Identification of Endophytic Microbiota of Phytoplasma-Infected Russian Olive Trees “Elaeagnus angustifolia L.” in the Northwest of Iran

Azizpour, Nadia; Nematollahi, Sevil; Khakvar, Reza; Jamshidi, Manizheh; Norouzi‐Beirami, Mohammad Hossein

doi:10.3390/f13101684

Cited by 3 publications

(5 citation statements)

References 23 publications

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“…The previously full genome of 'Ca. Phytoplasma asterisʼ was obtained as the causal agent of Russian olive witches'-broom disease in Iran [15]. However, in this research, in addition to 'Ca.…”

Section: Genomic Characterization Of Three Distinct Phytoplasma Speciesmentioning

confidence: 80%

“…In previous studies, the 'Ca. Phytoplasma asteris' was characterized as the causal agent of Russian olive witches 'broom disease in Iran [3,15]. However, MetaPhlAn2 analysis suggested that, in addition to 'Ca.…”

Section: Genomic Characterization Of Phytoplasmas With Russian Olive ...mentioning

confidence: 99%

“…Phytoplasma asteris' was recognized, associated with the infected trees [3], and then the genome of Iranian 'Ca. Phytoplasma asteris' was obtained using NGS analysis [15].…”

Section: Russian Olive Witches'-broom Disease Importance In the North...mentioning

confidence: 99%

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Characterization of ‘Ca. Phytoplasma asteris’, ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma mali’ Associated with Russian Olive Witches’-Broom Disease in Iran Using Next-Generation Sequencing

Zirak,

Khakvar

2023

OBM Genet

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Russian olive trees showing witches’-broom disease symptoms in urban green spaces and orchards in northwest Iran were sampled for phytoplasma detection. PCR assays and Sanger sequencing of 16S rRNA gene confirmed that ‘Ca. Phytoplasma asteris’ was associated with Russian olive witches’-broom disease. For genomic characterization of phytoplasma associated with disease, the total DNA of an infected tree was analyzed by Illumina next-generation sequencing (NGS). The NGS analysis generated 46011389 read pairs of raw data with about 6.8 × 109 bp sequences and 31% GC content. Then, MetaPhlAn2 analysis of NGS raw data predicted three phytoplasma species inside the infected Russian olive tree DNA. Finally, the genomes of ‘Ca. Phytoplasma asteris’ with 833199 bp length, ‘Ca. Phytoplasma australiense’ with 762261 bp length and ‘Ca. Phytoplasma mali’ with 518942 bp length were obtained from NGS raw data. This study represents the first report of ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma mali’ association with Russian olive witches’-broom disease using NGS analyses worldwide.

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Section: Genomic Characterization Of Three Distinct Phytoplasma Speciesmentioning

confidence: 80%

Section: Genomic Characterization Of Phytoplasmas With Russian Olive ...mentioning

confidence: 99%

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Characterization of ‘Ca. Phytoplasma asteris’, ‘Ca. Phytoplasma australiense’ and ‘Ca. Phytoplasma mali’ Associated with Russian Olive Witches’-Broom Disease in Iran Using Next-Generation Sequencing

Zirak,

Khakvar

2023

OBM Genet

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“…To predict bacterial genomes and profile the composition of microbial communities, the MetaPhlAn2 pipeline version 2.6.6.17 was applied to the raw data. 17 , 18 …”

Section: Methodsmentioning

confidence: 99%

“…To predict bacterial genomes and profile the composition of microbial communities, the MetaPhlAn2 pipeline version 2.6.6.17 was applied to the raw data. 17,18 To assemble bacterial genomes, the raw data were mapped to the reference genomes that had been previously deposited in GenBank, using Bowtie2 software version 2.5.0. The mapped reads were then assembled by metaSPAdes software version 3.15.4.…”

Section: Next-generation Sequencing Analysesmentioning

confidence: 99%

Genomic Characterization of Endosymbiotic Bacteria Associated With Helicoverpa armigera in Iran Using Next-Generation Sequencing

Sheibani,

Jamshidi,

Khakvar

et al. 2023

Bioinform Biol Insights

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Several species of the Helicoverpa genus have been recognized as major agricultural pests from different regions of the world, among which Helicoverpa armigera species has been reported as the most destructive and cosmopolitan species in most regions of the world, including Iran. This pest is a polyphagous species and can cause damage to more than 120 plant species. Studying the internal microbiome of pests is very important in identifying species’ weaknesses and natural enemies and potential biological control agents. For genomic characterization of the microbial community associated with H armigera, the whole genome of insect larvae collected from vegetable fields in the northwest of Iran was sequenced using next-generation sequencing Illumina platform. Finally, about 2 GB of raw data were obtained. Using the MetaPhlAn2 pipeline, it was predicted that 2 endosymbiont bacterial species including Buchnera aphidicola and Serratia symbiotica were associated with H armigera. Alignment of reference strains sequences related to both endosymbiotic bacteria with raw data and subsequently, assembly analyses resulted in 2 genomes with 657 623 bp length with GC content of 27.4% for B aphidicola and 1 595 135 bp length with GC content of 42.90% for S symbiotica. This research is the first report on the association of B aphidicola and S symbiotica as endosymbiotic bacteria with H armigera worldwide.

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Status of Cassava Witches’ Broom Disease in the Philippines and Identification of Potential Pathogens by Metagenomic Analysis

Landicho,

Montañez,

Camagna

et al. 2024

Biology

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Cassava witches’ broom disease (CWBD) is one of the most devastating diseases of cassava (Manihot esculenta Crantz), and it threatens global production of the crop. In 2017, a phytoplasma, Candidatus Phytoplasma luffae (Ca. P. luffae), was reported in the Philippines, and it has been considered as the causal agent, despite unknown etiology and transmission of CWBD. In this study, the nationwide occurrence of CWBD was assessed, and detection of CWBD’s pathogen was attempted using polymerase chain reaction (PCR) and next-generation sequencing (NGS) techniques. The results showed that CWBD has spread and become severe, exhibiting symptoms such as small leaf proliferation, shortened internodes, and vascular necrosis. PCR analysis revealed a low phytoplasma detection rate, possibly due to low titer, uneven distribution, or absence in the CWBD-symptomatic cassava. In addition, NGS techniques confirm the PCR results, revealing the absence or extremely low phytoplasma read counts, but a surprisingly high abundance of fastidious and xylem-limited fungus, Ceratobasidium sp. in CWBD-symptomatic plants. These findings cast doubt over the involvement of phytoplasma in CWBD and instead highlight the potential association of Ceratobasidium sp., strongly supporting the recent findings in mainland Southeast Asia. Further investigations are needed to verify the etiology of CWBD and identify infection mechanisms of Ceratobasidium sp. to develop effective diagnostic and control methods for disease management.

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Identification of Endophytic Microbiota of Phytoplasma-Infected Russian Olive Trees “Elaeagnus angustifolia L.” in the Northwest of Iran

Cited by 3 publications

References 23 publications

Characterization of ‘<em>Ca</em>. Phytoplasma asteris’, ‘<em>Ca</em>. Phytoplasma australiense’ and ‘<em>Ca</em>. Phytoplasma mali’ Associated with Russian Olive Witches’-Broom Disease in Iran Using Next-Generation Sequencing

Characterization of ‘<em>Ca</em>. Phytoplasma asteris’, ‘<em>Ca</em>. Phytoplasma australiense’ and ‘<em>Ca</em>. Phytoplasma mali’ Associated with Russian Olive Witches’-Broom Disease in Iran Using Next-Generation Sequencing

Genomic Characterization of Endosymbiotic Bacteria Associated With Helicoverpa armigera in Iran Using Next-Generation Sequencing

Status of Cassava Witches’ Broom Disease in the Philippines and Identification of Potential Pathogens by Metagenomic Analysis

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