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SRX8936961: UCE target enrichment of Nuncia_sp_MCZ:IZ:152213
1 ILLUMINA (Illumina HiSeq 2500) run: 4.9M spots, 1.5G bases, 488.1Mb downloads

Design: Libraries were prepared using the KAPA Hyper Prep Kit (Kapa Biosystems), using up to 250 ng DNA (i.e., half reaction of manufacturers protocol) as starting material. After end-repair and A-tailing, 5 M universal adapter stubs (University of Georgia, EHS DNA Lab) were ligated onto libraries. Libraries were then amplified in a 50 l reaction, which consisted of 15 l adapter- ligated DNA, 1X HiFi HotStart ReadyMix, and 0.5 M of each Illumina TruSeq dual- indexed primer (i5 and i7) with modified 8-bp indexes. Amplification conditions were 98 C for 45 s, then 16 cycles of 98 C for 15 s, 60 C for 30 s, and 72 C for 60 s, followed by a final extension of 72 C for 60 s. Samples were quantified to ensure amplification success. Equimolar amounts of libraries were combined into 1000 ng pools consisting of eight samples each. Target enrichment was performed on pooled libraries using the MYbaits Arachnida 1.1K version 1 kit following the Target Enrichment of Il- lumina Libraries v. 1.5 protocol (http://ultraconserved.org/#protocols). Hybridization was conducted at 65 C for 24 hours, then libraries were bound to streptavidin beads and washed. Following hybridization, pools were amplified in a 50 l reaction consisting of 15 l of hybridized pools, 1X Kapa HiFi HotStart ReadyMix, 0.25 M of each of TruSeq forward and reverse primers, and 5 l dH20. Amplification conditions consisted of 98 C for 45 s, then 16 cycles of 98 C for 15 s, 60 C for 30 s, and 72 C for 60 s, followed by a final extension of 72 C for 5 minutes. Following an additional cleanup, libraries were quantified using a Qubit fluorometer. Molarity was determined with an Agilent 2100 Bioanalyzer and equimolar mixes were prepared for sequencing.
Submitted by: Harvard University
Study: Phylogenomic reevaluation of Triaenonychoidea (Opiliones: Laniatores), and systematics of Triaenonychidae, including new families, genera, and species.
show Abstracthide Abstract
The Opiliones superfamily Triaenonychoidea currently includes two families, the monogeneric New Zealand-endemic Synthetonychiidae Forster, 1954 and Triaenonychidae Sorensen, 1886, a diverse family distributed mostly throughout the temperate Gondwanan terranes, with 110 genera and around 440 species currently described. Traditionally, Triaenonychidae has been divided into subfamilies diagnosed by very few morphological characters largely derived from the troublesome Roewerian system of morphology, and classifications based on this system led to many complications. Recent research within Triaenonychoidea using morphology and traditional multi-locus data has shown multiple deeply divergent lineages, non-monophyly of Triaenonychidae, and non-monophyly of subfamilies, necessitating a revision based on phylogenomic data. We used sequence capture of ultraconserved elements across 164 samples to create a 50 percent taxon occupancy matrix with 704 loci. Using phylogenomic and morphological examinations, we explored family level relationships within Triaenonychoidea including describing two new families, genera, and species. With our dataset we also explored phylogenomic relationships within Triaenonychidae with an extensive taxon set including samples representing about 80 percent of the genus-level diversity. Based on our results we discuss systematics of this family including the historical use of subfamilies, reassessment of morphology in context of our phylogeny, hypothesized placement for all unsampled genera, highlight lineages most in need of taxonomic revision, and provide an updated species level checklist. Aside from describing new taxa, our study provides the phylogenomic context necessary for future evolutionary and systematic research across this diverse lineage.
Sample:
SAMN15673370 • SRS7193210 • All experiments • All runs
Library:
Name: Nuncia_sp_MCZ:IZ:152213
Instrument: Illumina HiSeq 2500
Strategy: Targeted-Capture
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 4.9M spots, 1.5G bases, 488.1Mb
Run# of Spots# of BasesSizePublished
SRR124424294,941,7011.5G488.1Mb2021-12-01

ID:
11617978

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