The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq

Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of a wild species of sunflowers (Helianthus spp.) and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs) in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one distinct early generation hybrid. Then, we calculated the proportions of adaptive...目前鲜有研究探讨植物核基因间进化速率变异的成因，尤其是针对那些近期分化、仍可在野外发生杂交的物种。下一代测序（Next Generation Sequencing，NGS）技术的新近问世，使得研究者能够开展全基因组范围的蛋白质进化速率研究，以及解析选择在产生并维持物种分化中所发挥的作用。本研究借助单样本全转录组测序（RNAseq）技术，加深我们对野生向日葵属（Helianthus spp.）物种的种群基因组学的认知，并剖析影响蛋白质进化速率的各类因素。我们共比对了35吉字节的转录组测序数据，并在包含16312个基因的参考转录组中，鉴定出433257个单核苷酸多态性位点（Single Nucleotide Polymorphisms，SNPs）。借助单核苷酸多态性位点标记，我们鉴定出清晰的种群聚类结构，其大体对应本研究分析的三个物种：向日葵（Helianthus annuus）、海滨向日葵（Helianthus petiolaris）、薄皮向日葵（Helianthus debilis），仅存在一个独特的早期世代杂交个体。随后，我们计算了适应性进化...的比例