title: The repetitive landscape of the chicken genome.
abstract: Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, and low-copy fractions of the chicken genome. Sequencing high-copy DNA of chicken to about 2.7 x coverage of its estimated sequence complexity led to the initial identification of several new repeat families, which were then used for a survey of the newly released first draft of the complete chicken genome. The analysis provided insight into the diversity and biology of known repeat structures such as CR1 and CNM, for which only limited sequence data had previously been available. Cot sequence data also resulted in the identification of four novel repeats (Birddawg, Hitchcock, Kronos, and Soprano), two new subfamilies of CR1 repeats, and many elements absent from the chicken genome assembly. Multiple autonomous elements were found for a novel Mariner-like transposon, Galluhop, in addition to nonautonomous deletion derivatives. Phylogenetic analysis of the high-copy repeats CR1, Galluhop, and Birddawg provided insight into two distinct genome dispersion strategies. This study also exemplifies the power of the CBCS method to create representative databases for the repetitive fractions of genomes for which only limited sequence data is available.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wicker
authors.forename: Jon S
authors.initials: JS
authors.lastname: Robertson
authors.forename: Stefan R
authors.initials: SR
authors.lastname: Schulze
authors.forename: F Alex
authors.initials: FA
authors.lastname: Feltus
authors.forename: Vincent
authors.initials: V
authors.lastname: Magrini
authors.forename: Jason A
authors.initials: JA
authors.lastname: Morrison
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.forename: Robert
authors.initials: R
authors.lastname: Ivarie
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D015723:Gene Library; D005822:Genetic Vectors / Q000235:genetics; D016678:Genome; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D018626:Retroelements