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Identifikacija potencialnih tarč viroidnih malih RNA (vd-sRNA) v hmelju (Humulus lupulus L.)
ID Pokorn, Tine (Avtor), ID Jakše, Jernej (Mentor) Več o mentorju... Povezava se odpre v novem oknu

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Izvleček
Hmelj (Humulus lupulus L.) spada v družino konopljevk (Cannabaceae). Rastlina je dvodomna, gospodarsko je pomembna le ženska rastlina. Med njegove glavne rastlinske patogene uvrščamo tudi viroide. Poznamo štiri hmeljne viroide: hmeljev latentni viroid (HLVd), viroid zakrnelosti hmelja (HSVd), viroid grbavosti jabolk (AFCVd) in viroid razpokanosti skorje agrumov (CBCVd). V nalogi nas je zanimala interakcija med rastlino in viroidom. S pomočjo NGS tehnologij je že bilo potrjeno, da viroidne male RNA, ki v izjemno velikih količinah nastanejo pri okužbi z viroidoma HLVd ali CBCVd, predstavljajo celoten viroidni genom. S pomočjo NGS tehnologije smo ustvarili hmeljev transkriptom ter in-silico razrezali viroidna zaporedja na vse možne viroidne male RNA, velikosti 21, 22 in 24 bp. Transkriptom in razrezana viroidna zaporedja smo med seboj primerjali z uporabo dveh orodij – psRNATarget in UEA sRNA Workbench, pri čemer smo dobili množico tarč (1387 CBCVd in 1062 HLVd). Tarče smo izbirali po štirih kriterijih: 1) tarče, ki sodelujejo v metabolizmu rastlinskih hormonov, 2) tarče, ki sodelujejo v biogenezi malih RNA, 3) CBCVd tarče vd-sRNA z najvišjo pokritostjo regij viroida, in 4) geni z visoko homolognostjo z vd-sRNA. Izražanje tarčnih genov smo preverili s tehniko reverzne transkripcije in PCR v realnem času (RT-qPCR). Izbrane tarče so kazale spremenjene vzorce ekspresije v različnih tkivih hmelja. S pomočjo HLVd in CBCVd vd-sRNA smo za dva transkripta našli dokaze o morebitni zmanjšani ekspresiji, to sta LOX in GATA. Rezultati bodo lahko utrjevali nove raziskovalne poti v strategijah za boj proti viroidnim boleznim hmelja in drugih rastlin.

Jezik:Slovenski jezik
Ključne besede:rastlinska genetika, viroidi, male RNA, male viroidne RNA, hmelj, tarče, Humulus lupulus, NGS
Vrsta gradiva:Doktorsko delo/naloga
Tipologija:2.08 - Doktorska disertacija
Organizacija:BF - Biotehniška fakulteta
Založnik:[T. Pokorn]
Leto izida:2017
PID:20.500.12556/RUL-97741 Povezava se odpre v novem oknu
UDK:601.4:577.21:633.791:578.52(043.3)
COBISS.SI-ID:8871545 Povezava se odpre v novem oknu
Datum objave v RUL:08.11.2017
Število ogledov:1882
Število prenosov:579
Metapodatki:XML RDF-CHPDL DC-XML DC-RDF
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Sekundarni jezik

Jezik:Angleški jezik
Naslov:Identification of targets for viroid derived small RNAs (vd-sRNA) in hops (Humulus lupulus L.)
Izvleček:
Hop (Humulus lupulus L.) is a dioecious member of the Cannabaceae family, originating in China. Only the female plant is important economically. Our analyses focused on viroids, as important hop pathogens. Hop plant can be infected with four different viroids: hop latent viroid (HLVd), hop stunt viroid (HSVd), apple fruit crinkle viroid (AFCVd) and citrus bark cracking viroid (CBCVd). We focused on the interaction between viroid and plant using two viroids - one that causes mild symptoms (HLVd) and another that causes very serious and strongly expressed symptoms. To analyse the interaction between vd-sRNA and hop transcription, we first assembled the hop transcriptome and in-silico predicted all possible vd-sRNAs (21, 22 and 24 bp) of CBCVd and HLVd. Two tools were used to find hypothetical targets - psRNATarget and UEA sRNA Workbench. We focused our further work on potential targets belonging to one of the following categories 1) targets participate in the metabolism of plant hormones, 2) targets participate in small RNA biogenesis, 3) CBCVd targets of vd-sRNAs from extremely well covered regions of the viroid and 4) Genes with high homology with vd-sRNAs. Changes of target expression were monitored by reverse transcription coupled with quantitative PCR (RT-qPCR). The selected targets showed changed patterns of expression in various tissues of the hops. We found evidence of possible reduced expression for LOX and GATA transcripts. The results obtained in this study will consolidate new research pathways in strategies to combat viroid diseases of hops, as well as other plants.

Ključne besede:plant genetics, viroids, small RNA, viroid derived small RNA, hops, targets, Humulus lupulus, NGS

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