篦子三尖杉的种群转录组学研究：基于表达和序列变异分析由环境变化驱动的遗传分化

拟采用种群转录组学的方法研究篦子三尖杉种群由环境变化驱动的遗传分化。内容包括：（1）借助RNA-Seq在种群水平获得篦子三尖杉的转录组数据；将转录本归入直系同源基因簇，并筛选和环境相关的候选基因。（2）利用转录组数据开发SNP，基于表达水平和等位基因载荷鉴定差异表达和高度分化转录本，应用基因组扫描识别离群基因座。（3）根据差异表达和高度分化转录本的分布和变异，在表达和序列水平研究种群的遗传分化；检测离群基因座的功能类别、表达和序列变异，研究种群对环境的局部适应性。（4）对比差异表达和高度分化转录本，在所有转录本及在和环境相关的转录本中的分布式样、变异和分化程度，鉴定参与对环境变化做出响应的基因、研究环境对表达和序列变异的选择作用、评估表达和序列变异在种群分化中的相对重要性。（5）根据转录本所属的GO类别、直系同源基因簇和过代表性，研究种群分化涉及的基因范围，分辨驱动种群分化的环境因子。

This project aims to investigate the population genetic differentiation of Cephalotaxus oliveri Mast. that is driven by environmental changes by using population transcriptomic approaches. The main research contents are as follows: (1) We will apply RNA-Seq to generate the transcriptomic data of C. oliveri at the population level. Transcripts will be assigned to existing orthogroups, and a set of environmental factor-relevant candidate genes will be obtained by extensively searching published reports. (2) By studying the transcriptomic data, we will detect single nucleotide polymorphisms (SNPs); label distinctively expressed and highly divergent transcripts, respectively, according to their gene expression levels and allele loadings; and identify outlier loci by conducting a genome scan. (3) Expression- and sequence-based population divergence will be assessed on the basis of the distribution and variation of distinctively expressed and highly divergent transcripts. Meanwhile, the local adaptation of populations to environmental factors will be analyzed via an approach by incorporating both expression and sequence variation as well as the functional term of the outlier loci. (4) We will a conduct a comparative analysis of the distribution pattern, the variation level, and the divergence extent for distinctively expressed and highly divergent transcripts over all transcripts vs those restricted to environmental factor-relevant genes. Our objects are to identify the genes that are involved in the response to environmental changes, to reveal the effect of selection on the expression and sequence variation as a consequence of environmental influences, and to evaluate the relative contribution of the expression and sequence variation in shaping differentiation among populations. (5) We will also analyze the gene ontology (GO) terms, orthogroups, and over-representation of distinctively expressed and highly divergent transcripts in order to define the set of genes and to discriminate the environmental factors that contribute to population differentiation.