Multilocus sequence typing reveals two distinct populations of “Candidatus Phytoplasma sacchari” in China

Zhang, Rongyue; Wang, Xiaoyan; Shan, Hongli; Li, Jie; Li, Yinhu; Li, Wenfeng; He, Xin; Huang, Ying-Kun

doi:10.1007/s40858-023-00562-z

Cited by 5 publications

(6 citation statements)

References 30 publications

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“…Recently, multilocus sequence typing revealed that SCGS and SCWL phytoplasma isolates belonged to different populations of “ Ca . Phytoplasma sacchari,” but the classification was made without any genomic-level evidence (Abeysinghe et al, 2016 ; Zhang et al, 2023 ). In this study, we analyzed the phylogenetic relationships between isolates SCGS and SCWL at the genomic level and found that the ANI and dDDH values between their genomes were higher than the threshold values for taxon assignment of “ Ca .…”

Section: Discussionmentioning

confidence: 99%

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Complete genome sequence of “Candidatus Phytoplasma sacchari” obtained using a filter-based DNA enrichment method and Nanopore sequencing

Zhang,

Wang,

et al. 2023

Front. Microbiol.

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Phytoplasmas are phloem-limited plant pathogens, such as sugarcane white leaf (SCWL) phytoplasma, which are responsible for heavy economic losses to the sugarcane industry. Characterization of phytoplasmas has been limited because they cannot be cultured in vitro. However, with the advent of genome sequencing, different aspects of phytoplasmas are being investigated. In this study, we developed a DNA enrichment method for sugarcane white leaf (SCWL) phytoplasma, evaluated the effect of DNA enrichment via Illumina sequencing technologies, and utilized Illumina and Nanopore sequencing technologies to obtain the complete genome sequence of the “Candidatus Phytoplasma sacchari” isolate SCWL1 that is associated with sugarcane white leaf in China. Illumina sequencing analysis elucidated that only 1.21% of the sequencing reads from total leaf DNA were mapped to the SCWL1 genome, whereas 40.97% of the sequencing reads from the enriched DNA were mapped to the SCWL1 genome. The genome of isolate SCWL1 consists of a 538,951 bp and 2976 bp long circular chromosome and plasmid, respectively. We identified 459 protein-encoding genes, 2 complete 5S-23S-16S rRNA gene operons, 27 tRNA genes, and an incomplete potential mobile unit (PMU) in the circular chromosome. Phylogenetic analyses and average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values based on the sequenced genome revealed that SCWL phytoplasma and sugarcane grassy shoot (SCGS) phytoplasma belonged to the same phytoplasma species. This study provides a genomic DNA enrichment method for phytoplasma sequencing. Moreover, we report the first complete genome of a “Ca. Phytoplasma sacchari” isolate, thus contributing to future studies on the evolutionary relationships and pathogenic mechanisms of “Ca. Phytoplasma sacchari” isolates.

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Section: Discussionmentioning

confidence: 99%

“…Multilocus sequence typing revealed that SCWL and SCGS phytoplasmas belong to two different populations of “ Ca . Phytoplasma sacchari” (Abeysinghe et al, 2016 ; Zhang et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequence of “Candidatus Phytoplasma sacchari” obtained using a filter-based DNA enrichment method and Nanopore sequencing

Zhang,

Wang,

et al. 2023

Front. Microbiol.

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“…Phytoplasma sacchari) population structure which found two sequence types (STs). ST1 belonged to the 16SrXI-B and was found to be the main group and most widely distributed while ST2 belonged to the 16SrXI-D and was only found in Boashan area in China (Zhang et al 2023).…”

Section: Multilocus Sequence Genotyping (Mlst)mentioning

confidence: 97%

“…Hence, the use of several regions/genes of the phytoplasma genome, and multilocus sequence typing (MLST) were explored. Recently, multilocus sequence typing (MLST) up to 10 genes and whole genome sequences were reported (Zhang et al 2023;Jamshidi et al 2022;Abeysinghe et al 2016). In Thailand, the diversity of SCWL phytoplasma was studied based on RFLP of 1.35 bp of 16S rDNA covering 3' end of 16S rRNA, spacer region between the 16S rRNA and the tRNA (Ile) with enzyme HpaII and DNA sequencing which found sugarcane white leaf (SCWL) and sugarcane grassy shoot (SCGS) diseases caused from different phytoplasma (Wongkaew et al 1997).…”

Section: Introductionmentioning

confidence: 99%

Multilocal Genotyping of Sugarcane White Leaf phytoplasma in Thailand.

Watcharachaiyakup,

Burns,

Chaphakdee

et al. 2023

Preprint

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Sugarcan white leaf (SCWL) phytoplasma is a pathogen associated with sugarcane white leaf, a severe disease causing yield losses in sugarcane plantations, particularly in Asian countries. In this study, 174 SCWL symptomatic sugarcane samples were collected from sugarcane growing areas in the North, Northeastern and Central plain of Thailand. The genotyping was performed using partial 16s rDNA and partial internal transcribed spacer and multilocus sequence typing (MLST) based on six genes including tuf, secY, leuS, secA, AAA1 and GroES. The analysis indicated that partial 16s rDNA and partial internal transcribed spacer and other six genes could divide SCWL phytoplasma within sugarcane samples into two groups: 16SrXI-B and 16SrXI-D. Sugarcane samples found throughout the country consisted of SCWL phytoplasma in 16SrXI-B group (85.6%) while 16SrXI-D group was only found in the Northeastern regions. It was either found with 16SrXI-B in Roi et, Kalasin and Mookdahan provinces or alone in Surin province. The outcome of MLST offered extensive diversity studies of SCWL phytoplasma in Thailand which further information for disease management, detection method development and monitoring.

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“…Through various sequencing technologies and comparative genome assemblies, 27 complete genomes (Table S9) and 216 draft genomes have been published thus far (https://www.ncbi.nlm.nih.gov/datasets/taxonomy/33926/). In this study, we summarize the information on the 27 complete genomes, including 16SrI (Bai et al., 2006; Cao et al., 2021; Coetzee et al., 2019; Luo et al., 2022; Orlovskis et al., 2017; Oshima et al., 2004; Yan et al., 2023), II (Chang et al., 2015; Kirdat et al., 2023b; Li et al., 2023; Rodrigues Jardim et al., 2022; Tan et al., 2021), III (unpublished), V (Debonneville et al., 2022; Duckeck et al., 2023; Wang, Yang, et al., 2018), VIII (Huang et al., 2022), X (Kube et al., 2008), XI (Zhang et al., 2023), XII (Andersen et al., 2013; Tran‐Nguyen et al., 2008) and XIV (unpublished). Eight complete genomes were obtained for the 16SrI group.…”

Section: Genomic Information Of Phytoplasmasmentioning

confidence: 99%

Phytoplasma: A plant pathogen that cannot be ignored in agricultural production—Research progress and outlook

Wang,

Bai,

et al. 2024

Molecular Plant Pathology

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Phytoplasmas are phloem‐restricted plant‐pathogenic bacteria transmitted by insects. They cause diseases in a wide range of host plants, resulting in significant economic and ecological losses worldwide. Research on phytoplasmas has a long history, with significant progress being made in the past 30 years. Notably, with the rapid development of phytoplasma research, scientists have identified the primary agents involved in phytoplasma transmission, established classification and detection systems for phytoplasmas, and 243 genomes have been sequenced and assembled completely or to draft quality. Multiple possible phytoplasma effectors have been investigated, elucidating the molecular mechanisms by which phytoplasmas manipulate their hosts. This review summarizes recent advances in phytoplasma research, including identification techniques, host range studies, whole‐ or draft‐genome sequencing, effector pathogenesis and disease control methods. Additionally, future research directions in the field of phytoplasma research are discussed.

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Multilocus sequence typing reveals two distinct populations of “Candidatus Phytoplasma sacchari” in China

Cited by 5 publications

References 30 publications

Complete genome sequence of “Candidatus Phytoplasma sacchari” obtained using a filter-based DNA enrichment method and Nanopore sequencing

Complete genome sequence of “Candidatus Phytoplasma sacchari” obtained using a filter-based DNA enrichment method and Nanopore sequencing

Multilocal Genotyping of Sugarcane White Leaf phytoplasma in Thailand.

Phytoplasma: A plant pathogen that cannot be ignored in agricultural production—Research progress and outlook

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