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      Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization


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          Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.

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          Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

          High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences ("reads") resulting from a sequencing run are first "mapped" (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software.
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            Target-enrichment strategies for next-generation sequencing.

            We have not yet reached a point at which routine sequencing of large numbers of whole eukaryotic genomes is feasible, and so it is often necessary to select genomic regions of interest and to enrich these regions before sequencing. There are several enrichment approaches, each with unique advantages and disadvantages. Here we describe our experiences with the leading target-enrichment technologies, the optimizations that we have performed and typical results that can be obtained using each. We also provide detailed protocols for each technology so that end users can find the best compromise between sensitivity, specificity and uniformity for their particular project.
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              Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

              Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.

                Author and article information

                Ecol Evol
                Ecol Evol
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                11 June 2019
                June 2019
                : 9
                : 12 ( doiID: 10.1002/ece3.2019.9.issue-12 )
                : 6933-6948
                [ 1 ] Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas
                [ 2 ] Biodiversity Institute University of Kansas Lawrence Kansas
                [ 3 ] Department of Anatomy, School of Biomedical Sciences University of Otago Dunedin New Zealand
                [ 4 ] Department of Integrative Biology Oregon State University Corvallis Oregon
                [ 5 ] Department of Biology University of Rochester Rochester New York
                Author notes
                [*] [* ] Correspondence

                Grey T. Gustafson, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas.

                Email: gtgustafson@ 123456gmail.com

                Author information
                © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                : 08 April 2019
                : 26 April 2019
                : 28 April 2019
                Page count
                Figures: 9, Tables: 1, Pages: 16, Words: 12085
                Funded by: National Institutes of Health
                Award ID: 5K12GM063651
                Original Research
                Original Research
                Custom metadata
                June 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.5 mode:remove_FC converted:10.07.2019

                Evolutionary Biology
                bait design,genomics,phylogenetics,phylogenomics,probe design,ultraconserved elements


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