scholarly journals Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate ncRNAs

2015 ◽  
Vol 7 (3) ◽  
pp. 689-698 ◽  
Author(s):  
Andrew D. Kern ◽  
Daniel A. Barbash ◽  
Joshua Chang Mell ◽  
Daniel Hupalo ◽  
Amanda Jensen
Keyword(s):  
Ultraconserved Elements ◽  
Candidate Ncrnas

The phylogeny of robber flies (Asilidae) inferred from ultraconserved elements

2021 ◽  
Author(s):  
Chris M. Cohen ◽  
Katherine Noble ◽  
T. Jeffrey Cole ◽  
Michael S. Brewer
Keyword(s):  
Ultraconserved Elements ◽  
Robber Flies

scholarly journals Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

2015 ◽  
Vol 92 ◽  
pp. 140-146 ◽  
Author(s):  
Princess S. Gilbert ◽  
Jonathan Chang ◽  
Calvin Pan ◽  
Eric M. Sobel ◽  
Janet S. Sinsheimer ◽  
...  
Keyword(s):  
Gene Markers ◽  
Ultraconserved Elements ◽  
Genome Wide ◽  
Phylogenetic Informativeness

P41 Transcribed ultraconserved elements expression in tumour cell lines

2009 ◽  
Vol 7 (4) ◽  
pp. 34-35
Author(s):  
M. Blanco ◽  
M. Haz ◽  
M. Reboredo ◽  
V. Medina ◽  
I. Santamarina ◽  
...  
Keyword(s):  
Cell Lines ◽  
Tumour Cell ◽  
Ultraconserved Elements ◽  
Tumour Cell Lines

scholarly journals UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

2021 ◽  
Vol 9 ◽  
Author(s):  
Caio Ribeiro ◽  
Lucas Oliveira ◽  
Romina Batista ◽  
Marcos De Sousa
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Phylogenetic Trees ◽  
Computational Analysis ◽  
Data Matrix ◽  
Command Line ◽  
Command Line Interface ◽  
Ultraconserved Elements ◽  
Research Software ◽  
Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

scholarly journals More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

2012 ◽  
Vol 8 (5) ◽  
pp. 783-786 ◽  
Author(s):  
Nicholas G. Crawford ◽  
Brant C. Faircloth ◽  
John E. McCormack ◽  
Robb T. Brumfield ◽  
Kevin Winker ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Common Ancestor ◽  
Sister Group ◽  
Single Copy ◽  
Recent Analysis ◽  
Phylogenetic Position ◽  
Ultraconserved Elements ◽  
Sequence Capture ◽  
Genomic Scale ◽  
Nuclear Loci

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To test this hypothesis with data from many single-copy nuclear loci dispersed throughout the genome, we used sequence capture, high-throughput sequencing and published genomes to obtain sequences from 1145 ultraconserved elements (UCEs) and their variable flanking DNA. The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.

scholarly journals Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

2018 ◽  
Author(s):  
Tobias Andermann ◽  
Alexandre M. Fernandes ◽  
Urban Olsson ◽  
Mats Töpel ◽  
Bernard Pfeil ◽  
...  
Keyword(s):  
Ultraconserved Elements
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