The Repetitive Content in Lupin Genomes

In this chapter, we present the first detailed evaluation of the repetitive compartment in Lupinus genomes. Low-depth next-generation sequencing (NGS) genomic resources from four closely related smooth-seeded Mediterranean lupin species (L. albus, L. angustifolius, L. luteus, and L. micranthus), exhibiting remarkable differences in genome size and chromosome number have been investigated. The repetitive compartment is composed of a wide diversity of repeats and represents 23-51% of the genomes. This compartment is essentially comprised of transposable elements (43-85%), mainly represented by copia and gypsy LTR retrotransposon families. Among the latter, some prominent families (Tekay, Athila, Maximus-SIRE) significantly contribute to genome size differences among species and in shaping different species-specific repeat profiles, regardless of their chromosome numbers. Also particular lineages of these elements have been differentially and recently amplified within species, such as in L. luteus, L. albus, and L. angustifolius. Moreover, this study highlighted the diversity of tandem repeats in lupin genomes, with minisatellites and satellites mostly being species-specific, whereas microsatellites (SSRs) are ubiquitously distributed. Strikingly, L. angustifolius exhibited a tremendous amount of tandem repeats in its genome (26%), including a noteworthy accumulation of one particular hexamer SSR (15.24% of the genome), which demonstrate that also tandem repeats may greatly contribute to genome obesity and dynamics in lupins. Therefore, differential lineage-specific amplifications of retrotransposons and tandem repeats occurred among lupins. Accordingly, this strongly suggests that different processes and mechanisms regulating amplification, proliferation, and clearance of repeats have differentially operated within the same genus among closely related Mediterranean species over the last similar to 10-12 Myr. Further extension of such evaluation to various representatives of the lupins diversity and outgroups will provide a better overview of the repetitive compartment and its evolutionary dynamics in the genus. Additionally, the genomic resources generated by this work represent a valuable basis to start building a repeats database specifically dedicated to best understand the genomic landscape, repeats distribution, and localization in lupins. This will facilitate further investigations on the functional and evolutionary impact of repeats on genes of interest, such as those responsive for important agronomical, adaptive, and defense features.