果蝇microRNA适应性进化及其影响配子发生的比较基因组研究

D. melanogaster has undergone the tropical-to-temperate and wild-to-domestic habit shift, which makes it an excellent model organism to study the molecular mechanism underlying adaptation to new environments. The evolution of gene regulation and how it changes the fitness-related phenotypes are important topics in evolutionary genetics. On the basis of our previous work, we will use population genomic data to identify miRNAs that are subjected to positive selection in D. melanogaster. Then, we will focus on these adaptively evolving miRNAs and study their sequence, expression, and functional evolution by both comparative genomic and evolutionary genetics approaches. At the sequence level, we will survey the birth-and-death process and compare the nucleotide polymorphism patterns between D.melanogaster and D.simulans. At the expression level, we will analyze the tissue-specific expression pattern across closely related species in Drosophila. At the phenotype level, we will knockout these miRNAs in D. melanogaster and study their role in gametogenesis; furthermore, we will compare their functional divergence across species by anti-miRNA oligonucleotides. Finally, RNA-seq combined with bioinformatic analyses and target verification will be used to construct the miRNA regulatory networks in multiple species and the re-wiring of miRNA-target relationship between species will be studied. Using the genotype, expression, and phenotype data collectively, this work will contribute to the systematic understanding of adaptive evolution of miRNAs and its association with gametogenesis evolution in Drosophila. It will also reveal the role of natural selection in the evolution of gene regulatory network and shed light on the gene-gene interaction mechanism underlying the adaptation of D. melanogaster to new habitats at the genomic level.

黑腹果蝇经历了热带到温带、野生到家养的生境转变是研究生物对新环境适应机制的极好系统。基因调控的进化及影响表型的分子机制是进化遗传学研究的前沿课题。本项目将在已有工作基础上，以黑腹果蝇及其近缘种为材料，利用群体基因组数据，从全基因组水平鉴定黑腹果蝇中受正选择的miRNA；在序列水平，研究这些适应性进化的miRNA在果蝇属中的生灭过程及其在姐妹种间核苷酸变异模式的异同；在表达水平，分析适应性miRNA的组织特异性表达模式及演化；在表现型水平，利用基因敲除和反义寡核苷酸技术，研究适应性miRNA对雌雄配子发生的表型效应及其功能保守性；最终，利用转录组测序和分析，构建miRNA基因调控网络并探讨其演化规律。综合基因型、表达谱、表现型数据，阐明果蝇miRNA适应性进化的模式及其影响配子发生的基因组机制，揭示自然选择在基因调控网络进化中的作用，全面系统地认识黑腹果蝇适应新环境的多基因作用机制。

黑腹果蝇经历了热带到温带、野生到家养的生境转变是研究生物对新环境适应机制的极好系统。基因调控的进化及影响表型的分子机制是进化遗传学研究的前沿课题。我们利用果蝇群体基因组数据结合小RNA组测序，筛选鉴定黑腹果蝇中受选择的miRNA；利用基因敲除结合RNA-seq在姐妹种间探讨这些适应性进化的miRNA的功能演化及伴随的靶基因调控网络改变；同时鉴定了黑腹果蝇Z和M种系间适应性分化的miRNA靶位点，在体内外验证了这些位点的多态性对基因表达的影响。我们发现果蝇属新miRNA经历了产生、灭亡及适应性进化的循环，表明驱动miRNA进化的选择优势本身也是处在不断进化的过程中，这对理解miRNA的调控功能有重要意义；发现miR-310s通过多个靶基因不一致地控制表型，暗示miRNA对表型起到进化稳定的作用；发现年轻的miR-983对雄性生殖力的作用及其对转录组的影响在黑腹果蝇和拟果蝇间不保守，揭示适应性miRNA介导靶基因调控网络重建进而导致表型变异；发现种子序列和非种子序列的进化同时介导着miR-972基因簇调控网络的重建，基因簇成员靶基因库的保守性为返老还童miRNA功能的快速演化提供了便利，对理解miRNA功能演化有重要意义；发现M品系特异的正选择导致九个miRNA靶位点在Z和M品系间发生适应性分化，适应性靶位点多态性能导致靶基因表达量在品系间差异，揭示miRNA调控网络进化在M品系走出非洲的适应中起到重要作用。