Application of next-generation sequencing to very large genomes, such as chrysanthemum (Chrysanthemum sp.), faces challenges including repeated sequences, limited short-reads, and various contigs in massive fragments. Genotyping-by-sequencing (GBS) can overcome many of these drawbacks by high-multiplexing, and potential genotyping-sequencing approaches could have wide-ranging utilizations in chrysanthemum breeding. The study aimed to establish an approach for GBS application and to elucidate a phylogenomic structure in an individual with a large genome. We identified single nucleotide polymorphism (SNP) for SNP calling (279,189 markers) and SNP filtering (7758 markers) that will promote analysis of chrysanthemum population genetics. We conclude that GBS is the best approach for genotyping in chrysanthemum and can be applied in genetic breeding in various plants.

中文翻译：

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基因分型测序分析菊花遗传多样性

将二代测序应用于超大基因组，例如菊花（Chrysanthemum sp.），面临的挑战包括重复序列、有限的短读长和大量片段中的各种重叠群。基因分型测序 (GBS) 可以通过高复用来克服许多这些缺点，潜在的基因分型测序方法可以在菊花育种中得到广泛的应用。该研究旨在建立一种 GBS 应用方法，并阐明具有大基因组的个体的系统发育结构。我们确定了用于 SNP 调用（279,189 个标记）和 SNP 过滤（7758 个标记）的单核苷酸多态性 (SNP)，这将促进菊花种群遗传学的分析。