Diversity and distribution of potentially active Copia and Gypsy LTR retroelement families inhabiting the genome of Solanum lycopersicum cv. Heinz.

PAZ, RC; KOZACZEK, ME; ANDINO, NP; SANCHEZ PUERTA, MV

Cataratas del Iguazu

Congreso; XI International Congress of Plant Molecular Biology; 2015

Transposable elements (TEs) are the most abundant component of plant genomes and can dramatically induce genetic changes and genome evolution. In the genome of recently sequenced vegetable tomato (S. lycopersicum), the estimated fraction of TEs corresponding to retrotransposon is nearly 62%. Giving that tomato is the most important vegetable crop grown and consumed worldwide, the comprehension of retrotransposons dynamics and performing can provide answers about their evolution and domestication processes. In this study, we performed a genome-wide LTR retroelement annotation using data mining and bioinformatic strategies to generate a list of 737 complete LTR retroelements in the tomato genome that are potentially active and autonomous. Those retroelements were located along the 12 chromosomes and dispersion level and diversity were estimated. We identified 97 families of LTR retroelements, including 78 and 19 that belong to the superfamilies Copia and Gypsy, respectively. Phylogenetically analysis based on the protein RT was performed reveling the presence of major clades of LTR retroelements. Each family was characterized according their genome sizes and relative frequencies. Also, BLAST searches were made against S. lycopersicum EST database in order to estimate their transcriptional activity. Our retroelement list provides a valuable resource for the S. lycopersicum genome annotation and comparative genomics within Solanaceae, and may be used to discover active LTR retroelements for transposon-tagging in tomato.