Virus integration and tandem repeats in the genomes of Petunia
thesisposted on 14.02.2019, 09:48 by Osamah N. K. Alisawi
The integration of endogenous pararetroviruses (EPRVs) and tandemly repeated sequences were examined in whole genome raw reads, and two genome assemblies, in diploid Petunia species including hybrid-derivatives and their ancestors, using bioinformatics, molecular biology, cytogenetics and microscopy. Three types of EPRV clusters (petuvirus-, florendovirus- and caulimovirus-like sequences) were found. Chromosomal signals of PVCV (Petunia vein clearing virus) were seen by in situ hybridization in all Petunia species. Fragmented parts of four novel florendovirus-like sequences were found and the complete sequence was reconstructed, adding petunia to the 27 known host species. Chromosome III of P. axillaris and P. hybrida Rdc showed strong pericentromeric signal of PVCV and Florendovirus suggesting both EPRVs have similar positions, integration patterns and endogenization events (unlike P. integrifolia subsp inflata and P. axillaris subsp parodii). The caulimovirus-like sequence cluster was less abundant in genomes, with four novel members. RNA analysis from infected and healthy petunia samples revealed expression of endogenous PVCV and Caulimovirus sequences, unlike Florendovirus (not detected in RNA). The episomal form of vertically transmitted PVCV was integrated near the telomere of heterologous chromosomes. Transmission electron microscopy (TEM) showed differences in number and size of PVCV particles and inclusion bodies for both chlorotic spots and vein clearing symptoms, the latter correlated with PVCV particles in cytoplasm from vascular bundle cells. In plants with chlorotic symptoms, infected cells contained virions in parenchyma cells, while scattered virions were seen in chlorotic spots in P. hybrida W138 after heat induction of symptoms. Eight unique types of tandem repeat clusters were analysed within Petunia raw reads with variable genome proportions and different loci on mitotic chromosomes. Three were useful markers for chromosome identification. Taken together, the work shows the contribution of repetitive DNA to diversity and variation within petunia genomes, and has consequences for evolution, and both resistance and spread of some viruses.