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Title: To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

This repository contains Materials and designed UCE probe sets for the manuscript entitled "To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design".

 
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Award ID(s):
1942193
NSF-PAR ID:
10493726
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
Zenodo
Date Published:
Subject(s) / Keyword(s):
["phylogenomics, Coleoptera, UCE, probe set"]
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    Abstract

    Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design.

     
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    Thionitrous acid (HSNO), the smallest S‐nitrosothiol, is emerging as a potential key intermediate in cellular redox regulation linking two signaling molecules H2S and NO. However, the chemical biology of HSNO remains poorly understood. A major hurdle is the lack of methods for selective detection of HSNO in biological systems. Herein, we report the rational design, synthesis, and evaluation of the first fluorescent probe TAP‐1 for HSNO detection. TAP‐1 showed high selectivity and sensitivity to HSNO in aqueous media and cells, providing a useful tool for understanding the functions of HSNO in biology.

     
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