Analysis of the repetitive portion of Passifloraceae genomes

Abstract

Passiflora genus comprises a large group of plants popularly known as passion fruits, much appreciated for their exotic flowers and edible fruits. Species (~500) are morphologically variable and adapted to distinct tropical ecosystems. There are ~150 species native to Brazil, of which two are cultivated. Despite their relevance, there are few genomic data available. Our laboratory has been working on Passiflora genetics for more than two decades. Recently, we have generated the first genome of a wild passionflower, P. organensis. In addition, we have described the chloroplast genomes of several species of Passiflora, with representatives of the four subgenera (Astrophea, Decaloba, Deidamioides and Passiflora) and two species of Passifloraceae. These data became available for the identification and study of the repetitive portion of their nuclear genomes, using the RepeatExplorer tool. Preliminary results show the identification of the repetitive portion of the genome of the 22 species. The repetitive portion ranged from 22.2 to 81.7%. The species of the subgenus Decaloba had the smallest portion, and the species of the subgenus Passiflora had the largest one. LTR elements were the most frequent, specifically the Tekay lineage, followed by Angela and Athila. Interestingly, the Angela lineage is not present in Decaloba. Passiflora species are highly variable, with a great variation in genome size. In this study we will investigate in detail all types of repeat classes in a considerable number of species and this will provide a valuable resource for genomic studies on the genus, and support the Passiflora genome evolution investigation. Specifically, in this internship we intend to continue the analysis of the repetitive portions of Passifloraceae genomes, to manually verify the repeat classes identified, perform a comparative analysis between and within each subgenus, characterize the unclassified clusters and the DNA satellite families, and perform a phylogenetic inference based on repeat abundances. Moreover, it will be a great opportunity to learn with the team who had developed the Repeat Explorer tool. Our findings will be a valuable resource for genomic and evolutionary studies of the genus. (AU)