High-density linkage map to find snail genes that block schistosome transmission

描述(申请人提供)：血吸虫病是迄今为止人类最重要的蠕虫寄生虫病。疫苗是不可用的，唯一有效的治疗方法是反复使用一种药物(吡喹酮)，现在耐药性是一个令人担忧的问题。血吸虫是通过水生蜗牛传播的。了解蜗牛和血吸虫相互作用的分子机制是阻断传播的新策略的关键。为此，最近对蜗牛的基因组进行了测序。然而，由于0.9 GB基因组的50%是高度重复的，它仍然组装得很差。它由500,000个重叠群组成，其中一半的基因组包含在43kb以下的重叠群上(N50=大约一个基因的大小)。因此，任何与寄生虫免疫相关的遗传标记都不太可能在与它们相关联的因果基因的同一重叠群上找到。已知有六个与血吸虫抗性相关的标记存在于光滑小球虫中。但由于基因组组装不充分，与这些标记相关的大多数基因仍然是一个谜。因此，生物医学研究界最重要的目标之一--寻找与免疫相关的基因--目前受到严重阻碍。幸运的是，有一种替代方法可以完成基因组组装。基因组的重复部分在流行病学上几乎没有重要意义，因为我们预计它包含的功能元件或有用的遗传标记很少。基因组的非重复区域，包括绝大多数基因，可以通过强大的靶向序列捕获新方法与高密度连锁图谱组装在一起。鉴于我们在光滑假单胞菌的连锁作图方面的初步工作，以及我们过去在其他系统中高密度定向捕获方面的成功，我们唯一地准备好开发这一图谱。本申请的具体目标是(1)生成非重复序列的高密度连锁图谱 然后(2)使用该图谱来识别抗性标记周围的基因。该图谱将使用约40,000个遗传标记，将99%的独特基因组序列，包括95%的基因，整合到与18条蜗牛染色体相对应的大型连锁群中。创新：定向捕获是一种从未用于Biomphalaria的新方法。只关注基因组的单拷贝、包含基因的部分，避开了组装这样一个重复基因组的挑战，同时为特征图谱创建了高质量的基因组资源。这种方法也应该成为其他组装不良的基因组的模型。意义：到目前为止，蜗牛基因组计划并没有像预期的那样促进特征图谱的绘制。这一连锁图谱将消除快速识别控制蜗牛免疫和其他表型特征的基因的最后障碍。了解蜗牛免疫将揭示潜在干扰寄生虫的新方法(例如，针对蜗牛免疫系统所针对的寄生虫分子的治疗方法)，或者操纵蜗牛种群，使其成为能力较差的宿主。

DESCRIPTION (provided by applicant): Schistosomiasis is by far the most important helminth parasitic disease of humans. Vaccines are unavailable, the only effective treatment involves repeated dosing with a single drug (praziquantel), and now drug resistance is a concern. Schistosomes are transmitted by aquatic snails. Understanding the molecular mechanisms by which snails and schistosomes interact is key for new strategies to interrupt transmission. To this end, the genome of the snail Biomphalaria glabrata was recently sequenced. However, because >50% of the 0.9 Gb genome is highly repetitive, it remains very poorly assembled. It consists of >500,000 contigs, with half the genome contained on contigs under 43 kb (N50 = about the size of a gene). As a result, any genetic markers that associate with parasite immunity are unlikely to be found on the same contig as the causal gene to which they are linked. Six markers linked to schistosome resistance are known in B. glabrata. But most of the genes linked to those markers remain a mystery owing to the inadequate genome assembly. Thus, one of the most important goals of the Biomphalaria research community, to find genes associated with immunity, is currently severely hampered. Fortunately, there is an alternative to complete genome assembly. The repetitive portion of the genome is of little epidemiological importance because we expect it to contain few functional elements or useful genetic markers. The non-repetitive regions of the genome, which include the vast majority of genes, can be assembled with a high-density linkage map via the powerful new method of targeted sequence capture. We are uniquely poised to develop this map, given our preliminary work with linkage mapping in B. glabrata and our past success with high-density targeted capture in other systems. The specific objectives of this application are (1) to generate a high-density linkage map of the non-repetitive fraction of the B. glabrata genome, and then (2) use that map to identify genes surrounding resistance markers. This map will employ ~40,000 genetic markers to unite >99% of the unique genomic sequence, including >95% of genes, into large linkage groups corresponding to the 18 snail chromosomes. Innovation: Targeted capture is a new approach that has never been used with Biomphalaria. Focusing on just the single-copy, gene-containing fraction of the genome sidesteps the challenge of assembling such a repetitive genome, while creating a high-quality genomic resource for trait mapping. This approach should also be a model for other poorly-assembled genomes. Significance: The snail genome project has thus far failed to facilitate trait mapping as expected. This linkage map will remove the last barrier to rapidly identifying genes that control snail immunity and other phenotypic traits. Understanding snail immunity will reveal new ways to potentially interfere with the parasite (e.g. therapeutics targeting parasite molecules that are targeted by the snail immune system) or to manipulate snail populations to make them into less competent hosts.