Genetic Diversity and Phylogenetic Analysis of<i> Citrus tristeza virus</i> Isolates from Turkey

Erkiş-Güngör, Gözde; Çevik, Bayram

doi:10.1155/2019/7163747

Cited by 4 publications

(2 citation statements)

References 32 publications

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“…The positions of SNVs in the coding regions of CTV annotated ORFs were in the polyprotein ORF (13 SNVs), P33 ORF (1 SNV) and P18 ORF (1 SNV) ( Table 2 ). The CP genes were the most conserved and represented the same SNVs reported by previous studies [ 24 ]. Most SNVs in polyprotein were on papain-like proteins and four SNVs were observed in replication protein.…”

Section: Resultssupporting

confidence: 62%

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Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran

et al. 2023

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Citrus tristeza virus (CTV) is one of the economically destructive viruses affecting citrus trees worldwide, causing significant losses in fruit production. Comparative genomic studies have shown genetic diversity in various regions of the genome of CTV isolates, which has classified the virus into several genotypes. In recent years, some orange citrumelo-tolerant rootstocks showed yellowing, decline, and vein clearing in northern Iran (Mazandaran province, Sari). We confirmed the presence of CTV in the symptomatic trees by reverse transcription PCR (RT-PCR). The complete genome of a Sari isolate of CTV (Sari isolate) was sequenced using next-generation sequencing (NGS) technology. In addition, phylogenetic analysis, differential gene expression of the virus and identification of its variants in a population were studied. We obtained the final contigs of the virus (nt) and annotated all genomes to viral ORFs, untranslated regions (UTRs), intergenic regions, and 5’ and 3’ ends of the genome. Phylogenetic analysis of the Sari isolate and other genotypes of CTV showed that the Sari isolates were placed in a distinct cluster without a sister group. Based on the number of specific transcripts (TPM) in CTV RNA -Seq, P13 was the most highly expressed gene related to the host range of the virus and its systemic infection. The ORFs of the polyprotein, P33, and P18 showed variation in a single population of the sari isolate. The CTV has a potential for variation in a population in a host, and these variations may contribute to the best fit of the CTV in different situations. In Iran, whole genome sequencing of the CTV was performed for the first time, and we gained new insights into CTV variation in a population.

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Section: Resultssupporting

confidence: 62%

“…previous studies [24]. Most SNVs in polyprotein were on papain-like proteins and four SNVs were observed in replication protein.…”

Section: Plos Onementioning

confidence: 57%

Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran

et al. 2023

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Effects of graft and aphid transmission on the genetic diversity and population structure of Turkish citrus tristeza virus isolates

et al. 2021

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Variability of P26 and P10 genes in Colombian isolates of Potato yellow vein virus (PYVV)

Calderón¹,

Mosquera²,

Vargas³

2019

Agron. colomb.

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Potato yellow vein virus (PYVV) is the causal agent of the potato yellow vein disease and can reduce potato production up to 50%. This virus also infects tomatoes and can remain asymptomatic in plants. PYVV transmission is mediated by vegetative seed, the vector Trialeurodes vaporariorum, and grafts. Its genome has the P26 and P10 genes that are orthologues in the Crinivirus genus, which have been characterized as pathogenic factors and have not been studied in PYVV. We analyzed the variability of P26 and P10 from 45 and 48 sequences, which were obtained by RT-PCR amplification of the total RNA of symptomatic potato leaves from the provinces of Nariño, Cundinamarca, and Boyaca (Colombia). We included sequences of each gene of the PYVV genome of potato and tomato isolates from GenBank. The variability in these genes is influenced by the flow and uncontrolled use of vegetative seed between different provinces, that favor the dispersion of viral variants. In addition, the variability analysis based on maximum likelihood trees, haplotypes, and diversity indices showed that P26 is more variable than P10 and both are more variable in Andigena than in Phureja potatoes. The Tajima and Fu and Li tests revealedthat these genes are subject to negative selection.

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Genetic Diversity and Phylogenetic Analysis of Citrus tristeza virus Isolates from Turkey

Cited by 4 publications

References 32 publications

Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran

Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran

Effects of graft and aphid transmission on the genetic diversity and population structure of Turkish citrus tristeza virus isolates

Variability of P26 and P10 genes in Colombian isolates of Potato yellow vein virus (PYVV)

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