以线虫摄食器官进化为模型研究新生结构和行为的遗传发育机制

The developmental genetics mechanism of evolution of an inheritable trait is a core question of modern evolutionary synthesis and system biology. Studies in this field enable us to understand the flexibility and evolvability of basic biological processes. Current studies focus on genetic architecture of minor modification of traits or their degeneration. However, developmental mechanisms of evolution of a trait and genetic architecture of its gain-of-function remain elusive. During evolution, nematodes gain highly diverse feeding organs to adapt to different food. The classic model animal, nematode Caenorhabditis elegans, has been well studied on the cellular and developmental biology of its feeding organs, stoma and pharynx. This grant will use bacterivorous Caenorhabditis elegans and omnivorous Pristionchus pacificus as models to reveal developmental genetics mechanisms of gain-of-function of their feeding organs. A common molecular mechanism underlying evolution is modification of gene regulation. So based on high throughput and high resolution profiling of gene expression as a core methodology, this grant uses comparative functional genomics and combines well developed developmental genetics approaches in Caenorhabditis elegans to reveal genetic architecture and cellular and developmental mechanisms of gain of novel structures and behaviors of nematode’s stoma and pharynx. This grant expects to 1. reveal insights in molecular, cellular and developmental mechanisms underlying how organs evolve new function; 2. establish feeding organs of nematodes as evolution models for systematic studies.

性状进化的遗传发育机制是现代进化生物学和系统生物学的一个核心问题。这方面的研究使我们能够从复杂系统水平理解基础生物学过程的可调性和可进化性。但现有的研究主要是揭示性状微细修饰或退化的遗传机制，而较少研究新功能的获得及其发育生物学机制。线虫在适应不同食物的进化过程中获得高度多样化的摄食器官。其中经典模式生物秀丽隐杆线虫口咽的细胞发育生物学机制已有丰富研究。本课题将以食细菌的秀丽隐杆线虫和杂食的太平原管线虫的口咽为模型研究器官获得新功能的遗传发育机制。生物进化的一个常用分子机制是改变基因表达调控。因此，本课题以申请人开发的高通量高精度基因表达图谱技术为核心，通过比较功能基因组学，结合成熟的秀丽隐杆线虫发育遗传学手段，揭示导致线虫口咽获得新结构和行为的遗传结构和细胞发育生物学机制。本课题预期1.从分子细胞发育生物学水平理解器官如何进化出新的功能; 2.把线虫摄食器官建立为可以系统研究的进化模型。

长片段基因组文库如BAC和phasmid文库是重要的基因组学和遗传学研究资源。然而目前获取它们序列信息的方法需要昂贵的成本和时间。为了克服这个限制，我们生成了pBACode，一个BAC载体库。pBACode的每个载体都有一对随机序列在基因组插入位点两侧。把BAC文库的所有克隆混合在一起高通量测得基因组片段两端序列后，通过随机序列标记对配组基因组序列从而获得每个BAC克隆的基因组片段的两端序列配对。同时，通过多维混合法对标记序列进行高通量测序可以构建BAC克隆的物理图谱。还有，我们建立了一个计算流水线来提高BAC两端序列在基因组从头组装中的作用。作为验证性实验，我们已经用这个质粒库构建了牙鲆（Paralichthys olivaceus）的BAC基因组文库，高通量测序表明90%的BAC克隆可以通过这种随机序列标记法获得基因组片段的配对两端序列，并且定位它们在文库中的位置。高通量的BAC双端序列使得基因组草图的连续性提高了超过一个数量级，达到了10.8Mb。克隆物理图谱覆盖了91.8%的BAC克隆。对牙鲆、舌鳎和三棘背鳍鱼比较基因组分析和BAC克隆测序发现舌鳎的性别决定基因dmrt1和牙鲆的左右表达不对称基因myoD2在进化过程中通过染色体重排获得了新的上游序列。