Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. phytoplasma asteris" strains OY-M and AY-WB

L Tran-nguyen, M Kube, B Schneider, R Reinhardt, Karen Gibb

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris" strains OY-M and AY-WB showed that the gene order was more conserved between the closely related "Ca. Phytoplasma asteris" strains than to "Ca. Phytoplasma australiense." Differences observed between "Ca. Phytoplasma australiense" and "Ca. Phytoplasma asteris" strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function. Copyright � 2008, American Society for Microbiology. All Rights Reserved.
    Original languageEnglish
    Pages (from-to)3979-3991
    Number of pages13
    JournalJournal of Bacteriology
    Volume190
    Issue number11
    Publication statusPublished - 2008

    Fingerprint

    Phytoplasma
    Genome
    Bacteriophages
    Proteins
    Nucleotides
    Chromosomes
    Genes
    Carica
    Plant Diseases
    Chromosomes, Human, Pair 18
    Integrases
    Gene Order
    Insertional Mutagenesis
    Base Composition
    Microbiology
    DNA Replication
    DNA Repair
    Genetic Recombination
    DNA

    Cite this

    @article{2a8cdcb3f9334b02acf6e9c2881f9b7d,
    title = "Comparative genome analysis of {"}Candidatus Phytoplasma australiense{"} (subgroup tuf-Australia I; rp-A) and {"}Ca. phytoplasma asteris{"} strains OY-M and AY-WB",
    abstract = "The chromosome sequence of {"}Candidatus Phytoplasma australiense{"} (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27{\%}, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1{\%} of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of {"}Ca. Phytoplasma australiense{"} with {"}Ca. Phytoplasma asteris{"} strains OY-M and AY-WB showed that the gene order was more conserved between the closely related {"}Ca. Phytoplasma asteris{"} strains than to {"}Ca. Phytoplasma australiense.{"} Differences observed between {"}Ca. Phytoplasma australiense{"} and {"}Ca. Phytoplasma asteris{"} strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function. Copyright � 2008, American Society for Microbiology. All Rights Reserved.",
    keywords = "repetitive DNA, article, bacterial chromosome, bacterial gene, bacterial genome, bacterial strain, bacteriophage, candidatus phytoplama, chromosome size, cluster analysis, comparative study, DNA recombination, DNA repair, DNA replication, gene function, gene insertion sequence, genetic conservation, genomics, nonhuman, nucleotide metabolism, nucleotide sequence, nucleotide transport, papaya, Phytoplasma, plant disease, priority journal, protein function, ribosome, structure analysis, Amino Acid Sequence, Bacterial Proteins, Chromosomes, Bacterial, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genome, Bacterial, Molecular Sequence Data, Candidatus Phytoplasma, Candidatus Phytoplasma australiense, Carica papaya, Phytoplasma asteris, Vitis",
    author = "L Tran-nguyen and M Kube and B Schneider and R Reinhardt and Karen Gibb",
    year = "2008",
    language = "English",
    volume = "190",
    pages = "3979--3991",
    journal = "Journal of Bacteriology",
    issn = "0021-9193",
    publisher = "Global Science Books",
    number = "11",

    }

    Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. phytoplasma asteris" strains OY-M and AY-WB. / Tran-nguyen, L; Kube, M; Schneider, B; Reinhardt, R; Gibb, Karen.

    In: Journal of Bacteriology, Vol. 190, No. 11, 2008, p. 3979-3991.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. phytoplasma asteris" strains OY-M and AY-WB

    AU - Tran-nguyen, L

    AU - Kube, M

    AU - Schneider, B

    AU - Reinhardt, R

    AU - Gibb, Karen

    PY - 2008

    Y1 - 2008

    N2 - The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris" strains OY-M and AY-WB showed that the gene order was more conserved between the closely related "Ca. Phytoplasma asteris" strains than to "Ca. Phytoplasma australiense." Differences observed between "Ca. Phytoplasma australiense" and "Ca. Phytoplasma asteris" strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function. Copyright � 2008, American Society for Microbiology. All Rights Reserved.

    AB - The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris" strains OY-M and AY-WB showed that the gene order was more conserved between the closely related "Ca. Phytoplasma asteris" strains than to "Ca. Phytoplasma australiense." Differences observed between "Ca. Phytoplasma australiense" and "Ca. Phytoplasma asteris" strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function. Copyright � 2008, American Society for Microbiology. All Rights Reserved.

    KW - repetitive DNA

    KW - article

    KW - bacterial chromosome

    KW - bacterial gene

    KW - bacterial genome

    KW - bacterial strain

    KW - bacteriophage

    KW - candidatus phytoplama

    KW - chromosome size

    KW - cluster analysis

    KW - comparative study

    KW - DNA recombination

    KW - DNA repair

    KW - DNA replication

    KW - gene function

    KW - gene insertion sequence

    KW - genetic conservation

    KW - genomics

    KW - nonhuman

    KW - nucleotide metabolism

    KW - nucleotide sequence

    KW - nucleotide transport

    KW - papaya

    KW - Phytoplasma

    KW - plant disease

    KW - priority journal

    KW - protein function

    KW - ribosome

    KW - structure analysis

    KW - Amino Acid Sequence

    KW - Bacterial Proteins

    KW - Chromosomes, Bacterial

    KW - Gene Expression Regulation, Bacterial

    KW - Genes, Bacterial

    KW - Genome, Bacterial

    KW - Molecular Sequence Data

    KW - Candidatus Phytoplasma

    KW - Candidatus Phytoplasma australiense

    KW - Carica papaya

    KW - Phytoplasma asteris

    KW - Vitis

    M3 - Article

    VL - 190

    SP - 3979

    EP - 3991

    JO - Journal of Bacteriology

    JF - Journal of Bacteriology

    SN - 0021-9193

    IS - 11

    ER -