A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues
A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues
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DOI：
10.1111/1755-0998.13155
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发表时间：
2020-05-11
影响因子：
7.7
通讯作者：
MacManes, Matthew D.
中科院分区：
文献类型：
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作者：
Colella, Jocelyn P.;Tigano, Anna;MacManes, Matthew D.
高通量测序技术是获取历史标本分子数据的一种解决方案。然而，降解的DNA与短读组装的计算需求相结合，对从头基因组组装提出了重大的实验室和生物信息学挑战。链接读取或“合成长读取”测序技术，如10x Genomics，可能提供一种具有成本效益的替代解决方案，从降解的组织样本中组装更高质量的从头基因组。在这里，我们比较了使用链接阅读技术组装的四个鹿鼠（Peromyscus spp.）新基因组与从单个猎枪库组装的四个已发表基因组之间的组装质量（例如，基因组的连续性和完整性，正群的存在）。在相似的价格点上，这些方法产生了截然不同的组装，链接阅读组装具有更高的整体连续性和完整性，分别由较大的N50值和更多的基因组装数量来衡量。作为概念验证，我们使用来自4个Peromyscus链读组合和8个额外的啮齿动物分类群的注释基因来生成系统发育，以100%的支持重建物种之间的预期关系。虽然并非没有警告，但我们的结果表明，链接读取测序方法是从降解组织中构建从头基因组的可行选择，这可能对灭绝，稀有或难以收集的分类群特别有价值。
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 10x 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.