A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.
A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.
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DOI：
10.1534/g3.117.041319
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发表时间：
2017-07-05
期刊：
影响因子：
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通讯作者：
Blouin MS
中科院分区：
文献类型：
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作者：
Tennessen JA;Bollmann SR;Blouin MS
水生浮游蜗牛Biomphalaria glabrata是研究最多的软体动物之一，因为它在血吸虫病的传播中发挥作用。它的916 Mb基因组最近已被测序和注释，但它仍然组装不良。在这里，我们使用有针对性的捕获标记来绘制超过10，000个B。glabrata支架在94个F1后代的连锁杂交中，产生24个连锁群（LG）。我们添加了额外的支架，这些LG的基础上连锁不平衡（LD）分析有针对性的捕获和全基因组序列的96个无关的蜗牛。我们最终的连锁图谱由18，613个支架组成，包含515 Mb，代表56%的基因组和75%的基因和非重复区域。有18个大的（> 10 Mb）LG，可能代表预期的18个单倍体染色体，并且> 50%的基因组已被分配给至少17 Mb的LG。与其他腹足类基因组的比较揭示了同线和染色体重排的模式。关键免疫相关基因的连锁关系可能有助于阐明蜗牛-寄生虫相互作用。通过专注于基因和非重复区域之间的联系，我们已经产生了一个有用的资源关联蜗牛表型与因果基因，即使在没有一个完整的基因组组装。类似的方法可能会改善其他分类群中许多组装不良的基因组。这张地图将有助于今后对这种严重的人类寄生虫宿主的研究。
The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail–schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite.