Draft genome sequence of the New Jersey aster yellows strain of 'Candidatus Phytoplasma asteris'

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. A total of 177,847 reads were assembled into 75 contigs > 518 bp with a total base value of 652,092 and an overall [G+C] content of 27.1%. A total of 733 protein coding genes were identified. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession MAPF00000000. This draft genome was 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). NJAY and AY-WB exhibit approximately 0.5% dissimilarity at the nucleotide level among their shared genomic segments. 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. Apparent NJAY orthologs to the important AY-WB virulence factors, SAP11 and SAP54, were identified. A number of secreted proteins, both membrane-bound and soluble, were encoded, with many bearing similarity to known AY-WB effector molecules and others representing possible secreted proteins that may be novel to the NJAY lineage.

Fig 1

A) Neighbor-joining tree built using blast-based average nucleotide identity (ANIb) estimates calculated using JSpecies. Pairwise distances are provided in the inset table. As native ANIb values connote similarity measures; specifically, the proportion of identical residues among aligned segments expressed as a percentage; distance measures are obtained by taking complements with respect to 100%. ANIb considers similarity observed in all regions of the respective genomes where pairwise alignments using blastn are possible. B) Bayesian phylogeny produced using a codon-based model of DNA evolution applied to a concatemer of 29 reliably aligned, conserved protein-coding genes (6,618 codons in total). Branch lengths correspond to the number of nucleotide substitutions per codon. Posterior probabilities of the inferred branching patterns are indicated on the tree.

Fig 2

A) Venn diagram comparing species-specific Enzyme Commission (EC) code listings. Enzymatic category identifiers were obtained from NJAY using Prodigal-predicted proteins annotated with Blast2GO, and from AY-WB and OY-M using annotations currently available in KEGG per EC2KEGG. EC codes not mutual to all three taxa are indicated. B) As above, but using EC codes for AY-WB and OY-M following reannotation of their respective protein-coding genes via Prodigal and Blast2GO.