Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
27256582
DOI
10.1016/j.ydbio.2016.05.015
PII: S0012-1606(16)30050-1
Knihovny.cz E-resources
- Keywords
- Amphibian, BAC library, Genomics, Xenopus tropicalis,
- MeSH
- Genomics methods MeSH
- Gene Library * MeSH
- In Situ Hybridization, Fluorescence MeSH
- Liver chemistry MeSH
- Chromosome Mapping MeSH
- Xenopus Proteins genetics MeSH
- Sequence Analysis, DNA MeSH
- Chromosomes, Artificial, Bacterial genetics MeSH
- Xenopus genetics MeSH
- Animals MeSH
- Check Tag
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Xenopus Proteins MeSH
Large insert genomic DNA libraries are useful resources for genomic studies. Although the genome of Xenopus tropicalis stands as the amphibian reference genome because it benefitted from large-scale sequencing studies, physical mapping resources such as BAC libraries are lagging behind. Here we present the construction and characterization of a BAC library that covers the whole X. tropicalis genome. We prepared this BAC library from the genomic DNA of X. tropicalis females of the Adiopodoume strain. We characterized BAC clones by screening for specific loci, by chromosomal localization using FISH and by systematic BAC end sequencing. The median insert size is about 110kbp and the library coverage is around six genome equivalents. We obtained a total of 163,787 BAC end sequences with mate pairs for 77,711 BAC clones. We mapped all BAC end sequences to the reference X. tropicalis genome assembly to enable the identification of BAC clones covering specific loci. Overall, this BAC library resource complements the knowledge of the X. tropicalis genome and should further promote its use as a reference genome for developmental biology studies and amphibian comparative genomics.
CEA Institut de Génomique Genoscope Evry France
Department of Cell Biology Faculty of Science Charles University Prague Prague Czech Republic
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