Repeat Sequences in the Tomato Genome

Abstract

The sequencing of the tomato genome revealed that, though the moderated size when compared to most of the Solanaceae and other plant species, it comprises more than the 60 % of DNA repeats. This is in contrast with initial estimations assessing that the total genome comprised only about the 10-22 % of repetitive sequences. These preliminary hypotheses were probably biased by the presence of single-copy DNA within the repetitive portion of the genome and by the high sequence divergence of the repeat content. Though the release of the first version of the genome sequences in 2012, the complete view of the repeated regions in tomato at sequence level is still partial, because of difficulties due mainly to DNA repeat sequencing and assembling. However, deeper knowledge on the repeat content of the genome and its distribution was consistently supported by cytogenetics, molecular markers and reassociation kinetics, accompanied by advanced approaches such as Fluorescence In Situ Hybridization (FISH) and more recently Optical Mapping. These techniques helped to clarify many of the principal aspects related to the distribution and the organization of the major repeat classes in tomato, contributing to a consistent overview of this essential part of the genome. The main focus of this chapter is to describe the repeat content of the tomato genome as revealed from the sequencing effort and associated bioinformatics, mainly considering the distribution of highly and moderately repeated DNA sequences. We provide a general overview on plant genome complexity and repeat content, presenting the main repeat categories and their organization. Then we describe the bioinformatics for DNA repeats sequence analysis, focusing on most common approaches for investigations in large genomic sequences, as well as on major repeated sequence collections available to support plant genome annotations. Details on the methods employed to analyze the tomato genome sequences (assembly v. 2.40) published in 2012 will be presented. The description of what is known from tomato concerning the major DNA repeat classes is therefore overviewed highlighting the major results or confirmations obtained thanks to the genome sequencing effort. The discussion is mainly focused on the general description of repeat occurrence in the tomato genome, though questions on the specific role and evolution of these extended regions in tomato and in plant genomes, as well as in other eukaryotes, still remain open.