ABSTRACT

Target enrichment is a term that encompasses multiple related approaches where desired genomic regions are captured by molecular baits, leaving behind redundant or non-target regions in the genome, followed by amplification and next-generation sequencing of those captured regions. A molecular bait set was developed based on 426 single-copy, oomycete-specific orthologs and 3 barcoding genes. The bait set was tested on 27 oomycete samples (belonging to the Saprolegniales, Albuginales, and Peronosporales) derived from live and herbarium specimens, as well as control samples of true fungi and plants. Results show that (i) our method greatly enriches for the targeted orthologs on oomycete samples, but insignificantly on fungal and plant samples; (ii) an average of 263 out of 429 orthologs (61%) were recovered from oomycete live and herbarium specimens; (iii) sequencing roughly 100 000 read pairs per sample is sufficient for optimal ortholog recovery while maintaining low sequencing costs; and (iv) the expected relationships were recovered by phylogenetic analysis from the data generated. This is the first report of an oomycete-specific target enrichment method with broad potential applications for evolutionary and taxonomic studies. A key benefit of our target enrichment method is that it allows researchers to easily unlock the vast and unexplored oomycete genomic diversity stored in natural history collections.

摘要

目标富集是一个包含多种相关方法的术语，其中所需的基因组区域被分子诱饵捕获，在基因组中留下冗余或非目标区域，然后对这些捕获区域进行扩增和下一代测序。分子诱饵集是基于 426 个单拷贝、卵菌特异性直系同源物和 3 个条形码基因开发的。对来自活体和植物标本馆的 27 个卵菌目（属于水霉目、白斑目和霜霉目）以及真真菌和植物的对照样品测试了该诱饵组。结果表明（i）我们的方法极大地丰富了卵菌样本上的靶向直向同源物，但对真菌和植物样本的影响不大；(ii) 429 个直向同源物中平均有 263 个 (61%) 从卵菌活体和植物标本中回收；(iii) 每个样本测序大约 100 000 个读取对足以实现最佳直向同源物恢复，同时保持低测序成本；(iv) 通过系统发育分析从生成的数据中恢复了预期的关系。这是卵菌特异性目标富集方法的第一份报告，在进化和分类学研究中具有广泛的潜在应用。我们的目标富集方法的一个关键好处是，它允许研究人员轻松解锁存储在自然历史收藏中的大量未探索的卵菌基因组多样性。这是卵菌特异性目标富集方法的第一份报告，在进化和分类学研究中具有广泛的潜在应用。我们的目标富集方法的一个关键好处是，它允许研究人员轻松解锁存储在自然历史收藏中的大量未探索的卵菌基因组多样性。这是卵菌特异性目标富集方法的第一份报告，在进化和分类学研究中具有广泛的潜在应用。我们的目标富集方法的一个关键好处是，它允许研究人员轻松解锁存储在自然历史收藏中的大量未探索的卵菌基因组多样性。