Genome-Wide Analysis of Repetitive Elements in Papaya
Title | Genome-Wide Analysis of Repetitive Elements in Papaya |
Publication Type | Journal Articles |
Year of Publication | 2008 |
Authors | Nagarajan N, Navajas-Pérez R, Pop M, Alam M, Ming R, Paterson A, Salzberg S |
Journal | Tropical Plant Biology |
Volume | 1 |
Issue | 3 |
Pagination | 191 - 201 |
Date Published | 2008/// |
ISBN Number | 1935-9756 |
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 . |
URL | http://dx.doi.org/10.1007/s12042-008-9015-0 |