Data from: Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing

Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis.

三棘刺鱼（Gasterosteus aculeatus）的海洋种群已多次拓殖并快速适应淡水生境，为解析演化性状的遗传架构提供了极具价值的研究体系。本研究开发并应用了分箱式基因型分型测序（genotyping-by-sequencing, GBS）方法，依托两个各含350余尾个体的大型海洋-淡水杂交F₂群体，构建了刺鱼的高密度全基因组连锁图谱。所获得的连锁图谱显著优化了基因组组装：将78个新的基因组支架序列（scaffold）锚定至染色体、对40个基因组支架序列进行方向重定向，并在4个位点调整了基因组支架序列的排列顺序。在优化后的基因组组装结果中，94.6%的序列可被锚定至染色体上。为评估连锁图谱的质量，我们对控制侧骨板数量的数量性状位点（quantitative trait loci, QTL）进行定位，结果按预期将其定位至一个包含外胚层发育不良蛋白（Ectodysplasin）的200kb基因组区域，同时在7号染色体上定位到一个与此前已报道的修饰性QTL重叠的位点。最后，我们在两个杂交群体中定位了8个控制鳃耙长度趋同演化缩短的QTL，结果揭示这一经典适应性性状的遗传基础竟具有显著的模块化特征且并非平行演化模式。