Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum

PAZ, ROSALÍA CRISTINA; KOZACZEK, MELISA ELIANA; ROSLI, HERNÁN GUILLERMO; ANDINO, NATALIA PILAR; SANCHEZ-PUERTA, MARIA VIRGINIA

GENETICA

SPRINGER

Lugar: Berlin; Año: 2017

0016-6707

Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersi- cum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and con- sumed worldwide, understanding retrotransposon dynam- ics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for compara- tive genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.