Complete Genome Sequence of a Novel Recombinant
            <i>Citrus Tristeza Virus</i>
            , a Resistance-Breaking Isolate from Uruguay

Benítez-Galeano, María José; Vallet, Thomas; Carrau, Lucía; Hernández-Rodríguez, Lester; Bertalmío, Ana; Rivas, Fernando; Rubio, Leticia Fernández; Maeso, Diego; Vignuzzi, Marco; Moratorio, Gonzalo; Colina, Rodney

doi:10.1128/genomea.00442-18

Cited by 6 publications

(4 citation statements)

References 10 publications

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“…Both LMS6-6 and HA16-5 in our analysis fall in the HA16-5 clade in both nucleotide and protein trees with firm statistical support (Figures 4, 5). Four sequences are supposedly Poncirus-resistant breaking strains, namely, CA-RB-AT3 from California, United States (Yokomi et al, 2017), L13 from China (Wang et al, 2019), DSST17 from Uruguay (Benitez-Galeano et al, 2018), and B390-5 from South Africa (Cook et al, 2016) and have been classified under RB clade, which, in our analysis with both nucleotide and protein tree, form a strong clade together with HA16-5 and LMS6-6 (Figures 4, 5). The clade HA16-5 also accommodates several isolates from the southern part of India and the north-eastern region, including Assam and Darjeeling, together with at least three isolates from Bhutan (Bhu-Ts-15, Bhu-Wa-62, and Bhu-Ch-87) (Figures 4, 5).…”

Section: Ha16-5 Isolatementioning

confidence: 87%

A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World

Ghosh

Kokane

et al. 2022

Front. Microbiol.

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Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status.

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Section: Ha16-5 Isolatementioning

confidence: 87%

A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World

Ghosh

Kokane

et al. 2022

Front. Microbiol.

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“…The recombination frequency in CaAV-1 showed an inverse correlation with the level of asymmetric divergence in its genome, while such a correlation was not signi cant in CTV. However, new CTV phylogeny lineages generated by recombination, especially of the large fragment in the 3'-half moiety of the genome, have emerged in the long history of CTV evolution [24][25][26]. Moreover, the tree incongruities were only present in the 3'-half portions of the CaAV-1 genomes.…”

Section: Discussionmentioning

confidence: 99%

Viromics Unveils Extraordinary Genetic Diversity of the Family Closteroviridae in Wild Citrus

Liu

Zhang

Mei

et al. 2021

Preprint

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Background Our knowledge of citrus viruses is largely skewed toward virus pathology in cultivated orchards; comparatively little is known about the virus diversity and ecology in natural ecosystems. The metatranscriptomics approach were used to analyze wild citrus from the Ailao Mountain region in China, a region embracing huge biodiversity in an area where citrus species originated. We investigated the evolutionary history of citrus viruses to identify the factors facilitating outbreaks of emerging viruses. Results An independent wild citrus habitat were identified where citrus tristeza virus (CTV) exists along with three novel monopartite, graft-transmissible members of the family Closteroviridae differing from the managed agricultural systems that harbor other diverse citrus viruses. The viruses analyzed in 16 sequencing libraries of 32 citrus samples comprised five CTV genotypes, two inferred new ampelovirus species, and a monopartite ancestor type of the multipartite crinivirus that may represent a new taxon. Acquisition of heat shock protein genes (all viruses) and coat protein duplication (most), exchange of other exogenous genes (some), and alteration of expression strategy (rare) may reflect the significant historical nodes through which a Closteroviridae ancestor as the relic species has flourished. During viral expansion, genetic mutation coupled with recombination may be the essential impetus to update best-adapted sequences, as in the cases of our CTV and one of the ampeloviruses. Conclusions This research represents the first time of virus diversity in wild citrus. The findings deepen our knowledge of Closteroviridae modular evolution and diversification. Given the potential emergence of similar novel viruses as pathogens, the need for surveillance of their pathogenic and epidemiological characteristics and the presence of other novel citrus viruses among wild citrus is of utmost priority for global citrus production.

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“…aurantii , A . craccivora , and Myzus persicae [ 4 – 6 ]. Other spread pathways include graft transmission and plant material infested with aphid vectors [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

“…The CTV is distributed in the world as mild or severe strains. The main mode of transmission of CTV is through multiple aphid vectors including Aphis gossypii, Toxoptera citricida, A. citricola, T. aurantii, A. craccivora, and Myzus persicae [4][5][6]. Other spread pathways include graft transmission and plant material infested with aphid vectors [7].…”

Section: Introductionmentioning

confidence: 99%

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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Complete Genome Sequence of a Novel Recombinant Citrus Tristeza Virus , a Resistance-Breaking Isolate from Uruguay

Abstract: We report here the complete genome sequence of a Citrus tristeza virus (CTV) from Uruguay, sequenced by using Illumina and Sanger sequencing technology. This CTV DSST-17 genome clustered within genotype resistance breaking (RB) and presents two recombination events.

Cited by 6 publications

References 10 publications

A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World

A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World

Viromics Unveils Extraordinary Genetic Diversity of the Family Closteroviridae in Wild Citrus

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

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