Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

The Repetitive Landscape Of The Chicken Genome Analyzed Via Cot Based Cloning And Sequencing Of Repetitive DNA Fractions

Robert Ivarie¹ , Thomas Wicker² , Jon S. Robertson² , Stefan R. Schulze² , F. Alex Feltus² , Vincent Magrini³ , Jason A. Morrison³ , Elaine R. Mardis³ , Richard K. Wilson³ , Daniel G. Peterson⁴ , Andrew H. Paterson^1,2

¹  Department of Genetics, University of Georgia, Athens, Georgia 30602, USA

²  Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA

³  Genome Sequencing Center, Washington University Medical Center, Washington University, St. Louis, Missouri 63108, USA

⁴  Mississippi Genome Exploration Laboratory, Dept. of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA

Gene filtering methods have been developed typically for removing repetitive and foldback DNA fractions from genomic DNA to enrich for low copy or gene sequences. However, we used Cot-based cloning and sequencing (CBCS) to isolate and characterize repetitive elements of the chicken genome via DNA reassociation kinetics and high-throughput sequencing prior to the release of the first draft of the chicken genome. A "mini-genome" of 24.7 Mbp comprised mostly of availabe chicken BAC sequences was constructed to retrieve repetitive elements from known genomic sequence. The high-copy DNA of chicken was sequenced to ~2.7x coverage of its estimated sequence complexity and led to the identification of several new repeat families which were then used for a detailed survey of the released first draft of the chicken genome. The analysis not only provided significantly more information of known repeat structures (e.g., CR1 and CNM) but also identified 4 novel repeats (Birddawg, Hitchcock, Kronos, and Soprano) as well as new subfamilies of CR1 repeats. A single CR1 element was found encoding an intact reverse transcriptase which may explain why this LINE element is so prevalent in the chicken genome. A novel Mariner-like transposon, Galluhop, and its non-autonomous deletion derivatives were found in relatively high copy number but none encoded an intact transposase. Distinct dispersion strategies in the chicken genome were found from phylogenetic analysis of the high-copy repeats CR1, Galluhop and Birddawg. CBCS provides an important tool to analyze repetitive DNA elements in genomes not targeted for sequencing. This work was supported in large part by an NSF Partnership for Innovation grant to Andrew Paterson and Robert Ivarie.