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

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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.