The genome of a plant is composed of genes, but also of other elements, such as repetitive fraction. This repetitive component is made up of two types of sequences: transposons and tandem repeat sequences. Though in many cases this part occupies more than half of the plant genome, until recently it was known as the "junk genome" because it was believed to be useless. Now we are looking to identify its function, but to do this we must characterize and study this part, which until now had not been taken into account.
With the aim of clarifying the processes that led to the current structure of the cultivated olive genome, the quantity and composition of this repetitive fraction in the genus Olea and, ultimately, to trace the genealogy of the olive tree, researchers at the María de Maeztu Unit of Excellence - Department of Agronomy (DAUCO) Concepción Muñoz Díez and Carlos Trapero worked with a team at the University of Pisa led by Flavia Mascagni. For this purpose, they carried out an in-depth characterization of the olive repeat fraction in comparison with four other species belonging to the genus Olea, by means of bioinformatics and in situ hybridization analyses.
After quantification and comparison of the composition of the repeating fraction in Olea exasperata (from South Africa), Olea europaea subsp. europaea var. sativa (the cultivated olive tree), Olea europaea subsp. cuspidata, Olea europaea subsp. guanchica (which grows in the Canary Islands) and Olea paniculata (as the most distant taxon, an ancestor of the genus Olea that grows only in Australia) it was determined that in the four most closely related subspecies the repetitive part of the genome occupied about 50% of it, while in the most distant ancestor it occupied 70%.
Regarding the composition of this repetitive fraction, the team found that, while in the four most related Oleas tandem repeat sequences predominated, and not transposons, in Olea paniculata the situation was reversed. "The hypothesis is that there is competition between transposons and tandem repeat sequences, so that the genome somehow regulates this composition by taking into account an inverse relationship between the two groups," explained Concepción Muñoz.
The differences in the repetitive fraction between the four most related subspecies and the most distant species (O. paniculata) suggest that "these changes occurred after the divergence between paniculata and the other species studied", i.e., the increase in tandem repeats that is present in the rest of the Olea studied, but not in paniculata. In this way, the contribution of this hitherto forgotten part of the genome is helping to trace the olive tree'sgenealogical origins.
In addition, 11 major families of tandem repeats were identified in this study, 5 of which were novel discoveries.
Analyzing the genome (now easier thanks to the publication of the first complete genome of the olive tree in 2016, and more affordable techniques) makes it possible to infer genomic evolutionary events that have taken place before or after the splitting of a taxon, and to facilitate the drawing of this plant genus's family map.
This work sheds light on the evolution of the genus Olea and, in addition, highlights the role of the genome's repetitive fraction in its study.
Reference:
Mascagni F, Barghini E, Ceccarelli M, Baldoni L, Trapero C, Díez CM, Natali L, Cavallini A, Giordani T. The Singular Evolution of Olea Genome Structure. Front PlantSci. 2022 Mar 31;13:869048. doi: 10.3389/fpls.2022.869048