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Zhang RY, Wang XY, Li J, Shan HL, Li YH, Huang YK, He XH. Complete genome sequence of " Candidatus Phytoplasma sacchari" obtained using a filter-based DNA enrichment method and Nanopore sequencing. Front Microbiol 2023; 14:1252709. [PMID: 37849920 PMCID: PMC10577292 DOI: 10.3389/fmicb.2023.1252709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
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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Affiliation(s)
- Rong-Yue Zhang
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Xiao-Yan Wang
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Jie Li
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Hong-Li Shan
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Yin-Hu Li
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Ying-Kun Huang
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Xia-Hong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- School of Landscape and Horticulture, Southwest Forestry University, Kunming, China
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Bertaccini A. Plants and Phytoplasmas: When Bacteria Modify Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111425. [PMID: 35684198 PMCID: PMC9182842 DOI: 10.3390/plants11111425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 05/14/2023]
Abstract
Plant pathogen presence is very dangerous for agricultural ecosystems and causes huge economic losses. Phytoplasmas are insect-transmitted wall-less bacteria living in plants, only in the phloem tissues and in the emolymph of their insect vectors. They are able to manipulate several metabolic pathways of their hosts, very often without impairing their life. The molecular diversity described (49 'Candidatus Phytoplasma' species and about 300 ribosomal subgroups) is only in some cases related to their associated symptomatology. As for the other plant pathogens, it is necessary to verify their identity and recognize the symptoms associated with their presence to appropriately manage the diseases. However, the never-ending mechanism of patho-adaptation and the copresence of other pathogens makes this management difficult. Reducing the huge impact of phytoplasma-associated diseases in all the main crops and wild species is, however, relevant, in order to reduce their effects that are jeopardizing plant biodiversity.
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Affiliation(s)
- Assunta Bertaccini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, 40127 Bologna, Italy
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Kirdat K, Tiwarekar B, Thorat V, Sathe S, Shouche Y, Yadav A. 'Candidatus Phytoplasma sacchari', a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease. Int J Syst Evol Microbiol 2020; 71. [PMID: 33289626 DOI: 10.1099/ijsem.0.004591] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with 'Ca. Phytoplasma cynodontis' strain BGWL-C1 followed by 97.65 % similarity with 'Ca. P. oryzae' strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to 'Ca. P. cynodontis', were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon 'Candidatus Phytoplasma sacchari' is proposed.
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Affiliation(s)
- Kiran Kirdat
- Department of Microbiology, Tuljaram Chaturchand College, Baramati 413 102, Maharashtra, India
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Bhavesh Tiwarekar
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati 413 102, Maharashtra, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
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Kirdat K, Tiwarekar B, Thorat V, Narawade N, Dhotre D, Sathe S, Shouche Y, Yadav A. Draft Genome Sequences of Two Phytoplasma Strains Associated with Sugarcane Grassy Shoot (SCGS) and Bermuda Grass White Leaf (BGWL) Diseases. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:715-717. [PMID: 32040378 DOI: 10.1094/mpmi-01-20-0005-a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We performed whole-genome sequencing of two phytoplasmas associated with sugarcane grassy shoot (SCGS) and Bermuda grass white leaf diseases. These are the first draft genomes of SCGS phytoplasma (strain SCGS) and 'Candidatus Phytoplasma cynodontis' (strain LW01) and may help to delineate these phytoplasmas at a finer taxonomic level.
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Affiliation(s)
- Kiran Kirdat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413102, India
| | - Bhavesh Tiwarekar
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Nitin Narawade
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413102, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
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