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

DNA序列的变化如何导致新的适应和新物种的形成是进化生物学的核心问题，从自然变化中发展出来的方法在研究作物驯化过程中的进化变化方面也很重要。比较相关物种的基因组DNA并不能确定选择了哪些序列差异。利用物种之间和物种内部序列差异的统计群体遗传学方法可以精确定位可能导致适应性变化的DNA区域。然而，这些技术只有在待比较的基因组序列既不太相似也不太不相似时才有效，并且在动物或植物界甚至在真菌中还没有几对适合于分析的基因组序列。两个拟南芥科植物的基因组序列的即将完成，加上可用的基因组序列A。thaliana提供了在中等进化距离的植物物种中研究此类问题的机会，这对于进化过程的计算研究是理想的;这三个物种也适合功能研究。我们将通过研究全基因组范围内的序列进化，并通过研究进化的分子基础，在两个良好的特点和生态相关的性状，开花时间和自交不亲和性（SI），利用这一资源。我们将首先生成所有三个物种的序列比对，并编译所有的直向同源基因集，即从物种共同祖先的相同基因遗传而来。由于已知三个物种的遗传图谱非常相似，因此可以识别出基因组的大的正交延伸。比对将立即使我们能够检测出个别物种中存在/不存在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率（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率。比较所有基因之间的这些比率可以回答几个重要的问题，包括基因或区域之间的非同义替换率是否相似，如果不是，变异是否在大的基因组区域中是系统性的。适应性进化和/或有助于物种形成的候选基因将具有异常高的非同义替换率，相对于群体内的多态性水平（我们将从一组大的基因座作为“对照”进行估计）。其他感兴趣的候选基因可以从自然群体之间异常高或低的分化中鉴定出来。该序列分析将为开花时间和SI这两个适应性状的功能研究奠定基础。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，自然发生的A. lyrata种群将与已知A.拟南芥开花时间调节剂第二，我们将识别A。通过遗传作图的方法，确定了对开花时间有较大影响的琴菜基因组区域，然后通过操纵它们的活性来研究这些区域中的候选基因。我们将使用自交不亲和的物种A。lyrata研究自然种群向自交亲和性的转变，并将在C.风疹（SC）及其自交不亲和的姊妹种C. grandiflora的，包括建立一个永生映射人口从一个交叉的物种映射基因与SC/SI，和其他性状的进化意义，如花的大小等，我们的研究预计将回答几个有趣的进化和基因组进化的问题，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.