Molecular characterization of Coleus blumei viroids from coleus (Solenostemon scutellarioides (L.) Codd)

master's thesis

• Title: Molekularna karakterizacija Coleus blumei viroida iz ukrasne koprive (Solenostemon scutellarioides (L.) Codd)
• Author: Karlo Jezernik
• Mentor: Dijana Škorić (mentor)
• Committee member: Dijana Škorić (predsjednik povjerenstva)
• Committee member: Željka Vidaković-Cifrek (član povjerenstva)
• Committee member: Maja Matulić (član povjerenstva)
• Committee member: Antun Alegro (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2014-10-24, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Viroidi su patogeni jednostavniji od virusa. Do sada su pronađeni jedino u biljkama gdje se mogu replicirati bez vidljivih štetnih posljedica po biljku ili mogu uzrokovati simptome slične virusnima. Njihov genom se sastoji od male (246-401 nt), nekodirajuće, jednolančane kovalentno zatvorene molekule RNA. Za rasprostranjivanje ne trebaju viruse pomagače i imaju mogućnost autonomne replikacije što ih čini najmanjim poznatim RNA-replikonima. Ukrasna kopriva (Solenostemon scutellarioides (L.) Codd) domaćin je viroidima roda Coleviroid koji dijele središnju očuvanu regiju (Central Conserved Region, CCR) i pripadaju porodici Pospiviroidae. Cilj mog rada bio je istražiti prisutnost viroida roda Coleviroid u odabranim uzorcima ukrasnih kopriva i identificirati pronađene viroidne vrste. Iz listova tri kultivara biljaka S. scutellarioides ekstrahirana je ukupna RNA. Na njoj je provedena reverzna transkripcija i lančana reakcija polimeraze (RT-PCR) s univerzalnim početnicama za rod Coleviroid dizajniranima prema središnjoj očuvanoj regiji. Amplikoni približnih veličina 250 i 360 baznih parova su klonirani i analizirani metodom SSCP (Single-strand Conformation Polymorphism). Najreprezentativniji produkti su sekvencirani i bioinformatički analizirani. Nukleotidni sljedovi su otkrili prisutnost CbVd-1 i CbVd-3 po prvi puta u Hrvatskoj.

Abstract (english)

Viroids are pathogens simpler than viruses found only in plants where they can replicate without adverse effects or can cause virus-like symptoms. Viroid genome comprises one small (246-401 nt), non-coding, single stranded covalently closed RNA molecule. Viroids do not depend on helper viruses for spreading and have autonomous replication which makes them the smallest known RNA-replicons. Solenostemon scutellarioides (L.) Codd hosts several viroids from genus Coleviroid that have common Central Conserved Region (CCR) and are members of the familiy Pospiviroidae. The aim of this work was to investigate the occurrence of Coleviroids in selected S. scutellarioides plants and to identify detected viroid species. Total RNA was extracted from leaf samples of three S. scutellarioides cultivars and subjected to reverse transcription and polymerase chain reaction (RT-PCR) with the use of universal primers designed specifically for Coleviroid CCR. Amplicons of about 250 and 360 base pairs were cloned and analyzed with SSCP (Single-strand Conformation Polymorphism) method. The most representative products were sequenced. Obtained sequences were analyzed and revealed the presence of two Coleviroides, namely, CbVd-1 and CbVd-3, for the first time in Croatia.

• Keywords: Coleviroid; CbVd-1; CbVd-3; ukrasna kopriva; RT-PCR; SSCP
• Keywords (english): Coleviroid; CbVd-1; CbVd-3; RT-PCR; SSCP
• Language: croatian
• URN:NBN: urn:nbn:hr:217:198849
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-04-26 09:45:17