Characterisation of chromosome derived circular DNA elements from blood and muscle tissue of pigeon.

Extrachromosomal circular DNA elements (eccDNAs) of chromosomal origin are known to be common in a number of eukaryotic species. However, it remains to be addressed whether genomic features such as genome size, load of repetitive elements within the genome and/or animal physiology affects the number of eccDNAs. Here we use the pigeon Columba livia as a model to investigate the genomic distribution and abundance of eccDNAs in a condensed genome. By sequencing the eccDNA in blood and breast muscle from three pigeon breeds at various ages and with different flight behavior, we characterize thirty thousand unique eccDNAs. Comparison between pigeon and human eccDNA from skeletal muscle reveals higher numbers of unique eccDNAs per human nucleus. The fraction of eccDNA sequences, derived from repetitive elements, exist in proportions similar to genome content, i.e. human 72.4% (expected 52.5%) and pigeon 8.7% (expected 5.5%). In humans, SINEs, simple repeats and satellites are overrepresented by ~2-fold and repeats from tRNA and rRNA are ~5-fold enriched. In pigeons, coding regions (exons and genes) are overrepresented and repeats of LINEs and LTRs are ~2-fold enriched. We identify genomic regions that are potential hotspots for DNA circularization in breast muscle, including genes involved in muscle development. We find the biological age of pigeons does not correlate with eccDNA counts while the number of unique eccDNAs in a non-flying breed (King pigeons) is significantly higher (9-fold) than two other breeds. Our results suggest that eccDNA counts correlate with the content of repetitive elements in a genome and the sum of unique eccDNA types per nucleus can differ between species as well as subspecies.