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× 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.

High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes

“…All copies of CR1 (chicken LINE) interspersed within non-tandemly organised centromeric Cen5, CenZ and Cen27 sequences were found to be 5′-truncated and thus devoid of active promoters. Such distribution of CR1 interspersed repeat is in correspondence with modern data on distribution and functional activity of LINE class repeats in chicken genome, which contains around 26,000 copies of the CR1 element with the vast majority of copies being inactive (ICGSC 2004;Wicker et al 2005;Lee et al 2009). …”

Transposable elements as drivers of genomic and biological diversity in vertebrates

“…Taken together, these observations suggest a massive reduction of diversity of retrotransposable elements in the tetrapod lineage, possibly before the split of mammals and birds 300 million years ago. Subsequently, the L1 and L2 families might have been eliminated in the chicken lineage after divergence from mammals (Wicker et al 2005). Extinction of families of transposable elements can also occur within major vertebrate lineages.…”

“…However, differences well correlated with variations in haploid genome size are observed between mammals: the genome of the short-tailed opossum contains more transposable elements (52% of the genome) than the genome of primates (45Y50%), mouse and rat (39Y40%) and dog (34%) (Gentles et al 2007 and references therein). In birds, the small genome of the domestic chicken (about 40% of the human genome) contains only 10% of mobile DNA (Wicker et al 2005). In fish, the genome of the medaka (about 25% of the human genome), contains 7% transposable elements (Kasahara et al 2007).…”

“…Another family with lineagedependent success is L3/CR1. In chicken, this family with 96 000 copies represents the major group of transposable elements (74% in copy number), covering 3.1% of the genome (Wicker et al 2005). L3/CR1 elements have been less successful in the larger genome of placental mammals (8000 copies in mouse for 0.05% of the genome and 37 000 copies in human for 0.31% of the genome) and in fish (Volff et al 2003), but are well represented in opossum (317 000 copies for 2% of the genome; Gentles et al 2007).…”

Isolation and characterization of sixty sequences of cot-1 DNA from the Asiatic black bear, Ursus thibetanus

“…Combining the established principles of DNA reassociation kinetics with high-throughput sequencing also known as Cot-based cloning and sequencing (Peterson et al, 2002), is a powerful tool for isolating and characterizing the various repetitive components of any genome. This technique has been used to describe the repetitive DNA sequences in Panax ginseng (Ho and Leung, 2002) as well as the repetitive landscape of the chicken genome (Wicker et al, 2005). Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms.…”