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Research Project: Genome-Based Strategies and Physiological Biomarkers for Detection and Identification of plant Pathogenic Phytoplasmas and Spiroplasmas

Location: Molecular Plant Pathology Laboratory

Title: Draft genome sequence of the New Jersey aster yellows strain of ‘Candidatus Phytoplasma asteris’

Author
item Sparks, Michael
item Bottner, Kristi
item Gundersen-rindal, Dawn
item Lee, Ing Ming

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/20/2018
Publication Date: 2/6/2018
Citation: Sparks, M., Bottner-Parker, K.D., Gundersen, D.E., Lee, I. 2018. Draft genome sequence of the New Jersey aster yellows strain of ‘Candidatus Phytoplasma asteris’. PLoS One. https://doi.org/10.1371/journal.pone.0192379.
DOI: https://doi.org/10.1371/journal.pone.0192379

Interpretive Summary: Phytoplasmas are cell wall-less plant pathogenic bacteria, which infect more than 1000 plant species and cause numerous economically important diseases. There are a vast number of diverse phytoplasma strains that are distributed on all continents. Because of the inability to cultivate them readily in cell-free media, provisional Genus Phytoplasma and ‘Candidatus Phytoplasma spp.’ were proposed to accommodate their classification. For finer classification of phytoplasmas, a scheme was proposed based on RFLP analysis of 16Sr RNA sequence that, thus far, includes 32 16S ribosomal (16Sr) groups and more that 200 subgroups. Group 16SrI represents one of the most diverse groups. ‘Candidatus Phytoplasma asteris’ strain NJAY belongs to subgroup 16SrI-A which causes severe yellowing diseases of lettuce in New Jersey. In order to understand the pathogenic nature of phytoplasmas, genomic sequencing of phytoplasmas has been the focus. But thus far, only several phytoplasmas genomes (belonging to 16SrI, 16SrX, and 16SrXII groups) have been fully sequenced. In the aster yellows group (16SrI), complete genomes of ‘Candidatus Phytoplasma asteris’ strains AY-WB (aster yellows witches’-broom ) and OY-M (onion yellows-M), belonging to subgroups 16SrI-A and 16SrI-B, respectively, and two draft genomes belonging to subgroup 16SrI-B strains, OY-V (onion yellows-V) and MBSP (maize bushy stunt phytoplasma), were published. In the present study, we present the draft genome sequence of ‘Candidatus Phytoplasma asteris’ strain NJAY (16SrI-A) with 652,092 nucleotide bases and 733 protein coding genes. The availability of 16SrI-A strain NJAY draft genome sequence combined with the other existing draft genome sequences of group 16SrI will facilitate the identification of specific genomic feature of this group that may be responsible for the pathogeneses inflicted by various 16SrI group phytoplasma strains. This information will aid disease control and will interest graduate students and scientists.

Technical Abstract: The NJAY (New Jersey aster yellows) strain of ‘Candidatus Phytoplasma asteris’ is a significant plant pathogen responsible for causing severe lettuce yellows in the U.S. state of New Jersey. A draft genome sequence was prepared for this organism and used for genome- and gene-based comparative phylogenetic analyses with other phytoplasmas, including the closely related ‘Ca. Phytoplasma asteris’ strain, aster yellows witches’- broom (AY-WB). Evidence indicated that NJAY harbors four plasmids homologous to those known to encode pathogenicity determinants in AY-WB, as well as a chromosome-encoded mobile unit. An NJAY ortholog to the important AY-WB virulence factor, SAP11, was identified, exhibiting perfect sequence identity with its AY-WB counterpart. A number of secreted proteins, both membrane-bound and soluble, were identified, with many bearing similarity to known AY-WB effector molecules and others representing elements potentially novel to the NJAY lineage.