Spider-specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae)
Spider-specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae)
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DOI：
10.1111/1755-0998.13099
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发表时间：
2019-10-28
影响因子：
7.7
通讯作者：
Hormiga, Gustavo
中科院分区：
文献类型：
--
作者：
Kulkarni, Siddharth;Wood, Hannah;Hormiga, Gustavo
系统基因组学方法已被证明可用于解决蜘蛛生命树中的深层节点和顽固性群体。在蛛形纲动物中，转录组学方法可以产生数千个基因座，而使用先前设计的蛛形纲动物特异性探针集的靶标捕获方法最多可以靶向约1000个基因座。在这里，我们为蜘蛛开发了一个专门的目标捕获探针集，其中包含超过2000个超保守元素（UCEs），然后通过测序和系统发育分析证明了该探针集的实用性。我们利用三种蜘蛛基因组（Loxosceles， Parasteatoda和Stegodyphus）设计了“蜘蛛特异性”探针集，并确保新设计的探针集包含先前设计的Arachnida探针集的UCEs。新的“蜘蛛特异性”探针用于对51个标本的UCE位点进行测序。剩余样本包括5个蜘蛛基因组和分类群，这些基因组和分类群使用Arachnida探针集进行富集。“蜘蛛特异性”探针还用于收集蜘蛛目共84个代表性分类群的基因座。在将这84个类群与蛛形纲探针集进行定位时，我们最多捕获了710个UCE位点，而蜘蛛特异性探针集从同一类群样本中捕获了1547个UCE位点。使用最大似然和聚结方法的系统发育分析证实了最近转录组学分析解决的大多数节点，但不是全部（例如UCE数据表明“symphytognathoids”是单一的）。我们基于拓扑学测试的首选假设表明，“联齿纲”（微型圆球织工）是单一的，而在以前的研究中，这一假设只得到形态和行为特征的结合的支持。
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target-capture methods, using the previously designed arachnid-specific probe set, can target a maximum of about 1,000 loci. Here, we develop a specialized target-capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the 'spider-specific' probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe set includes UCEs from the previously designed Arachnida probe set. The new 'spider-specific' probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The 'spider-specific' probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider-specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using maximum likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g. UCE data suggest monophyly of 'symphytognathoids'). Our preferred hypothesis based on topology tests, suggests monophyly of the 'symphytognathoids' (the miniature orb weavers), which in previous studies has only been supported by a combination of morphological and behavioural characters.