In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae)

Yi-Fan Chiu,Cheng-Yu Wu,Yu-Cen Wan,Jer-Min Tsai,Yen-Po Lin,Han-Yun Li,Natapot Warrit,Yi-Yen Li,Ren-Chung Cheng,Yong-Chao Su

doi:10.3390/d14030184

Abstract

Reduced-representation sequencing (RRS) has made it possible to identify hundreds to thousands of genetic markers for phylogenomic analysis for the testing of phylogenetic hypotheses in non-model taxa. The use of customized probes to capture genetic markers (i.e., ultraconserved element (UCE) approach) has further boosted the efficiency of collecting genetic markers. Three UCE probe sets pertaining to spiders (Araneae) have been published, including one for the suborder Mesothelae (an early diverged spider group), one for Araneae, and one for Arachnida. In the current study, we developed a probe set specifically for the superfamily Araneoidea in spiders. We then combined the three probe sets for Araneoidea, Araneae, and Arachnid into a fourth probe set. In testing the effectiveness of the 4 probe sets, we used the captured loci of the 15 spider genomes in silico (6 from Araneoidea). The combined probe set outperformed all other probe sets in terms of the number of captured loci. The Araneoidea probe set outperformed the Araneae and Arachnid probe sets in most of the included Araneoidea species. The reconstruction of phylogenomic trees using the loci captured from the four probe sets and the data matrices generated from 50% and 75% occupancies indicated that the node linked to the Stegodyphus + RTA (retrolateral tibial apophysis) clade has unstable nodal supports in the bootstrap values, gCFs, and sCFs. Our results strongly indicate that developing ad hoc probe sets for sub-lineages is important in the cases where the origins of a lineage are ancient (e.g., spiders ~380 MYA).

Highlights

IntroductionHigh-throughput sequencing is widely used for the generation of genomic data in phylogenomic research [1–4]
Using Stegodyphus mimosarum as the base genome in accordance with the methods outlined by Faircloth et al [9], we detected 12,679 probes related to 1374 UCE loci using Argyrodes miniaceus, Latrodectus hesperus, Loxosceles reclusa, Trichonephila clavipes, and
This study suggests that even when dealing with a monophyletic group (e.g., Araneae), an ancient evolutionary origin (e.g., ~380 MYA), the use of a specific probe set to test phylogenetic hypotheses within a sub-lineage could benefit via more lineage-specific loci, and potentially, more captured loci

Summary

Introduction

High-throughput sequencing is widely used for the generation of genomic data in phylogenomic research [1–4]. Reduced-representation sequencing (RRS) methods [5] have made it possible to collect hundreds to thousands of genetic markers at a fraction of the cost of whole-genome sequencing [6]. The ultraconserved elements approach (UCE approach), a form of target DNA sequencing, is becoming prevalent [7–9]. The UCE approach using customized probes makes it possible for researchers to capture thousands of genetic markers from non-model taxa, thereby making it possible to test hypotheses about phylogeny from shallow (e.g., 200 MYA) divergence times [10]

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Discussion

Conclusion