Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the C. gigas genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs, i.e., adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process.

连锁和连锁作图的研究已有100多年的先进遗传和生物学知识。如今，除了它们日益重要的作用外，在将表型映射到基因型中，密集的连锁图还可以帮助验证基因组装配。以前，我们显示太平洋牡蛎Crassostrea gigas的第一个基因组组装中的支架中有40％是嵌合的，包含映射到不同连接基团的单核苷酸多态性（SNP）。在这里，我们将14个由按序列基因分型（GBS）方法生成的SNP构建的连锁图与五个先前构建的连锁图合并，以创建具有高置信度的近6.9万个SNP简编。我们使用该纲要来评估C. gigas的最近可用的染色体级装配基因组，对301个重叠群中的275个重叠群中的SNP进行定位，并通过连锁比较这些重叠群的顺序与通过Hi-C测序方法对其组装进行比较。我们发现，尽管26％的重叠群包含SNP的嵌合嵌段，即比其重叠群中大多数SNP映射到不同连锁基团的相邻SNP，但这些明显的错配仅占基因组序列的0.08％。此外，通过连锁和测序定位的275个重叠群中有近90％的组装相同。对于剩余的10％重叠群，两个程序集之间的不一致似乎是由于链接信息不足而导致的。因此，我们对连锁图的汇编强烈支持了牡蛎基因组的这种染色体水平的装配。最后，我们使用该程序集首次估算了风生孢子虫，