Identifikacija čekićastog viroida jabuke u retrospektivnoj studiji ekstrakata ukupnih nukleinskih kiselina iz jabuka

undergraduate thesis

• Title (english): Apple hammerhead viroid identification in retrospective analysis of total nucleic acids extracts from apples
• Author: Jana Matijević
• Mentor: Dijana Škorić (mentor)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2023-07-17, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Čekićasti viroid jabuke (eng. apple hammerhead viroid, AHVd) pripada porodici Avsunviroidae i
rodu Pelamoviroid. Primarno inficira jabuke (Malus domestica Borkh.), no njegova prisutnost je
potvrđena i u nešpuli (Eriobotrya japonica (Thunb.) Lindl.). Cilj rada bio je potvrditi prisutnost
AHVd-a u prethodno istraživanim izolatima kultivara jabuka na području Hrvatske. Analizirano je
15 prethodno istraživanih izolata jabuka i tri izolata pripremljena za potrebe ovog rada. Iz
ekstrakata ukupnih nukleinskih kiselina jabuka metodom reverzne transkripcije i lančane reakcije
polimeraze (RT-PCR) uz primjenu početnica specifičnih za AHVd u elektroforetskom agaroznom
gelu detektirana je prisutnost viroidnih amplikona u čak sedam uzoraka. Iz šest uzorka dobivene
su konsenzus-sekvence parcijalnog AHVd-genoma. Viroid je pronađen u raznim sortama jabuka
na različitim lokacijama, a njegova prisutnost u izolatima jabuka potvrđena je Sangerovim
sekvenciranjem i filogenetskom analizom, te usporedbom sekundarnih struktura viroidnih genoma.
Većina hrvatskih AHVd-varijanti se na filogenetskom stablu grupirala zajedno zbog blizine
lokacija jabuka iz kojih su prikupljani uzorci, dok su se dva uzorka izdvojila i grupirala sa
sekvencama iz drugih država. Zbog blizine uzgojne lokacije jabuke Mađarskoj jedan je uzorak
AHVd u skupini s uzorcima iz Mađarske i Češke, dok je drugi uzorak grupiran s kanadskim
uzorcima vjerojatno zbog uvoznog porijekla te sorte jabuke.

Abstract (english)

Apple hammerhead viroid (AHVd) belongs to the family Avsunviroidae and the genus
Pelamoviroid. It primarily infects apples (Malus domestica Borkh.). This research was conducted
in order to confirm the presence of AHVd in the previously investigated isolates of apple cultivars
in Croatia. In the scope of this study, 15 previously researched apple isolates and three samples
isolated for the purpose of this work were analyzed. The presence of viroid amplicons in
electrophoresis gels was detected in seven total nucleic acids extracts from apple after reverse
transcription and polymerase chain reaction (RT-PCR) with primers specific for AHVd. Six
consensus sequences of the partial AHVd genome were obtained. The viroid was found in various
apple varieties in different locations and its presence was confirmed by phylogenetic analysis of
Sanger sequences and the comparison of secondary structures. Most of the Croatian samples were
grouped together on the phylogenetic tree due to the proximity of the apple cultivation sites, while
two samples grouped with sequences from other countries. One isolate of AHVd from apple
growing near the Hungarian border grouped with samples from Hungary and the Czech Republic,
whereas the other was grouped with Canadian samples probably due to the origin of the apple
variety that was most likely imported.

• Keywords: AHVd; Hrvatska; Pelamoviroid; prvi nalazi
• Keywords (english): AHVd; Croatia; Pelamoviroid; first report
• Language: croatian
• URN:NBN: urn:nbn:hr:217:186179
• Study programme: Title: Ecology; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/prvostupnica (baccalaureus/baccalaurea) biologije (sveučilišni/a prvostupnik/prvostupnica (baccalaureus/baccalaurea) biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Embargoed access; Embargo expiration date: 2024-07-17
• Created on: 2023-07-24 09:16:45