Evolutionary history of endogenous viral elements (EVEs) in Citrus species and their putative involvement in genome structure and functions

Repeated sequences, such as transposable elements (TEs) and endogenous viral elements (EVEs), are ubiquitous components of plant genomes.
They sometimes accumulate in large copy numbers and can influence the structure and expression of host genomes.
Therefore, they are considered important drivers of plant genome evolution and species diversification.
EVEs are viral genomic sequences that became integrated into the genome of their host upon viral infection.
In vascular plants, most EVEs belong to the Caulimoviridae family and are termed endogenous caulimovirids (ECVs). ECVs appear to be highly repetitive in some plant genomes.
However, despite their abundance, their involvement in evolutionary processes remains unclear.
New high-quality genome sequences were recently assembled for C. micrantha, C. reticulata, C. medica, and C. maxima, the ancestors of cultivated Citrus species.
Taking advantage of these new genome sequences, we carried out a comprehensive annotation of repeated sequences.
Our results showed that more than half of the analysed Citrus genomes are composed of repeated sequences (42-47% TEs, 3-5% ECVs, 0.50-2% satellite DNA and 4-5% simple sequence repeats). The highest ECV copy numbers were found in the C. medica and C. maxima genome assemblies.
Satellite DNA sequences were concentrated in telomeric regions, whereas TEs and ECVs were preferentially localized in centromeric and pericentromeric regions.

XV International Citrus Congress

D. Giraud, N. Choisne, S. Sidibe-Bocs, H. Vassilieff, G. Costantino, G. Droc, P.Y. Teycheney, F. Maumus, P. Ollitrault, F. Luro

citrus, transposable elements, endogenous caulimovirids, satellite DNA, genome annotation

https://doi.org/10.17660/ActaHortic.2026.1448.7