Identification of genes in the tomato big bud phytoplasma and comparison to those in sweet potato little leaf-V4 phytoplasma

Claire Streten-Joyce, Karen Gibb

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    Genetic relatedness of phytoplasmas is commonly defined on the basis of differences in the highly conserved 16S rRNA gene, which may not resolve closely related phytoplasmas. An example of this is the closely related tomato big bud (TBB) and sweet potato little leaf strain V4 (SPLL-V4) phytoplasmas, which cannot easily be differentiated by their 16S rRNA gene sequences. This study aimed to identify genes on the TBB phytoplasma chromosome which could be used to examine genetic variation between these two closely related phytoplasmas. Random clones generated from TBB phytoplasma genomic DNA were sequenced and characterized by database analysis. Twenty-three genes were identified within 19 random clones, which contained approximately 18.0 kbp of TBB phytoplasma genomic DNA. Half of the TBB phytoplasma genes identified were involved in DNA replication, transcription and translation. The remaining TBB phytoplasma genes were involved in protein secretion, cellular processes and energy metabolism. Phylogenetic analysis of representative genes showed that the TBB phytoplasma grouped with the mycoplasmas with the exception of the TBB phytoplasma secA gene, which grouped with the onion yellows phytoplasma. PCR primers were designed based on the new genes and tested on isolates of the TBB and SPLL-V4 phytoplasmas. Most primers amplified a product from TBB and SPLL-V4 phytoplasma samples. When amplified products were subjected to RFLP analysis, the restriction patterns were the same as the respective original clones. This result confirmed that the same sequence had been amplified by PCR and showed that these isolates were indistinguishable using the new genes. This study showed that in fact the TBB and SPLL-V4 phytoplasmas are closely related even with the analysis of new genes. These new genes have, however, provided insight into the biology of the TBB and SPLL-V4 phytoplasmas.
    Original languageEnglish
    Pages (from-to)1797-1805
    Number of pages9
    JournalMicrobiology
    Volume149
    Issue number7
    Publication statusPublished - 2003

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    Phytoplasma
    Ipomoea batatas
    Lycopersicon esculentum
    Genes
    Clone Cells
    rRNA Genes
    Polymerase Chain Reaction

    Cite this

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    abstract = "Genetic relatedness of phytoplasmas is commonly defined on the basis of differences in the highly conserved 16S rRNA gene, which may not resolve closely related phytoplasmas. An example of this is the closely related tomato big bud (TBB) and sweet potato little leaf strain V4 (SPLL-V4) phytoplasmas, which cannot easily be differentiated by their 16S rRNA gene sequences. This study aimed to identify genes on the TBB phytoplasma chromosome which could be used to examine genetic variation between these two closely related phytoplasmas. Random clones generated from TBB phytoplasma genomic DNA were sequenced and characterized by database analysis. Twenty-three genes were identified within 19 random clones, which contained approximately 18.0 kbp of TBB phytoplasma genomic DNA. Half of the TBB phytoplasma genes identified were involved in DNA replication, transcription and translation. The remaining TBB phytoplasma genes were involved in protein secretion, cellular processes and energy metabolism. Phylogenetic analysis of representative genes showed that the TBB phytoplasma grouped with the mycoplasmas with the exception of the TBB phytoplasma secA gene, which grouped with the onion yellows phytoplasma. PCR primers were designed based on the new genes and tested on isolates of the TBB and SPLL-V4 phytoplasmas. Most primers amplified a product from TBB and SPLL-V4 phytoplasma samples. When amplified products were subjected to RFLP analysis, the restriction patterns were the same as the respective original clones. This result confirmed that the same sequence had been amplified by PCR and showed that these isolates were indistinguishable using the new genes. This study showed that in fact the TBB and SPLL-V4 phytoplasmas are closely related even with the analysis of new genes. These new genes have, however, provided insight into the biology of the TBB and SPLL-V4 phytoplasmas.",
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    Identification of genes in the tomato big bud phytoplasma and comparison to those in sweet potato little leaf-V4 phytoplasma. / Streten-Joyce, Claire; Gibb, Karen.

    In: Microbiology, Vol. 149, No. 7, 2003, p. 1797-1805.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Identification of genes in the tomato big bud phytoplasma and comparison to those in sweet potato little leaf-V4 phytoplasma

    AU - Streten-Joyce, Claire

    AU - Gibb, Karen

    PY - 2003

    Y1 - 2003

    N2 - Genetic relatedness of phytoplasmas is commonly defined on the basis of differences in the highly conserved 16S rRNA gene, which may not resolve closely related phytoplasmas. An example of this is the closely related tomato big bud (TBB) and sweet potato little leaf strain V4 (SPLL-V4) phytoplasmas, which cannot easily be differentiated by their 16S rRNA gene sequences. This study aimed to identify genes on the TBB phytoplasma chromosome which could be used to examine genetic variation between these two closely related phytoplasmas. Random clones generated from TBB phytoplasma genomic DNA were sequenced and characterized by database analysis. Twenty-three genes were identified within 19 random clones, which contained approximately 18.0 kbp of TBB phytoplasma genomic DNA. Half of the TBB phytoplasma genes identified were involved in DNA replication, transcription and translation. The remaining TBB phytoplasma genes were involved in protein secretion, cellular processes and energy metabolism. Phylogenetic analysis of representative genes showed that the TBB phytoplasma grouped with the mycoplasmas with the exception of the TBB phytoplasma secA gene, which grouped with the onion yellows phytoplasma. PCR primers were designed based on the new genes and tested on isolates of the TBB and SPLL-V4 phytoplasmas. Most primers amplified a product from TBB and SPLL-V4 phytoplasma samples. When amplified products were subjected to RFLP analysis, the restriction patterns were the same as the respective original clones. This result confirmed that the same sequence had been amplified by PCR and showed that these isolates were indistinguishable using the new genes. This study showed that in fact the TBB and SPLL-V4 phytoplasmas are closely related even with the analysis of new genes. These new genes have, however, provided insight into the biology of the TBB and SPLL-V4 phytoplasmas.

    AB - Genetic relatedness of phytoplasmas is commonly defined on the basis of differences in the highly conserved 16S rRNA gene, which may not resolve closely related phytoplasmas. An example of this is the closely related tomato big bud (TBB) and sweet potato little leaf strain V4 (SPLL-V4) phytoplasmas, which cannot easily be differentiated by their 16S rRNA gene sequences. This study aimed to identify genes on the TBB phytoplasma chromosome which could be used to examine genetic variation between these two closely related phytoplasmas. Random clones generated from TBB phytoplasma genomic DNA were sequenced and characterized by database analysis. Twenty-three genes were identified within 19 random clones, which contained approximately 18.0 kbp of TBB phytoplasma genomic DNA. Half of the TBB phytoplasma genes identified were involved in DNA replication, transcription and translation. The remaining TBB phytoplasma genes were involved in protein secretion, cellular processes and energy metabolism. Phylogenetic analysis of representative genes showed that the TBB phytoplasma grouped with the mycoplasmas with the exception of the TBB phytoplasma secA gene, which grouped with the onion yellows phytoplasma. PCR primers were designed based on the new genes and tested on isolates of the TBB and SPLL-V4 phytoplasmas. Most primers amplified a product from TBB and SPLL-V4 phytoplasma samples. When amplified products were subjected to RFLP analysis, the restriction patterns were the same as the respective original clones. This result confirmed that the same sequence had been amplified by PCR and showed that these isolates were indistinguishable using the new genes. This study showed that in fact the TBB and SPLL-V4 phytoplasmas are closely related even with the analysis of new genes. These new genes have, however, provided insight into the biology of the TBB and SPLL-V4 phytoplasmas.

    KW - gene product

    KW - genomic DNA

    KW - RNA 16S

    KW - article

    KW - bud

    KW - cell activity

    KW - chromosome analysis

    KW - controlled study

    KW - cytoplasm

    KW - DNA replication

    KW - DNA sequence

    KW - DNA transcription

    KW - energy metabolism

    KW - gene amplification

    KW - gene identification

    KW - gene isolation

    KW - gene sequence

    KW - genetic analysis

    KW - genetic conservation

    KW - genetic variability

    KW - molecular biology

    KW - molecular cloning

    KW - molecular phylogeny

    KW - Mycoplasma

    KW - nonhuman

    KW - nucleotide sequence

    KW - onion

    KW - plant leaf

    KW - polymerase chain reaction

    KW - priority journal

    KW - protein secretion

    KW - randomization

    KW - restriction fragment length polymorphism

    KW - RNA translation

    KW - sequence analysis

    KW - sequence database

    KW - strain difference

    KW - sweet potato

    KW - tomato

    KW - Acholeplasmataceae

    KW - Adenosine Triphosphatases

    KW - ATP-Dependent Proteases

    KW - Bacterial Proteins

    KW - Base Sequence

    KW - DNA, Bacterial

    KW - Energy Metabolism

    KW - Escherichia coli Proteins

    KW - Genes, Bacterial

    KW - Genome, Bacterial

    KW - Ipomoea batatas

    KW - Lycopersicon esculentum

    KW - Membrane Proteins

    KW - Membrane Transport Proteins

    KW - Molecular Sequence Data

    KW - Phylogeny

    KW - Species Specificity

    KW - Allium cepa

    KW - Bacteria (microorganisms)

    KW - Mycoplasmatales

    KW - Onion yellows phytoplasma

    KW - Phytoplasma

    KW - Prokaryota

    KW - Solanum tuberosum

    KW - Tomato big bud phytoplasma

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    M3 - Article

    VL - 149

    SP - 1797

    EP - 1805

    JO - Microbiology

    JF - Microbiology

    SN - 1350-0872

    IS - 7

    ER -