Targeted sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Following our recent development of a genome assembly for the Pink Ipê tree (Handroanthus impetiginosus), a widely distributed Neotropical timber species, we now report the development of a set of 24,751 capture probes for single-nucleotide polymorphisms (SNPs) characterization and genotyping across 18,216 distinct loci, sampling more than 10 Mbp of the species genome. This system identifies nearly 200,000 SNPs located inside or in close proximity to almost 14,000 annotated protein-coding genes, generating quality genotypic data in populations spanning wide geographic distances across the species native range. To provide recommendations for future developments of similar systems for highly heterozygous plant genomes we investigated issues such as probe design, sequencing coverage and bioinformatics, including the evaluation of the capture efficiency and a reassessment of the technical reproducibility of the assay for SNPs recall and genotyping precision. Our results highlight the value of a detailed probe screening on a preliminary genome assembly to produce reliable data for downstream genetic studies. This work should inspire and assist the development of similar genomic resources for other orphan crops and forest trees with highly heterozygous genomes.

中文翻译：

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设计和评估用于高度杂合植物基因组的全基因组SNP基因分型的序列捕获系统：以Keystone Neotropical阔叶树基因组为例的案例研究。

靶向序列捕获与高通量测序相结合已成为研究全基因组序列变异的有效方法。继我们最近为广泛分布的新热带木材物种的粉红色Ipê树（Handroanthus impetiginosus）的基因组装配开发之后，我们现在报告开发了一套24,751个捕获探针，用于18,216个单核苷酸多态性（SNP）表征和基因分型独特的基因座，采样了超过10 Mbp的物种基因组。该系统可识别位于大约14,000个带注释的蛋白质编码基因内部或附近的近200,000个SNP，从而在跨越物种本地范围的广泛地理距离的种群中生成高质量的基因型数据。为了为高度杂合的植物基因组的类似系统的未来开发提供建议，我们调查了诸如探针设计，测序覆盖率和生物信息学等问题，包括对捕获效率的评估以及对SNP召回和基因分型精度的测定技术可重复性的重新评估。我们的结果强调了在初步的基因组组装上进行详细探针筛选的价值，以为下游遗传研究提供可靠的数据。这项工作应启发并协助开发其他具有高度杂合基因组的孤儿作物和林木的类似基因组资源。包括对捕获效率的评估以及对SNP召回率和基因分型精度的测定技术可重复性的重新评估。我们的结果强调了在初步的基因组组装上进行详细探针筛选的价值，以为下游遗传研究提供可靠的数据。这项工作应启发并协助开发其他具有高度杂合性基因组的孤儿作物和林木的类似基因组资源。包括对捕获效率的评估以及对SNP召回率和基因分型精度的测定技术可重复性的重新评估。我们的结果强调了在初步的基因组组装上进行详细探针筛选的价值，以为下游遗传研究提供可靠的数据。这项工作应启发并协助开发其他具有高度杂合性基因组的孤儿作物和林木的类似基因组资源。