@article {16271, title = {Genome-Wide Analysis of Repetitive Elements in Papaya}, journal = {Tropical Plant Biology}, volume = {1}, year = {2008}, month = {2008///}, pages = {191 - 201}, abstract = {Papaya ( Carica papaya L.) is an important fruit crop cultivated in tropical and subtropical regions worldwide. A first draft of its genome sequence has been recently released. Together with Arabidopsis , rice, poplar, grapevine and other genomes in the pipeline, it represents a good opportunity to gain insight into the organization of plant genomes. Here we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes. These repetitive sequences account for \~{}56\% of the papaya genome with TEs being the most abundant at 52\%, tandem repeats at 1.3\% and high copy number genes at 3\%. Most common types of TEs are represented in the papaya genome with retrotransposons being the dominant class, accounting for 40\% of the genome. The most prevalent retrotransposons are Ty3-gypsy (27.8\%) and Ty1-copia (5.5\%). Among the tandem repeats, microsatellites are the most abundant in number, but represent only 0.19\% of the genome. Minisatellites and satellites are less abundant, but represent 0.68\% and 0.43\% of the genome, respectively, due to greater repeat length. Despite an overall smaller gene repertoire in papaya than many other angiosperms, a significant fraction of genes (\>2\%) are present in large gene families with copy number greater than 20. This repeat database clarified a major part of the papaya genome organization and partly explained the lower gene repertoire in papaya than in Arabidopsis .}, isbn = {1935-9756}, url = {http://dx.doi.org/10.1007/s12042-008-9015-0}, author = {Nagarajan,Niranjan and Navajas-P{\'e}rez,Rafael and Pop, Mihai and Alam,Maqsudul and Ming,Ray and Paterson,Andrew and Salzberg,Steven} }