Comparative Analysis of the Peanut Witches'-Broom Phytoplasma Genome Reveals Horizontal Transfer of Potential Mobile Units and Effectors

Wan-Chia Chung,Wen-Sui Lo,Ling-Ling Chen,Chih-Horng Kuo,Chan-Pin Lin,Marc Robinson-Rechavi

doi:10.1371/journal.pone.0062770

Abstract

Phytoplasmas are a group of bacteria that are associated with hundreds of plant diseases. Due to their economical importance and the difficulties involved in the experimental study of these obligate pathogens, genome sequencing and comparative analysis have been utilized as powerful tools to understand phytoplasma biology. To date four complete phytoplasma genome sequences have been published. However, these four strains represent limited phylogenetic diversity. In this study, we report the shotgun sequencing and evolutionary analysis of a peanut witches'-broom (PnWB) phytoplasma genome. The availability of this genome provides the first representative of the 16SrII group and substantially improves the taxon sampling to investigate genome evolution. The draft genome assembly contains 13 chromosomal contigs with a total size of 562,473 bp, covering ∼90% of the chromosome. Additionally, a complete plasmid sequence is included. Comparisons among the five available phytoplasma genomes reveal the differentiations in gene content and metabolic capacity. Notably, phylogenetic inferences of the potential mobile units (PMUs) in these genomes indicate that horizontal transfer may have occurred between divergent phytoplasma lineages. Because many effectors are associated with PMUs, the horizontal transfer of these transposon-like elements can contribute to the adaptation and diversification of these pathogens. In summary, the findings from this study highlight the importance of improving taxon sampling when investigating genome evolution. Moreover, the currently available sequences are inadequate to fully characterize the pan-genome of phytoplasmas. Future genome sequencing efforts to expand phylogenetic diversity are essential in improving our understanding of phytoplasma evolution.

Highlights

Phytoplasmas are a group of phytopathogenic bacteria that are transmitted by sap-feeding insect vectors [1,2,3]
With the recent advancements in genomic sciences, genome sequencing has been adopted as a powerful tool to characterize the gene content of these uncultivated bacteria [5,6,7,8,9]
Comparative analyses of the available phytoplasma genome sequences have improved our knowledge of their evolutionary history and facilitated experimental works to investigate the mechanisms of pathogenicity [10,11,12,13]

Summary

Introduction

Phytoplasmas are a group of phytopathogenic bacteria that are transmitted by sap-feeding insect vectors [1,2,3]. To provide an alternative method of estimating the completeness, we identified a list of protein-coding genes that are conserved among the four complete phytoplasma genomes (Table 1) and checked for their presence in our draft assembly. The number of protein-coding genes in the PnWB phytoplasma is similar to ‘Ca. P. mali’ and relatively low compared to ‘Ca. P. asteris’ and ‘Ca. P. australiense’ (Table 1).

Results

Conclusion