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

PAZ ROSALIA CRISTINA; MELISA ELIANA KOZACZEK; HERNÁN GUILLERMO ROSLI; NATALIA PILAR ANDINO; MARÍA VIRGINIA SANCHEZ PUERTA

GENETICA

SPRINGER

Lugar: Berlin; Año: 2017 vol. 145 p. 417 - 430

0016-6707

Transposableelements are the most abundant components of plant genomes and can dramaticallyinduce genetic changes and impact genome evolution. In the recently sequenced genomeof tomato (Solanum lycopersicum), theestimated fraction of elements corresponding to retrotransposons is nearly 62%.Given that tomato is one of the most important vegeTtablecrop cultivated and consumed worldwide, understanding retrotransposon dynamicscan provide insight into its evolution and domestication processes. In this study,we performed a genome-wide in silico searchof full-length LTR retroelements in the tomato nuclear genome and annotated 736full-length Gypsy and Copia retroelements. The dispersion level across the 12chromosomes, the diversity and tissue-specific expression of those elements wereestimated. Phylogenetic analysis based on the retrotranscriptase region revealedthe presence of 12 major lineages of LTR retroelements in the tomato genome. Weidentified 97 families, of which 77 and 20 belong to the superfamilies Copiaand Gypsy, respectively. Each retroelement family was characterized according totheir element size, relative frequencies and insertion time. These analyses representa valuable resource for comparative genomics within the Solanaceae,transposon-tagging and for the design of cultivar-specific molecular markers intomato.