Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald.

Hui-Li Zhang,Mbuya Sylvain Ntambo,Gongyou Chen,Mei-Ting Huang,Philippe C Rott,San-Ji Gao,Li-Lan Chen

doi:10.3390/microorganisms8020182

Abstract

Leaf scald (caused by Xanthomonas albilineans) is an important bacterial disease affecting sugarcane in most sugarcane growing countries, including China. High genetic diversity exists among strains of X. albilineans from diverse geographic regions. To highlight the genomic features associated with X. albilineans from China, we sequenced the complete genome of a representative strain (Xa-FJ1) of this pathogen using the PacBio and Illumina platforms. The complete genome of strain Xa-FJ1 consists of a circular chromosome of 3,724,581 bp and a plasmid of 31,536 bp. Average nucleotide identity analysis revealed that Xa-FJ1 was closest to five strains from the French West Indies and the USA, particularly to the strain GPE PC73 from Guadeloupe. Comparative genomic analysis between Xa-FJ1 and GPE PC73 revealed prophage integration, homologous recombination, transposable elements, and a clustered regulatory interspaced short palindromic repeats (CRISPR) system that were linked with 16 insertions/deletions (InDels). Ten and 82 specific genes were found in Xa-FJ1 and GPE PC73, respectively, and some of these genes were subjected to phage-related proteins, zona occludens toxin, and DNA methyltransferases. Our findings highlight intra-species genetic variability of the leaf scald pathogen and provide additional genomic resources to investigate its fitness and virulence.

Highlights

Xanthomonas is a genus in the gamma subdivision of the Proteobacteria that contains a large number of plant pathogens
X. albilineans colonizes the vascular system of sugarcane leaves and stalks, but is capable of infecting the parenchyma cells of sugarcane, a unique characteristic differing from other bacterial pathogens with a reduced genome [3]
The genome of strain GPE PC73—the only other X. albilineans strain with a complete genome sequence in NCBI—contained 3115 putative genes with an average length of 1059 bp (Table 1)

Summary

Introduction

Xanthomonas is a genus in the gamma subdivision of the Proteobacteria that contains a large number of plant pathogens. X. albilineans colonizes the vascular system of sugarcane leaves and stalks, but is capable of infecting the parenchyma cells of sugarcane, a unique characteristic differing from other bacterial pathogens with a reduced genome [3]. This bacterial pathogen induces various leaf and stalk symptoms during disease progress [2]. In the initial phase of the disease, X. albilineans causes the appearance of white, narrow, sharply defined leaf stripes which is followed by necrosis and wilting of infected leaves, resulting in plant death [4,5]. Albicidin is a potent DNA gyrase inhibitor that inhibits chloroplast DNA replication and blocks chloroplast differentiation, resulting in the white stripe and chlorotic symptoms on infected leaves [6]

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Conclusion