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Rattner R, Thapa SP, Dang T, Osman F, Selvaraj V, Maheshwari Y, Pagliaccia D, Espindola AS, Hajeri S, Chen J, Coaker G, Vidalakis G, Yokomi R. Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors. BMC Genomics 2021; 22:373. [PMID: 34022804 PMCID: PMC8140453 DOI: 10.1186/s12864-021-07637-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen's wide host range serve as drivers of genetic diversity. This diversity was examined in silico by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC-2, C5, C189, LB 319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas. RESULTS Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-2 and C5; C189 and R8-A2; BR12, BLH-MB, BLH-13 and LB 319. Strain GII3-3X remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish, and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. CONCLUSIONS The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1597-2232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3-3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.
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Affiliation(s)
- Rachel Rattner
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Shree Prasad Thapa
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Vijayanandraj Selvaraj
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Yogita Maheshwari
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Deborah Pagliaccia
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Andres S Espindola
- Department of Entomology & Plant Pathology and Institute of Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, 93274, USA
| | - Jianchi Chen
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Raymond Yokomi
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA.
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Carle P, Saillard C, Carrère N, Carrère S, Duret S, Eveillard S, Gaurivaud P, Gourgues G, Gouzy J, Salar P, Verdin E, Breton M, Blanchard A, Laigret F, Bové JM, Renaudin J, Foissac X. Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Appl Environ Microbiol 2010; 76:3420-6. [PMID: 20363791 PMCID: PMC2876439 DOI: 10.1128/aem.02954-09] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 03/25/2010] [Indexed: 11/20/2022] Open
Abstract
The assembly of 20,000 sequencing reads obtained from shotgun and chromosome-specific libraries of the Spiroplasma citri genome yielded 77 chromosomal contigs totaling 1,674 kbp (92%) of the 1,820-kbp chromosome. The largest chromosomal contigs were positioned on the physical and genetic maps constructed from pulsed-field gel electrophoresis and Southern blot hybridizations. Thirty-eight contigs were annotated, resulting in 1,908 predicted coding sequences (CDS) representing an overall coding density of only 74%. Cellular processes, cell metabolism, and structural-element CDS account for 29% of the coding capacity, CDS of external origin such as viruses and mobile elements account for 24% of the coding capacity, and CDS of unknown function account for 47% of the coding capacity. Among these, 21% of the CDS group into 63 paralog families. The organization of these paralogs into conserved blocks suggests that they represent potential mobile units. Phage-related sequences were particularly abundant and include plectrovirus SpV1 and SVGII3 and lambda-like SpV2 sequences. Sixty-nine copies of transposases belonging to four insertion sequence (IS) families (IS30, IS481, IS3, and ISNCY) were detected. Similarity analyses showed that 21% of chromosomal CDS were truncated compared to their bacterial orthologs. Transmembrane domains, including signal peptides, were predicted for 599 CDS, of which 58 were putative lipoproteins. S. citri has a Sec-dependent protein export pathway. Eighty-four CDS were assigned to transport, such as phosphoenolpyruvate phosphotransferase systems (PTS), the ATP binding cassette (ABC), and other transporters. Besides glycolytic and ATP synthesis pathways, it is noteworthy that S. citri possesses a nearly complete pathway for the biosynthesis of a terpenoid.
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Affiliation(s)
- Patricia Carle
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Colette Saillard
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Nathalie Carrère
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Sébastien Carrère
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Sybille Duret
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Sandrine Eveillard
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Patrice Gaurivaud
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Géraldine Gourgues
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Jérome Gouzy
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Pascal Salar
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Eric Verdin
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Marc Breton
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Alain Blanchard
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Frédéric Laigret
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Joseph-Marie Bové
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Joel Renaudin
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
| | - Xavier Foissac
- INRA, UMR1090 Génomique Diversité Pouvoir Pathogène, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France, Université Victor Segalen Bordeaux 2, UMR1090, F-33883 Villenave d'Ornon, France, INRA, CNRS, Laboratoire Interactions Plantes Micro-Organismes UMR441/2594, F-31320 Castanet Tolosan, France, INRA, UR419 Espèces Fruitières, 71 Avenue Edouard Bourlaux, BP81, F-33883 Villenave d'Ornon Cedex, France
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