Analysis of the genetic diversity of genome sequences of variants of apple hammerhead viroid

Sanderson, Daniel; James, D.

doi:10.1080/07060661.2019.1614672

Cited by 4 publications

(5 citation statements)

References 15 publications

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“…The genome of AHVd variants ranged in size from 434 nt to 440 nt, with clear distinct nucleotides at specific positions as indicated from the secondary structure. The nucleotide variability observed and phylogenetic analysis among the two isolates confirmed intra-isolate variability as observed by other workers [ 30 , 31 ]. The clustering of the identified viruses and viroids with viruses from countries such as Japan, Italy, China and the USA indicates the possible introduction of these viruses from these countries to India via the exchange of planting material either through cultivars or rootstocks.…”

Section: Discussionsupporting

confidence: 89%

“…For RT-PCR, specific primer pairs ( Table S1 ) reported earlier was used to amplify genomic regions corresponding to the coat protein or replicase genes. RT-PCR was performed in a 30-cycle program with denaturation at 94 °C for 30 s, annealing at 50 °C for ApNMV, 53 °C for ApMV [ 35 ], 50 °C for ASGV and 55 °C for ASPV and AHVd for 45 s [ 31 , 37 ], followed by extension at 72 °C for 30 s with a final extension at 72 °C for 7 min. The reagents were the same except the cDNA template and forward and reverse primers of specific viruses/viroids.…”

Section: Methodsmentioning

confidence: 99%

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High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid

Nabi

Rao

Mansoor

et al. 2022

Plants

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Many viruses have been found associated with apple mosaic disease in different parts of the world. In order to reveal and characterize the viruses and viroids in symptomatic apple plants, next-generation sequencing (RNA seq.) of rRNA-depleted total RNA using Illumina Hiseq2500 was applied to two cultivars, Oregon Spur and Golden Delicious, with symptoms of mosaic and necrosis and one cultivar, Red Fuji, which was asymptomatic. The RNA sequencing detected five viruses, viz., apple necrotic mosaic virus (ApNMV), apple mosaic virus (ApMV), apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), and one viroid i.e., apple hammerhead viroid (AHVd). RT-PCR amplification and sequencing also confirmed the presence of all these five viruses and viroids detected in HTS of total RNA. The complete genomes of five viruses and AHVd were reconstructed. The phylogenetic analysis of these viruses and AHVd revealed genetic diversity by forming subclusters with isolates from other countries. Recombination events were observed in all five viruses while single-nucleotide variants were detected only in ApMV and ApNMV. The absence of ApMV and ApNMV in asymptomatic samples from the same cultivars in an RT-PCR assay indicated that these two viruses are associated with mosaic disease of apples in India. This is the first viral genome analysis of symptomatic and asymptomatic apple plants and the first report of genome characterization of viruses associated with apple mosaic disease from India. High-throughput RNA sequencing is a powerful tool to characterize the genome of viruses and viroids in plants previously undetected by conventional methods. This would also help in the indexing and certification of large-scale germplasm.

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Section: Discussionsupporting

confidence: 89%

Section: Methodsmentioning

confidence: 99%

High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid

Nabi

Rao

Mansoor

et al. 2022

Plants

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“…AGCaV, identified from Australia and Canada, was reported in Korea (Cho et al, 2016). AHVd had been reported in the United States, Japan, Italy, Spain, and New Zealand since it had been identified as a new viroid species (Szostek et al, 2018;Chiumenti et al, 2019;Sanderson and James, 2019). ALV-1 and ARWV-1, identified from the United States, were confirmed to be co-infected with more than two other viruses in apple rootstocks in Korea (Lim et al, 2019).…”

Section: Biology Progress After the Discovery Of New Fruit Tree Virusmentioning

confidence: 92%

“…Eight publications focused on genome diversity related to six species: AHVd, CYVCV, BCLCaV, BlMaV, MBV1, and AcV-1. Two publications analyzed the genetic diversity of genome sequences from variants of AHVd (Chiumenti et al, 2019;Sanderson and James, 2019). Genetic stability among CYVCV isolates from different geographic origins were analyzed (Zhen et al, 2015;Chen et al, 2017).…”

Section: Biology Progress After the Discovery Of New Fruit Tree Virusmentioning

confidence: 99%

Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

Hou

Massart

2020

Front. Microbiol.

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High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.

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“…First identified in China in 2014 [ 32 ], AHVd is now globally widespread [ 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. More research is needed to quantify the possible harmful effects of AHVd in apple trees [ 35 , 37 , 38 , 39 , 40 ].…”

Section: Introductionmentioning

confidence: 99%

Thermotherapy Followed by Shoot Tip Cryotherapy Eradicates Latent Viruses and Apple Hammerhead Viroid from In Vitro Apple Rootstocks

Bettoni

Fazio²,

Costa

et al. 2022

Plants

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Virus and viroid-free apple rootstocks are necessary for large-scale nursery propagation of apple (Malus domestica) trees. Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV) are among the most serious apple viruses that are prevalent in most apple growing regions. In addition to these viruses, a new infectious agent named Apple hammerhead viroid (AHVd) has been identified. We investigated whether thermotherapy or cryotherapy alone or a combination of both could effectively eradicate ACLSV, ASGV, and AHVd from in vitro cultures of four apple rootstocks developed in the Cornell-Geneva apple rootstock breeding program (CG 2034, CG 4213, CG 5257, and CG 6006). For thermotherapy treatments, in vitro plants were treated for four weeks at 36 °C (day) and 32 °C (night). Plant vitrification solution 2 (PVS2) and cryotherapy treatments included a shoot tip preculture in 2 M glycerol + 0.8 M sucrose for one day followed by exposure to PVS2 for 60 or 75 min at 22 °C, either without or with liquid nitrogen (LN, cryotherapy) exposure. Combinations of thermotherapy and PVS2/cryotherapy treatments were also performed. Following treatments, shoot tips were warmed, recovered on growth medium, transferred to the greenhouse, grown, placed in dormancy inducing conditions, and then grown again prior to sampling leaves for the presence of viruses and viroids. Overall, thermotherapy combined with cryotherapy treatment resulted in the highest percentage of virus- and viroid-free plants, suggesting great potential for producing virus- and viroid-free planting materials for the apple industry. Furthermore, it could also be a valuable tool to support the global exchange of apple germplasm.

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Analysis of the genetic diversity of genome sequences of variants of apple hammerhead viroid

Cited by 4 publications

References 15 publications

High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid

High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid

Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

Thermotherapy Followed by Shoot Tip Cryotherapy Eradicates Latent Viruses and Apple Hammerhead Viroid from In Vitro Apple Rootstocks

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