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FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales.

التفاصيل البيبلوغرافية
العنوان: FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales.
المؤلفون: Hutter CR; Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA., Cobb KA; Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA., Portik DM; California Academy of Sciences, San Francisco, California, USA., Travers SL; Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA.; Department of Biological Sciences, Rutgers University-Newark, Newark, New Jersey, USA., Wood PL Jr; Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA., Brown RM; Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA.
المصدر: Molecular ecology resources [Mol Ecol Resour] 2022 Apr; Vol. 22 (3), pp. 1100-1119. Date of Electronic Publication: 2021 Oct 12.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Blackwell Country of Publication: England NLM ID: 101465604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1755-0998 (Electronic) Linking ISSN: 1755098X NLM ISO Abbreviation: Mol Ecol Resour Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Oxford, England : Blackwell
مواضيع طبية MeSH: Anura*/genetics , Genetics, Population*, Animals ; Genome ; Genomics ; Phylogeny
مستخلص: Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait  kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.
(© 2021 John Wiley & Sons Ltd.)
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معلومات مُعتمدة: 0907996 National Science Foundation; 1540502 National Science Foundation; 1654388 National Science Foundation; 1451148 National Science Foundation; 1557053 National Science Foundation; K12GM093854 Foundation for the National Institutes of Health; 0743491 National Science Foundation; 1701952 National Science Foundation; 2300207 KU Research Investment Council
فهرسة مساهمة: Keywords: UCEs; amphibians; anura; exon capture; genomics; target capture
تواريخ الأحداث: Date Created: 20210927 Date Completed: 20220308 Latest Revision: 20240628
رمز التحديث: 20240628
DOI: 10.1111/1755-0998.13517
PMID: 34569723
قاعدة البيانات: MEDLINE
الوصف
تدمد:1755-0998
DOI:10.1111/1755-0998.13517