The genomic basis of adaptation and species divergence in Senecio

该项目将利用DNA测序和分析技术的最新发展，研究植物Senecio （ragworts）的适应和物种形成的基因组基础。这项工作的主要目的是确定物种适应不同环境的基因编码和调控区域差异的相对重要性，我们的零假设是这些基因组区域对适应和物种分化的贡献相同。为此，我们将比较分别适应西西里岛埃特纳火山高海拔和低海拔地区的Senecio aethensis和S.菊花和它们之间形成的杂交种S. squalidus（牛津ragwort）基因组的蛋白质编码和调控区域的核苷酸序列，后者是300年前从埃特纳火山的杂交带引进植物到牛津后在英国进化而来的。所有三种Senecio物种都适应非常不同的栖息地，这些表型差异将通过新的比较基因组技术检测到的基因型差异来反映。事实上，我们之前nerc资助的研究已经揭示了三种物种之间基因表达的差异与表型适应相关。本项目将进一步分析这些遗传差异，并通过分析3个物种基因组的整个基因丰富部分（蛋白质编码和调控序列）来扩大基因组比较。为了做到这一点，我们将建立一个部分参考基因组测序的基因空间，基因组的非重复部分，塞内西奥squalidus。这将允许鉴定蛋白质编码和调控区域（例如启动子和microRNA结合位点）。使用生物信息学方法可以相对容易地识别基因的蛋白质编码区域，但识别调节区域需要使用新技术进行额外的分析，旨在识别：i) RNA聚合酶和转录因子结合位点（染色质免疫沉淀[ChIP-]测序），ii) microRNAs（最近发现的普遍存在的基因调节因子）及其结合位点。一旦确定，这些区域就可以在所有3个物种的多个个体中广泛测序，以确定它们之间的差异。进化遗传分析将用于比较DNA多态性模式，以检测可能涉及局部适应和物种形成的蛋白质编码和调控区域的自然选择“足迹”，并进一步研究3种Senecio物种的进化史。此外，我们将研究3种Senecio物种之间启动子结合、DNA甲基化（基因沉默）和microRNA表达/靶向的变化，这些变化可能参与适应。最后，我们将测试（使用生长在不同紫外线条件下的植物）候选基因对高紫外线的局部适应的改变表达/调节是否由物种差异或表型可塑性决定（在高海拔地区）。该项目将率先在进化基因组学领域开辟新天地：1)使用功能和进化基因分析来分析植物的整个基因空间，以探测与适应和物种形成相关的选择“足迹”；2)探索microrna在适应和物种形成中的作用；3)对植物物种进行大规模chip测序。因此，这项工作将为我们目前对基因组变化在适应和物种形成中的作用的理解提供前所未有的进展。

This project will exploit the latest developments in DNA sequencing and analysis technologies to study the genomic bases of adaptation and speciation in the plant genus Senecio (ragworts). The principal aim of this work is to determine the relative importance of differences in the coding and regulatory regions of genes in adaptation of species to contrasting environments, our null hypothesis being that these genomic regions contribute equally to adaptation and species divergence. To do this we will compare the nucleotide sequences of protein-coding and regulatory regions of the genomes of Senecio aethnensis and S. chrysanthemifolius, adapted to high and low altitudes, respectively, on Mt. Etna, Sicily, and a hybrid formed between them, S. squalidus (Oxford ragwort), which evolved in Britain following introduction of plants to Oxford from a hybrid zone on Mt. Etna 300 years ago. All 3 Senecio species are adapted to very different habitats and these phenotypic differences will be reflected by genotypic differences detectable by new comparative genomic technologies. Indeed, our previous NERC-funded research has revealed differences in gene expression between the 3 species correlated with phenotypic adaptation. This project will analyse these genetic differences further, and expand genomic comparison through an analysis of the entire gene-rich portion (protein-coding and regulatory sequences) of the genomes of the 3 species. To do this we will establish a partial reference genome by sequencing the gene-space, the non-repetitive fraction of the genome, of Senecio squalidus. This will allow identification of protein-coding and regulatory regions (e.g. promoters and microRNA binding sites). Protein-coding regions of genes can be identified relatively easily using bioinformatic approaches, but identification of regulatory regions requires additional analyses using new technologies designed to identify: i) RNA polymerase- and transcription factor-binding sites (chromatin immunoprecipitation [ChIP-] sequencing), ii) microRNAs (recently discovered ubiquitous gene-regulatory factors) and their binding sites. Once identified, these regions can then be sequenced extensively in multiple individuals of all 3 species to identify differences between them. Evolutionary genetic analysis will then be used to compare patterns of DNA polymorphism to detect 'footprints' of natural selection in protein-coding and regulatory regions that may have been involved in local adaptation and speciation, and also to further investigate the evolutionary history of the 3 Senecio species. In addition, we will investigate changes to promoter binding, DNA methylation (gene silencing) and microRNA expression/targeting between the 3 Senecio species that may be involved in adaptation. Finally, we will test (using plants grown at different UV-regimes) whether altered expression/regulation of candidate genes for local adaptation to high UV light (in high altitude S. aethnensis) is determined by species divergence or phenotypic plasticity. This project will break new ground in evolutionary genomics by being the first to: 1) use functional and evolutionary genetic analyses to analyse the entire gene-space of a plant to detect 'footprints' of selection correlated with adaptation and speciation; 2) explore the role of microRNAs in adaptation and speciation; 3) use large-scale ChIP-sequencing in a plant species. This work will therefore provide unprecedented advances in our current understanding of the role of genomic change in adaptation and speciation.