Covering all bases: a universal Metazoan UCE probe set to democratize phylogenomics.

IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
Shahan Derkarabetian, Arianna Lord, Katherine Angier, Julia G Cosgrove, Ella Frigyik, Sara González-Delgado, Breanna Jordan, Paula C Rodríguez-Flores, Shoyo Sato, Lily Shapiro, Gonzalo Giribet
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引用次数: 0

Abstract

Biology is in a genomics era, but many researchers may still be alienated from these techniques as a lack of genomic resources remain for many animal groups, necessitating further democratization. Hybrid capture is a popular phylogenomic approach in molecular systematics, with ultraconserved elements (UCEs) being the most popular. However, access to UCE data is more expensive per sample relative to other commonly used genetic/genomic approaches. Using published genomes, we developed a Metazoan UCE probe set, the universality of which allows multiple research groups working on vastly different animal lineages to share costs and resources across labs. We demonstrated the utility of this probe set both in silico against 58 published metazoan genomes and in vitro with 130 samples representing 33 metazoan phyla, showing that these probes target loci useful for both deep and shallow level relationships. The proportion of target UCEs sequenced by the Metazoa probe is equivalent to that of taxon-specific probe sets, but from across all animal phyla. We explored general patterns of UCE recovery across Metazoa using published genomes and the majority of publicly available UCE probe sets. The Metazoa probe set is commercially available in two forms: the full set, containing 19,986 probes targeting 2146 loci; and the reduced cost set, containing 5098 probes targeting 466 loci. The development of a universal UCE probe set should expand the use of genomic data to a much larger segment of the zoological community, with strong potential for broad applications in phylogenomics across all animal phyla.

覆盖所有的基础:一个通用的Metazoan UCE探针设置民主化系统基因组学。
生物学正处于基因组学时代,但由于许多动物群体缺乏基因组资源,许多研究人员可能仍然与这些技术疏远,这需要进一步的民主化。混合捕获是分子系统学中一种流行的系统基因组学方法,其中超保守元件(UCEs)最为流行。然而,与其他常用的遗传/基因组方法相比,获取UCE数据的每个样本成本更高。利用已发表的基因组,我们开发了一套Metazoan UCE探针集,它的通用性允许多个研究小组在实验室中研究截然不同的动物谱系,共享成本和资源。我们证明了该探针集在计算机上对58个已发表的后生动物基因组和代表33个后生动物门的130个样本的体外效用,表明这些探针针对的位点对深层和浅层关系都有用。Metazoa探针测序的目标UCEs的比例与分类群特异性探针集的比例相当,但来自所有动物门。我们使用已发表的基因组和大多数公开可用的UCE探针集探索了跨后生动物的UCE恢复的一般模式。mettazoa探针集在商业上有两种形式:全套,包含19,986个探针,靶向2146个位点;而缩减后的成本集包含5098个探针,目标为466个位点。通用UCE探针集的开发应该将基因组数据的使用扩展到动物群落的更大部分,在所有动物门的系统基因组学中具有广泛应用的强大潜力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genome Biology and Evolution
Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY
CiteScore
5.80
自引率
6.10%
发文量
169
审稿时长
1 months
期刊介绍: About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.
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