Draft Genome Sequence Resource of AldY-WA1, a Phytoplasma Strain Associated with Alder Yellows of <i>Alnus rubra</i> in Washington, U.S.A.

Cai, Weili; Nunziata, Schyler O.; Srivastava, Subodh; Wilson, Telissa; Chambers, Nathaniel; Rivera, Yazmín; Nakhla, Mark K.; Costanzo, Stefano

doi:10.1094/pdis-10-21-2350-a

Cited by 4 publications

(6 citation statements)

References 17 publications

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“…The occurrence of a wide array of different map genotypes in alder trees in southern Italy further supports data of previous investigations by which a higher diversity of the mentioned genotypes was found in alder trees and O. alni than in grapevine and S. titanus, all sampled in various areas of five European countries [24]. Prior to this work, only one and two ALY strains had been examined at imp and groEL gene sequence level, respectively [9,50]. On the other hand, sequence and phylogenetic analyses of both genes have been widely used to characterize and differentiate strains of 'Ca.…”

Section: Discussionsupporting

confidence: 85%

“…Alder yellows (ALY) is a phytoplasma disease of Alnus species which is known to occur in several European countries (for reviews see [ 4 , 5 ]). It has also been observed in Washington state (USA) and Ontario (Canada) on red alder ( A. rubra ) [ 6 , 7 , 8 , 9 ]. Symptoms of ALY include yellowing, premature autumn coloration, sparse foliage, small leaves, shoot proliferation, stunting, dieback, and decline.…”

Section: Introductionmentioning

confidence: 99%

“…Symptoms of ALY include yellowing, premature autumn coloration, sparse foliage, small leaves, shoot proliferation, stunting, dieback, and decline. Latent infections are also common [ 6 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]. ALY is associated with the ALY phytoplasma, a member of the elm yellows (EY) phytoplasma group or 16SrV group, subgroup 16SrV-C [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

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Occurrence, Impact, and Multilocus Sequence Analysis of Alder Yellows Phytoplasma Infecting Common Alder and Italian Alder in Southern Italy

Marcone,

Pierro,

Palmieri

2024

Microorganisms

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Alder yellows (ALY) phytoplasma (16SrV-C) is associated with ALY, a disease of several Alnus (alder) species in Europe and A. rubra in North America. In all affected species, the symptoms are similar. However, latent infections are common. ALY phytoplasma includes different strains which may be occasionally transmitted to grapevines leading to some grapevine yellows diseases. In the current study, visual symptom assessment and PCR-based methods using universal and group-specific phytoplasma primers were used to update and extend knowledge on the occurrence, impact, and genetic diversity of ALY phytoplasma in declining and non-symptomatic A. glutinosa and A. cordata trees in the Basilicata and Campania regions of southern Italy. ALY phytoplasma was detected in 80% of alder trees examined. In symptomatic trees, no other cause of disease was observed. More than half of alder trees that tested phytoplasma-positive proved to be latently infected. A considerable genetic variability was observed among the newly recorded ALY phytoplasma strains in southern Italy in almost of the genes examined. These included 16S rRNA, 16S/23S rDNA spacer region, ribosomal protein rpsV (rpl22) and rpsC (rps3), map, imp, and groEL genes. Eleven new genotypes were identified at map gene sequence level. However, the genetic differences observed were not related to plant host species, geographical origin, and symptoms shown by infected alder trees. Also, this study indicates that ALY phytoplasma is more widespread than previously thought.

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Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Occurrence, Impact, and Multilocus Sequence Analysis of Alder Yellows Phytoplasma Infecting Common Alder and Italian Alder in Southern Italy

Marcone,

Pierro,

Palmieri

2024

Microorganisms

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“…The first complete genome of phytoplasma (onion yellows phytoplasma mild strain (OY-M) was published in 2004 [ 6 ] (data deposited into GenBank in 2003). So far, 47 phytoplasma genomes (35 draft and 12 complete) have been sequenced involving 13 groups and 29 subgroups ( Figure 2 and Table 1 , [ 6 , 7 , 14 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 ]). The size of the complete ge-nomes ranges from 576 to 960 Kb.…”

Section: Phytoplasma Nomenclature: Delineation Of Candidatu...mentioning

confidence: 99%

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

Wei

Zhao

2022

Biology

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Phytoplasmas are pleomorphic, wall-less intracellular bacteria that can cause devastating diseases in a wide variety of plant species. Rapid diagnosis and precise identification of phytoplasmas responsible for emerging plant diseases are crucial to preventing further spread of the diseases and reducing economic losses. Phytoplasma taxonomy (identification, nomenclature, and classification) has lagged in comparison to culturable bacteria, largely due to lack of axenic phytoplasma culture and consequent inaccessibility of phenotypic characteristics. However, the rapid expansion of molecular techniques and the advent of high throughput genome sequencing have tremendously enhanced the nucleotide sequence-based phytoplasma taxonomy. In this article, the key events and milestones that shaped the current phytoplasma taxonomy are highlighted. In addition, the distinctions and relatedness of two parallel systems of ‘Candidatus phytoplasma’ species/nomenclature system and group/subgroup classification system are clarified. Both systems are indispensable as they serve different purposes. Furthermore, some hot button issues in phytoplasma nomenclature are also discussed, especially those pertinent to the implementation of newly revised guidelines for ‘Candidatus Phytoplasma’ species description. To conclude, the challenges and future perspectives of phytoplasma taxonomy are briefly outlined.

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“…WGS will be performed on patients in both the SoC and intervention arm and provided by the Victorian Genetics Health Service. The sequencing will then be run through several software programmes to confirm the diplotype status including Stargazer, 11 Aldy 12 and Cyrius. 13 Two tools for genotyping pharmacogenes will be used on each sequencing set to develop a consensus call.…”

Section: Methods: Data Collection Management Analysismentioning

confidence: 99%

Minimising Adverse Drug Reactions and Verifying Economic Legitimacy-Pharmacogenomics Implementation in Children (MARVEL- PIC): protocol for a national randomised controlled trial of pharmacogenomics implementation

Conyers,

Halman,

Moore

et al. 2024

BMJ Open

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IntroductionDNA-informed prescribing (termed pharmacogenomics, PGx) is the epitome of personalised medicine. Despite international guidelines existing, its implementation in paediatric oncology remains sparse.Methods and analysisMinimising Adverse Drug Reactions and Verifying Economic Legitimacy-Pharmacogenomics Implementation in Children is a national prospective, multicentre, randomised controlled trial assessing the impact of pre-emptive PGx testing for actionable PGx variants on adverse drug reaction (ADR) incidence in patients with a new cancer diagnosis or proceeding to haematopoetic stem cell transplant. All ADRs will be prospectively collected by surveys completed by parents/patients using the National Cancer Institute Pediatric Patient Reported [Ped-PRO]-Common Terminology Criteria for Adverse Events (CTCAE) (weeks 1, 6 and 12). Pharmacist will assess for causality and severity in semistructured interviews using the CTCAE and Liverpool Causality Assessment Tool. The primary outcome is a reduction in ADRs among patients with actionable PGx variants, where an ADR will be considered as any CTCAE grade 2 and above for non-haematological toxicities and any CTCAE grade 3 and above for haematological toxicities Cost-effectiveness of pre-emptive PGx (secondary outcome) will be compared with standard of care using hospital inpatient and outpatient data along with the validated Childhood Health Utility 9D Instrument. Power and statistics considerations: A sample size of 440 patients (220 per arm) will provide 80% power to detect a 24% relative risk reduction in the primary endpoint of ADRs (two-sided α=5%, 80% vs 61%), allowing for 10% drop-out.Ethics and disseminationThe ethics approval of the trial has been obtained from the Royal Children’s Hospital Ethics Committee (HREC/89083/RCHM-2022). The ethics committee of each participating centres nationally has undertaken an assessment of the protocol and governance submission.Trial registration numberNCT05667766.

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Draft Genome Sequence Resource of AldY-WA1, a Phytoplasma Strain Associated with Alder Yellows of Alnus rubra in Washington, U.S.A.

Cited by 4 publications

References 17 publications

Occurrence, Impact, and Multilocus Sequence Analysis of Alder Yellows Phytoplasma Infecting Common Alder and Italian Alder in Southern Italy

Occurrence, Impact, and Multilocus Sequence Analysis of Alder Yellows Phytoplasma Infecting Common Alder and Italian Alder in Southern Italy

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

Minimising Adverse Drug Reactions and Verifying Economic Legitimacy-Pharmacogenomics Implementation in Children (MARVEL- PIC): protocol for a national randomised controlled trial of pharmacogenomics implementation

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