UCE target enrichment of Uraspis_secunda_AM_I46017 - SRA

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SRX22109017: UCE target enrichment of Uraspis_secunda_AM_I46017
1 ILLUMINA (Illumina HiSeq 4000) run: 505,106 spots, 152.5M bases, 72Mb downloads

Design: We prepared dual-indexed libraries for targeted enrichment using the HyperPrep Kit (KAPA Biosystems, Wilmington, MA) following the manufacturers protocols. We used a probe set targeting 1314 UCE loci informative for phylogenetic analyses of Carangiformes and other acanthomorph fishes across evolutionary time scales. We enriched libraries following protocols for the MYcroarray MYBaits kit v3.02 (Arbor Biosciences, Ann Arbor, MI) with three modifications: 1) we added 100 ng of MYBaits were added to each reaction, 2) we used 500ng custom blocking oligos that included 8 inosines to block the 8 nucleotide index sequences, and 3) we used chicken C0t-1 DNA (Applied Genetics Laboratories, Melbourne, FL) in place of the human C0t-1. We ran the hybridization reaction at 65C for 24 hours. Following hybridization, all pools were bound to streptavidin beads (MyOne C1; Life Technologies) and washed according to a standard target enrichment protocol (Blumenstiel et al. 2010). Samples were re-suspended with 30 L ddH20 while still bound to the streptavidin beads, and we proceeded immediately to PCR recovery of the enriched libraries. The PCR protocol used 15 L of streptavidin bead-bound, enriched library in water with 25 L HiFi HotStart Taq (Kapa Biosystems), 5 L of Illumina TruSeq primer mix (5 M each), and 5 L of ddH2O. We amplified each library using the following thermal profile: 98 C for 45s; 16 cycles of 98 C for 15s, 60 C for 30s, 72 C for 60s; and a final extension of 72 C for 5m. We performed a 1X cleanup of the enriched DNA using Speed Beads and re-hydrated the resulting enriched DNA in 33 L of ddH2O. To remove adapter-dimers <150 bp, we performed a clean-up step using the GeneRead Size selection kit (Qiagen, Inc.) on all enriched libraries, followed by quantification with a Qubit fluorometer. We estimated the size of the enriched pools by running each on an Agilent Bioanalyzer. Enriched libraries were sequenced using 150 base pair paired-end sequencing on an Illumina HiSeq 4000 (Oklahoma Medical Research Foundation Clinical Genomics Center).

Submitted by: University of Alaska Fairbanks

Study: Widespread sympatry in a species-rich clade of marine fishes (Carangoidei)

PRJNA1028788 • SRP466664 • All experiments • All runs

show Abstracthide Abstract

Carangoidei is an ecologically important clade of marine fishes that utilize coral reef and pelagic environments. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a time-calibrated phylogeny of Carangoidei and its parent clade, Carangiformes. With a dataset averaging 958 UCE loci and representing 80% of the known species diversity within Carangoidei, we provide phylogenomic resolution for the relationships within this clade. Our tests of phylogenetic covariance suggest that the evolution of certain morphological and ecological traits has been conserved during carangoid lineage diversification. The prevalence of sympatry coincides with evidence of morphological and environmental niche-partitioning in body size and depth in the water column between sister taxa.

Sample:

SAMN37852365 • SRS19173823 • All experiments • All runs

Organism: Uraspis secunda

Library:

Name: Uraspis_secunda_AM_I46017

Instrument: Illumina HiSeq 4000

Strategy: Targeted-Capture

Source: GENOMIC

Selection: Hybrid Selection

Layout: PAIRED

Runs: 1 run, 505,106 spots, 152.5M bases, 72Mb

Run	# of Spots	# of Bases	Size	Published
SRR26403285	505,106	152.5M	72Mb	2023-10-30

ID:: 30040879

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