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Virus Integration and Tandem Repeats in the Genomes of Petunia a Thesis

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Virus Integration and Tandem Repeats in the Genomes of Petunia a Thesis Virus integration and tandem repeats in the genomes of Petunia A thesis submitted to the University of Leicester for the degree of Doctor of Philosophy By Osamah Nadhim Kadhim Alisawi M.Sc. January 2019 Department of Genetics and Genome Biology i Abstract 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. i Declaration I hereby declare that no part of this thesis has been previously submitted to this or any other university as part of the requirements for a higher degree. The study described in this thesis, unless otherwise acknowledged in the text or by reference, was conducted by the undersigned who is fully responsible. This work was achieved in the Department of Genetics and Genome Biology, University of Leicester and Julius Kühn-Institut (JKI), Braunschweig, Germany (see Appendix 4.1), during the period from January 2015 to December 2018. Signed:…………………………... Date:……………………………… Osamah Nadhim Kadhim Alisawi ii Dedication Thanks to ALLAH for blessing me much more than I deserve This work is dedicated to the sacred two date palm trees grown on Euphrates river beach, covered me with their fronds, and taken care of me for my entire life, proud of you both my great father and mother Nadhim Kadhim Alisawi and Rabab Waheed Alisawi My lovely, amazing wife Wasan Riyadh Alisawi, who brilliantly supported me to build up this story. Future men, my little boys, Zaid, Yazan and newborn baby Taim. My beloved sisters (Israa and Rawaa) and brothers (Ahmed and Yaseen). I would also send my fulfilment and sincerity to my great grandfather who passed away and left behind a massive heritage for the whole tribe (Al-Isa) and Iraqi community. Al Sheikh Haj Waheed Abood Alisawi (1927-2012) , my respected uncles Dr. Abood Waheed Alisawi and Dr. Riyadh Waheed Alisawi Finally, thanks must go to my homeland where the first ever civilization established IRAQ iii Acknowledgements First and foremost, I would like to express my sincere gratitude and appreciation to my three supervisors Prof. Pat Heslop-Harrison, Dr. Trude Schwarzacher and Dr. Katja Richert- Pöggeler, for their support, guidance, kindness and generosity over the whole time of study. I am indebted to Prof. David Twell and Dr. Richard Gornall for their positive comments and notes. I would also like to acknowledge my thanks to Mr. Ramesh Patel and my colleagues in lab 201 Dr. Sarbast Ihsan Mustafa, Dr. Jotyar Jassim Muhammed, Dr. Rubar M. Salih, Dr. Nouf Fakieh Alsayied and Noorhariza Mohd Zaki. My special thanks go to very gentle members of Dr. Katja Richert-Pöggeler’s lab in Julius Kühn-Institut (JKI), Braunschweig, Germany; Mr. Dirk Schmalowski, Ms. Christina Maaß (Grille) and Ms. Sabine Schuhmann for their assistance and fruitful cooperation. I highly appreciate the full cooperation of Assistant Prof. Aureliano Bombarely, Department of Horticulture, Virginia Tech, USA, who provided me with raw reads and assemblies of Petunia species. I wish to thank my Iraqi friends Dr. Wadhah Mahbooba, Dr. Ghazwan Al Hassan, Dr. Pshtiwan Bebane, Dr. Tariq A. Kareem, Mr. Imad Younis, Mr. Muhammed Abdul Sattar, Mr. Wisam Aziz and Mr. Maitham Al-Jalali for their kind help. I would like to thank my sponsorship; the Iraqi Ministry of Higher Education and Scientific research and my home department; Plant Protection Department, Faculty of Agriculture, University of Kufa for their funding and giving me this great opportunity. Last, and by no means least, I wish to thank all people who have pushed me forward to be in progress all time. iv Contents Abbreviations ....................................................................................................................................... viii Chapter I. Introduction ............................................................................................................................ 1 1.1 The genus Petunia ............................................................................................................................. 1 1.2 The karyotype of petunia chromosomes ....................................................................................... 8 1.3 Repetitive DNA .......................................................................................................................... 10 1.3.1 Types of Repetitive DNA sequences ................................................................................... 11 1.4 Virus definition and taxonomy ................................................................................................... 13 1.5 Transposable elements (TEs) ...................................................................................................... 14 1.5.1 Retrotransposons (Class I elements) .................................................................................... 15 1.5.2 DNA transposons (Class II elements) .................................................................................. 18 1.5.3 Transposable elements in petunia ........................................................................................ 19 1.6 Fluorescence in situ hybridization .............................................................................................. 19 1.7 Bioinformatic techniques ............................................................................................................ 20 1.7.1 Whole genome sequencing data ........................................................................................... 20 1.7.2 k-mer counting ..................................................................................................................... 21 1.7.3 Graph-based clustering of raw read sequences .................................................................... 22 1.8 Aims and objectives .................................................................................................................... 25 Chapter II. Materials and methods ........................................................................................................ 26 2.1 Plant material and cultivation ..................................................................................................... 26 2.2 Standard solutions and media ..................................................................................................... 27 2.3 Methods....................................................................................................................................... 31 2.3.1 Genomic DNA extraction .................................................................................................... 31 2.3.2 DNA quantification .............................................................................................................. 32 2.3.3 PCR amplification ................................................................................................................ 32 2.3.4 Purification of DNA fragments from agarose gel ................................................................ 33 2.3.5 Cloning of PCR products ..................................................................................................... 33 2.3.6 Probe labelling ..................................................................................................................... 37 2.3.7 Petunia chromosome preparations ....................................................................................... 37 2.3.8 Fluorescent in situ hybridization .........................................................................................
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