Complete Genome Sequence of Spiroplasma citri Strain R8-A2
            <sup>T</sup>
            , Causal Agent of Stubborn Disease in
            <i>Citrus</i>
            Species

Davis, Robert E.; Shao, Jonathan; Zhao, Yan; Gasparich, Gail E.; Gaynor, Brady J.; Donofrio, Nicole

doi:10.1128/genomea.00206-17

Cited by 14 publications

(10 citation statements)

References 20 publications

(20 reference statements)

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“…Additionally, the number of predicted protein coding regions was higher in U.S. strains compared to R8-A2 T genome. One set of rRNA genes and 32 tRNA genes were predicted in U.S. strains, which is consistent with the R8-A2 T strain [26].…”

Section: Discussionsupporting

confidence: 75%

“…Prior to advances in long-read sequencing, the best assembly of S. citri was strain GII3-3X, which contained 39 chromosomal contigs [22]. The rst sequence of S. citri containing a single chromosomal contig was reported from Morocco in 2017, S. citri R8-A2 T [26]. Complete genomes, with single chromosomal contigs, of six more strains of S. citri isolated in the United States were reported in 2020 [14,15] and a seventh strain, C5, isolated from carrot, is reported in this study.…”

Section: Discussionmentioning

confidence: 99%

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Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Rattner

Thapa

Dang

et al. 2020

Preprint

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Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horseradish, carrot, sesame, and also infect 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 by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC2, C5, C189, LB319, 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-12 and C5; C189 and R8-A2; BR12, BLH-MB, BLH13 and LB 319. Strain GII3-3 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 1,597-2,232 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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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Rattner

Thapa

Dang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Prior to advances in long-read sequencing, the best assembly of S. citri was strain GII3–3X, which contained 39 chromosomal contigs [ 24 ]. The first sequence of S. citri containing a single chromosomal contig was reported in 2017 for Moroccan S. citri strain R8-A2 T [ 31 ]. Complete genomes, with single chromosomal contigs, of six more strains of S. citri isolated in the United States were reported in 2020 [ 14 , 15 ] and a seventh strain, C5, isolated from carrot, is reported in this study.…”

Section: Discussionmentioning

confidence: 99%

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

et al. 2021

View full text Add to dashboard Cite

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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“…To determine any genomic differences that may occur between S. citri populations, the bacterium was isolated and cultured from different times and hosts, and S. citri DNA purified and subjected to PacBio sequencing. The whole genome sequence was assembled for five strains to add to the two S. citri sequences in the public database [8,9]. The genome sequences reported here will be used for comparative genomics and to better understand the etiology, relationships and evolution among the spiroplasmas.…”

Section: Objectivementioning

confidence: 99%

Whole genome sequence of five strains of Spiroplasma citri isolated from different host plants and its leafhopper vector

et al. 2020

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Objectives: Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in North America. Five strains of S. citri were cultured from citrus, horseradish, and N. tenellus from different habitats and times. DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution. Data description: The whole genome sequence of five strains of S. citri are described herein. The S. citri chromosome was circularized for all five strains and ranged from 1,576,550 to 1,742,208 bp with a G + C content of 25.4-25.6%.

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Complete Genome Sequence of Spiroplasma citri Strain R8-A2 ^T , Causal Agent of Stubborn Disease in Citrus Species

Cited by 14 publications

References 20 publications

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Whole genome sequence of five strains of Spiroplasma citri isolated from different host plants and its leafhopper vector

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Complete Genome Sequence of Spiroplasma citri Strain R8-A2 T , Causal Agent of Stubborn Disease in Citrus Species

Cited by 14 publications

References 20 publications

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Whole genome sequence of five strains of Spiroplasma citri isolated from different host plants and its leafhopper vector

Contact Info

Product

Resources

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Complete Genome Sequence of Spiroplasma citri Strain R8-A2 ^T , Causal Agent of Stubborn Disease in Citrus Species