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Sathees, Kanitha, 2016. Complete genome characterization of barley yellow dwarf virus-OYV. Second cycle, A1E. Uppsala: SLU, Department of Plant Biology (from 140101)



Barley yellow dwarf-associated viruses (BYD-associated viruses) belong to the family Luteoviridae and are of high economical relevance for cultivation of cereals. BYD-associated viruses are phloem-restricted pathogens that cause yellowing and reddening of leaves, plant dwarfing and reduction in size and number of grains. The viruses are transmitted only by aphids and have a genome of single-stranded positive sense RNA (+ssRNA). BYDV-oat yellowing virus (BYDV-OYV) was discovered in Latvia in a study on molecular variability of the coat protein gene (CP gene) of BYD-associated viruses from Latvia and Sweden. The virus was proposed to be a new species within the family Luteoviridae. Recently, BYDV-OYV has also been found in Sweden. In my previous study, a partial genome sequence, which comprised 2,792 nucleotides (nt) of the 3´ end of BYDV-OYV, was determined to investigate the relationship with other isolates of BYD-associated viruses. A phylogenetic analysis with the partial genome sequence of BYDV-OYV and other isolates of family Luteoviridae showed that BYDV-OYV is a new variant within the family Luteoviridae. BYDV-OYV shared higher nucleotide identity with the groups PAV-IIIa and PAV-IIIb than to the groups PAV-I and PAV-II. In the current study, a molecular investigation of BYDV-OYV was carried out by determining also the 5´ part of the genome sequence to explore genome organization, relationship with other viruses of family Luteoviridae, recombination events and taxonomic classification. The total determined sequence contained 5,132 nt and covered an almost complete genome except the un-translated region 1 (UTR1), the 5' end of open reading frame 1 (ORF1) and the 3' end of UTR4. The genome organization of BYDV-OYV is similar to other members of the genus Luteovirus. BYDV-OYV differs enough in sequence from other isolates of the genus Luteovirus to be regarded as a separate species. Overall genome sequence identity was only 72 - 83 % between BYDV-OYV and other viruses of genus Luteovirus. BYDV-PAS-129 (GenBank accession no AY218796) belonging to group PAV-II, had the highest nucleotide identity (83 %). Nucleotide identities of individual ORFs and UTRs showed more complex relationship between BYDV-OYV and other viruses of genus Luteovirus and ranged from 50 - 97%. ORF1, ORF2 and UTR2 are more closely related to those of BYDV-PAS-129, while other regions are more closely related to those of BYDV-PAV-CN and BYDV-PAV isolate 05ZZ1 in group PAV-III. One putative recombination event was detected when the genome sequence of BYDV-OYV was analysed together with 12 other isolates of the genus Luteovirus. The recombinant seem to originate from BYDV-PAS-129 (minor) and BYDV-PAV-CN (major) with the recombinant region starting and ending at nt positions 772 and 1,013, respectively. The genome of BYDV-OYV has thus probably evolved through recombination between ancestors of BYDV-PAS-129 and BYDV-PAV-CN. BYDV-PAS-129 also seems to be a recombinant with a virus related to BYDV-OYV as minor parent. The recombination event in the genome of BYDV-OYV was detected within the ORF1 and ORF2 region, which is a hot spot in the evolution of the family Luteoviridae.

Main title:Complete genome characterization of barley yellow dwarf virus-OYV
Authors:Sathees, Kanitha
Supervisor:Kvarnheden, Anders
Examiner:Meijer, Johan
Series:Examensarbete / Institutionen för växtbiologi, SLU
Volume/Sequential designation:153
Year of Publication:2016
Level and depth descriptor:Second cycle, A1E
Student's programme affiliation:NM008 Plant Biology - Master's Programme 120 HEC
Supervising department:(NL, NJ) > Department of Plant Biology (from 140101)
Keywords:complete nucleotide sequence, genome organization, barley yellow dwarf virus-OYV (BYDV-OYV), Luteovirus, recombination
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Subject. Use of subject categories until 2023-04-30.:Plant diseases
Deposited On:12 Dec 2016 12:55
Metadata Last Modified:12 Dec 2016 12:55

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