High‐throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short‐read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked‐read or “synthetic long‐read” sequencing technologies, such as 10× Genomics, may provide a cost‐effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four new deer mouse (Peromyscus spp.) genomes assembled using linked‐read technology and four published genomes assembled from a single shotgun library. At a similar price‐point, these approaches produce vastly different assemblies, with linked‐read assemblies having overall higher contiguity and completeness, measured by larger N50 values and greater number of genes assembled, respectively. As a proof‐of‐concept, we used annotated genes from the four Peromyscus linked‐read assemblies and eight additional rodent taxa to generate a phylogeny, which reconstructed the expected relationships among species with 100% support. Although not without caveats, our results suggest that linked‐read sequencing approaches are a viable option to build de novo genomes from degraded tissues, which may prove particularly valuable for taxa that are extinct, rare or difficult to collect.

中文翻译：

---

音乐组学的链接阅读方法：来自降解组织的更高质量的从头基因组组装。

高通量测序技术是一种用于访问历史样本中分子数据的提议解决方案。但是，降解的DNA与短读装配的计算要求相结合，对从头基因组装配提出了重大的实验室和生物信息学挑战。链接阅读或“合成长阅读”测序技术（例如10x基因组学）可能提供一种经济高效的替代解决方案，以从降解的组织样品中组装更高质量的从头基因组。在这里，我们比较了四只新的鹿鼠（Peromyscus）之间的装配质量（例如，基因组连续性和完整性，正交群的存在）spp。）基因组是使用链接阅读技术组装的，而四个已发布基因组则是从一个shot弹枪文库中组装的。在类似的价格点上，这些方法产生的装配完全不同，链接读取的装配具有更高的连续性和完整性，分别通过更大的N50值和更大数量的已装配基因来衡量。作为概念验证，我们使用了来自四个Peromyscus的带注释的基因链接阅读的程序集和另外八个啮齿类动物分类以产生系统发育，在100％支持下重建了物种之间的预期关系。尽管并非没有警告，但我们的结果表明，连锁阅读测序方法是从降解组织构建从头构建基因组的可行选择，这对于灭绝，稀有或难于收集的分类群可能特别有价值。