉴定。首先，拟南芥自然种群开花时间的变化将与已知拟南芥开花时间调控因子同源基因的序列变化相关。其次，我们将通过遗传作图的方法确定对开花时间影响较大的基因组区域，并通过调控这些区域的活性来研究候选基因。我们将利用自交不亲和种a . lyrata研究一些自然种群向自交不亲和（SC）的过渡，并将对风疹C. rubella （SC）及其自交不亲和姊妹种C. granflora进行类似的研究，包括建立一个从物种杂交的永活定位群体来定位与SC/SI相关的基因，以及其他具有进化意义的性状，如花的大小等。总之，我们的研究有望回答几个有趣的进化和基因组进化问题，也应该推进作物育种计划。

The question of how changes in DNA sequence result in novel adaptations and in the formation of new species is at the heart of evolutionary biology, and approaches developed from natural changes are also important in studying evolutionary changes during crop domestication. Comparing the genomic DNA of related species does not identify which sequence differences were selected. Statistical population genetic approaches using sequence differences between and within species can pinpoint regions of the DNA that may underlie adaptive changes. However, these techniques are only effective if the genome sequences to be compared are neither too similar nor too dissimilar, and few pairs of genome sequences suitable for the analyses are yet available in the animal or plant kingdoms, or even in fungi. The impending completion of the genome sequences of the two Brassicaceae Arabidopsis lyrata and Capsella rubella, together with the available genome sequence of A. thaliana, offers opportunities to study such questions in plant species at the intermediate evolutionary distances that are ideal for computational studies of evolutionary processes; these three species are also suitable for functional studies. We will exploit this resource by studying sequence evolution on a genome-wide scale and by studying the molecular basis of evolution in two well-characterized and ecologically relevant traits, flowering time and self-incompatibility (SI). We will first generate sequence alignments of all three species and compile all sets of orthologous genes, i.e. descended from the same gene in the species' common ancestor. As the genetic maps of the three species are known to be very similar, large orthologous stretches of genome can be identified. The alignments will immediately allow us to detect the especially interesting category of genes that are present/absent in individual species, allowing study of genome evolution. We will next estimate rates of synonymous sequence changes (not changing the amino-acid sequence of the proteins encoded) and non-synonymous changes between pairs of genes present in each species pair. Comparing these rates across all genes can answer several important questions, including whether rates of non-synonymous substitutions are similar between genes or regions, and if not, whether variation is systematic across large genomic regions. Candidates for having evolved adaptively and/or contributed to speciation will be genes with unusually high rates of non-synonymous substitutions, relative to polymorphism levels within populations (which we shall estimate from a large set of loci to serve as 'controls'). Other interesting candidate genes can be identified from unusually high or low differentiation between natural populations. The sequence analyses will provide a foundation for functional studies of two adaptive traits, flowering time and SI. Genes affecting flowering time will be identified with two complementary approaches. First, variation in flowering time in naturally occurring A. lyrata populations will be correlated with sequence changes in orthologues of known A. thaliana flowering time regulators. Second, we will identify A. lyrata genomic regions with large effects on flowering time by genetic mapping, and then study candidate genes in these regions by manipulating their activity. We will use the self-incompatible species A. lyrata to study the transition to self-compatibility (SC) in some natural populations, and will do similar studies in C. rubella (SC) and its self-incompatible sister species C. grandiflora, including establishing an immortalized mapping population from a cross of the species to map genes associated with SC/SI, and other traits of evolutionary significance, such as flower size, etc. Together, our studies are expected to answer several interesting evolutionary and genome evolution questions, and should also advance breeding programmes in crops.