The IGBB is a member of the NIH-funded Mississippi IDeA Network of Biomedical Research Excellence (Mississippi INBRE or MS-INBRE), a program designed to build biomedical infrastructure throughout the state. Through MS-INBRE, Mississippi students and faculty at Mississippi's undergraduate institutions are (1) trained in biomedical research techniques, (2) given the opportunity to work with top researchers at Mississippi's major research universities, (3) afforded access to state-of-the-art bioscience equipment, and (4) provided with assistance in preparing grant proposals. The IGBB serves as the MS-INBRE proteomics/computational biology core. For more information about MS-INBRE, click here.
Dr. Natàlia Garcia-Reyero VinasAdjunct Research Professor
FACULTY
email(601) 634-3764
Vicksburg, MS
The repetitive landscape of the chicken genome
IGBB Authors:
Daniel G. PetersonPUBLICATION YEAR:
2005IMPACT FACTOR:
9.896CITATION COUNT:
145Wicker TM, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH, Ivarie R (2005) The repetitive landscape of the chicken genome.
Genome Research 15: 126-136.
DOI:
10.1101/gr.2438004EID:
2-s2.0-19944432437PMID: 15256510
DOWNLOAD PDFABSTRACTCot-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.
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