In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae)
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) approa...
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MDPI AG
2022-03-01
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| Online Access: | https://www.mdpi.com/1424-2818/14/3/184 |
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| author | Yi-Yen Li Jer-Min Tsai Cheng-Yu Wu Yi-Fan Chiu Han-Yun Li Natapot Warrit Yu-Cen Wan Yen-Po Lin Ren-Chung Cheng Yong-Chao Su |
| author_facet | Yi-Yen Li Jer-Min Tsai Cheng-Yu Wu Yi-Fan Chiu Han-Yun Li Natapot Warrit Yu-Cen Wan Yen-Po Lin Ren-Chung Cheng Yong-Chao Su |
| author_sort | Yi-Yen Li |
| collection | DOAJ |
| description | 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 <i>Stegodyphus</i> + 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). |
| first_indexed | 2024-03-09T19:55:47Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-09T19:55:47Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-2d80432477d9467586a4039ac8429c052023-11-24T00:57:17ZengMDPI AGDiversity1424-28182022-03-0114318410.3390/d14030184In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae)Yi-Yen Li0Jer-Min Tsai1Cheng-Yu Wu2Yi-Fan Chiu3Han-Yun Li4Natapot Warrit5Yu-Cen Wan6Yen-Po Lin7Ren-Chung Cheng8Yong-Chao Su9Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, TaiwanDepartment of Information and Communication, Kun Shan University, Tainan 710, TaiwanDepartment of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, TaiwanDepartment of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, TaiwanDepartment of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, TaiwanCenter of Excellence in Entomology and Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, ThailandDepartment of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, TaiwanDepartment of Life Sciences, National Chung Hsing University, Taichung 40227, TaiwanDepartment of Life Sciences, National Chung Hsing University, Taichung 40227, TaiwanDepartment of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, TaiwanReduced-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 <i>Stegodyphus</i> + 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).https://www.mdpi.com/1424-2818/14/3/184target sequencingreduced representation sequencing (RRS)spider phylogenomicsdeep phylogeny |
| spellingShingle | Yi-Yen Li Jer-Min Tsai Cheng-Yu Wu Yi-Fan Chiu Han-Yun Li Natapot Warrit Yu-Cen Wan Yen-Po Lin Ren-Chung Cheng Yong-Chao Su In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae) Diversity target sequencing reduced representation sequencing (RRS) spider phylogenomics deep phylogeny |
| title | In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae) |
| title_full | In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae) |
| title_fullStr | In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae) |
| title_full_unstemmed | In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae) |
| title_short | In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae) |
| title_sort | in silico assessment of probe capturing strategies and effectiveness in the spider sub lineage araneoidea order araneae |
| topic | target sequencing reduced representation sequencing (RRS) spider phylogenomics deep phylogeny |
| url | https://www.mdpi.com/1424-2818/14/3/184 |
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