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Ali, Ayesha, 2021. Mechanisms of biogenesis of novel RNA species associated with viral infections. Second cycle, A2E. Uppsala: SLU, Department of Plant Biology (from 140101)


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Abstract

Sugar beet is an important crop and covers 20 % of the global production of sucrose. The crop is damaged by many pathogens and, especially, by viruses including beet necrotic yellow vein virus (BNYVV) and beet soil-borne mosaic virus (BSBMV). BSBMV and BNYVV are closely related, and sequence analysis revealed the presence of a 20-nucleotide-long ‘coremin’ region in RNA3 (of BSBMV and BNYVV), RNA4 (of BSBMV) and RNA5 (of BNYVV). Previously, an attempt to amplify full-length cDNA of BSBMV RNA2 genomic segment generated two additional PCR products, which upon sequencing appeared to represent RNA recombination products. Here, we studied the accumulation of these novel RNA species associated with BSBMV infection and how the 20-nt ‘coremin’ region and the secondary structure of BSBMV RNA affect accumulation of the novel RNAs if silent mutations are introduced into BSBMV full-length clones to disrupt these structures. Nicotiana benthamiana plants were agroinfiltrated with the corresponding BSBMV mutants and accumulation of viral RNA2 and the novel RNAs was quantified by RT-qPCR. The levels of novel BSBMV RNAs were significantly reduced or being undetectable in plants systemically infected with those constructs suggesting that the coremin region and the secondary structure of BSBMV RNA2 are required for the formation of the novel RNAs upon BSBMV infection. Additionally, we showed that chimeric RNAs did not accumulate in N. benthamiana plants silenced for a ribonuclease responsible for production of shorter versions of RNA3 and RNA4. Altogether, the data support our hypothesis that biogenesis of the novel RNAs associated with BSBMV infection depends on RNA2 secondary structure and “kissing RNAs”.

Main title:Mechanisms of biogenesis of novel RNA species associated with viral infections
Authors:Ali, Ayesha
Supervisor:Savenkov, Eugene
Examiner:Kvarnheden, Anders
Series:Examensarbete / Institutionen för växtbiologi, SLU
Volume/Sequential designation:188
Year of Publication:2021
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:SM006 Plant Biology for Sustainable Production - Master's programme, 120.0hp
Supervising department:(NL, NJ) > Department of Plant Biology (from 140101)
Keywords:BSBMV, BNYVV, Coremin, Non-coding RNAs, Exoribonuclease, VIGS
URN:NBN:urn:nbn:se:slu:epsilon-s-17363
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-17363
Subjects:Plant diseases
Language:English
Deposited On:11 Nov 2021 11:45
Metadata Last Modified:12 Nov 2021 02:00

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