To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design
To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design
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DOI：
10.1093/isd/ixad014
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发表时间：
2023-07-01
影响因子：
3.4
通讯作者：
Gunter，Nicole L.
中科院分区：
文献类型：
--
作者：
Gustafson，Grey T.;Glynn，Rachel D.;Gunter，Nicole L.
已经证明，针对焦点分类群定制超保守元件（UCE）探针组设计可以改善基因座恢复和重复基因组推断。然而，除了进行昂贵的体外测试之外，目前还不清楚如何最好地确定现有的UCE探针组是否可能足以进行基因组推断，或者是否需要定制的探针设计。在这里，我们研究了8种不同的UCE探针集的金龟子的硅微生物学基因组推断的效用。测试的探针组在以下方面不同：（i）在探针设计过程中使用的探针组与金龟总科分类群的亲缘关系如何，（ii）探针组设计的系统发育推断的宽度，以及（iii）探针设计的方法。作为这项研究的一部分，2个新的UCE探针集的甲虫家庭金龟子和超家庭Hydrophiloidea。我们证实，探针组的效用随着与目标分类群的系统发育距离的增加而降低。此外，缩小探针设计的系统发育宽度降低了系统发育捕获范围。我们还证实了以前的研究结果，优化UCE探头设计的方法。最后，我们提出了建议，评估需要从头探头设计。
Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design.