Au Family Short Retroposons Contribute to Transcriptional and Phenotypic Diversity in Tomato (Solanaceae)

Abstract

Here we report the current gene impact of the Au family of SINEs in tomato. The genome of Solanum lycopersicum ‘Heinz 1706’ SL3.0 -NCBI annotation release 103- was reference searched and the Au profile was characterized in-depth. Tomato genome comprises ca. 670 Au copies, of entire length-18.5%- or truncated, randomly inserted and eroded, forming three well supported (>80%) super clusters which disperse along the 12 chromosomes mirroring the subtelomeric gene distribution bias of the species. In tomato, the Au clade is largely localized at protein coding genes-69.5% introns, 7.8% 3UTRs, 2.1% 5UTRs, 1.2% CDSs- followed by genomic copies-18.3%-, long non coding RNA genes-1.4%- and pseudogenes-0.8%-. The 419 tomato genes harboring intronic Au are diverse, weakly associated considering biological processes and molecular functions, but include important traits such as stress response, hormone response or phenotype plasticity. Au was found to be transcribed inside circular RNAs derived from 12 genic loci. Exonic Au affect the transcriptional and/or translational profiles of 67 tomato genes, including biological/agronomical important ones, contributing to UTR length and composition, UTR transcript variants, CDS boundary definitions, protein domains and variants. We propose that biased survival of Au in tomato genes is an adaptive feature.