基于蛔科多物种比较基因组分析的程序性DNA消除研究

Programmed DNA Elimination(PDE) is the procedure that part of the genomic DNA was actively eliminated during the early development of embryos which results in the much smaller genome size in somatic cells in comparison to the germline cells. The PDE was first discovered in parasite nematode Parascaris univalens and later confirmed its existence in other species including insects, copepods, mammals, fishes, birds and lampreys. Despite the PDE was early discovered in 1887, the biological significances and the inner mechanism was still not clearly unveiled. In the recent studies, the PDE was found to have relations with extremely gene silencing and sex determination. Meanwhile, in one organism, the location of eliminated sequences on the genome was stable, but no identical conserved sequences found between eliminated segments, which suggests that the mechanism of identification of sequences to be eliminated may be very complicated. The current study of PDE remains many difficulties: First, more organisms that have PDE were still uncovered on the genome level; Second, the current assemblies used for PDE analysis were still fragmented and some of the eliminated sequences were even ‘invisible’ (unassembled), thus some of the truth about the PDE were still unknown and further studies were affected. In this project, we will update the current assemblies and build new assemblies from candidate organisms from Ascarididae. By concentrating on the gene silencing by PDE and comparative genomic analysis between the target worms, we hope to study the possible effect of speeding the differentiation of species by PDE. This project will improve our knowledge on the mechanism and biological significance of PDE, as well as the knowledge of stability of the infrastructure of genome and chromosome. This project will also provide useful resources for other parasite nematode studies. Moreover, this project will contribute to the development of potential genome editing tools based on the mechanism of PDE in the future.

程序性DNA消除是在胚胎发育过程中，一部分基因组DNA发生了程序性的消除，导致体细胞基因组远小于胚系基因组的现象。该现象于1887年在马蛔虫中发现，但其生物学意义和形成机制一直并未得到明确答案。近期研究表明，程序性DNA消除或与基因沉默、性别决定有关，但在不同物种之间机制差异较大。由于众多可能存在该现象的物种尚未被发掘，且缺乏全面的比较基因组学研究，对该现象的认识尚停留在初级阶段。本项目拟在现有研究基础上，完善蛔科代表物种基因组资源，通过比较基因组学方法，研究程序性DNA消除对物种分化可能起到的推动作用。本项目拟更新对程序性DNA消除现象的现有认识，并希望为开发潜在的基于程序性DNA消除机制的基因组编辑工具的奠定理论基础。

程序性DNA消除现象是在胚胎发育过程中，一部分细胞基因组DNA发生了程序性的消除，导致体细胞基因组小于完整基因组的现象。程序性DNA消除是一种极端的基因敲除机制，伴随着体细胞中基因组的丢失，将部分基因在体细胞中直接删除。目前该现象的成因和机制均尚不明确，需要进行大量的基因组比较分析来找出该现象在进化上的来源。蛔科物种是典型的具有程序性DNA消除的物种，也是目前研究该现象的代表物种，但目前已测序的蛔虫物种数量非常稀少，且大多数基因组质量较差，严重阻碍了对该现象的深入研究。本项目通过文献调研和综合判断，确定并完成了3个蛔虫物种的从头组装。首先，大幅提升了犬弓首蛔虫基因组的组装质量；其次，完成了西氏贝蛔虫完整染色体级别基因组；最后，完成了鸡蛔虫基因组草图组装。同时，在两个质量较好的基因组上，初步鉴定出了具有程序性DNA消除现象的区域。通过本项目获得的基因组资源，进一步提升了可用于程序性DNA消除分析的蛔虫基因组数量，为将来深入研究程序性DNA消除的成因和机制奠定了重要基础。此外，由于西氏贝蛔虫宿主为大熊猫，具有比较独特的研究意义，因此利用本项目构建的西氏贝蛔虫基因组，我们进一步合作完成了西氏贝蛔虫的基因组特征分析，发现蛔虫可能具有独特且普遍的宿主转移机制，揭示了蛔虫在基因快速进化下形成的快速适应能力，并提出了针对大熊猫蛔虫病的防控建议，有益于野生大熊猫的保护。