Encapsidation of the host RNAs by broad bean mottle virus (BBMV) and cowpea chlorotic mottle virus (CCMV)

Advisors: Jozef Julian Bujarski.Committee members: Melvin R. Duvall; Gabriel P. Holbrook.Includes bibliographical references.Includes illustrations.Encapsidation of the viral genome into capsid is a highly specific process. Despite the viral RNA specificity, evidence of the host cellular RNA co-encapsidation have been shown in some insect viruses like Flock house virus (FHV) and plant viruses like Cucumber necrotic virus (CNV). This study is dedicated to finding the similar evidence of host RNA encapsidation by the two members, BBMV and CCMV of the Bromovirus family -- model virus system. The Next Generation RNA sequencing (NGS RNA-seq) can be implemented to sequence the RNAs encapsidated by the highly purified virions. We mapped and aligned the reads obtained from sequencing to the viral references to filter out the co-encapsidated non-viral reads. These co-encapsidated non-viral reads are then classified into different categories on the basis of their origin from the host plants. BBMV and CCMV co-encapsidated 1.465% and 1.323% of the host RNAs respectively. Majorities of the host RNAs encapsidated are nuclear including ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs). Among the co-encapsidated plant RNAs, 21.228% and 35.220% reads are from transposable elements (TEs) in BBMV and CCMV respectively, which make these virions a potential carrier for the horizontal gene transfer (HGT) in plants.M.S. (Master of Science