The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

Abstract

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in freeliving organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

Recent advances in the molecular biology ofLeifsonia xylisubsp.xyli, causal organism of ratoon stunting disease

“…In addition, this bacterium harbours homologues of photolyase and flagellar operons, two ABC glycine and betaine transporters, genes that protect against changes in the osmotic condition and genes for carotenoid biosynthesis. These all suggest that at one time it had a free-living life form (Monteiro-Vitorello et al 2004).…”

“…Evidence that L. xyli subsp. xyli is, or used to be, able to survive outside of sugarcane xylem vessels, free-living in the environment, is shown by the fact that there are a large number (n = 30) of ABC transporter homologues, indicating it can utilise a large range of carbohydrates (Monteiro-Vitorello et al 2004). In addition, this bacterium harbours homologues of photolyase and flagellar operons, two ABC glycine and betaine transporters, genes that protect against changes in the osmotic condition and genes for carotenoid biosynthesis.…”

“…xyli is undergoing genome decay, based on what appear to be 310 pseudogenes (i.e. gene fragments arising from frameshifts or deletions or caused by point mutations that introduce or remove stop codons, or incomplete genes), comprising 13% of the total number of predicted genes in this organism's genome (Monteiro-Vitorello et al 2004) (Table 1). Other actinomycetes also undergoing genome decay, such as Mycobacterium leprae, causal organism of leprosy, have more pseudogenes (905, or 34.1% of its genes) (Cole et al 2001), but L. xyli subsp.…”

“…xyli has the highest level seen in any of the plant-associated bacteria whose genomes have been sequenced. Monteiro-Vitorello et al (2004) believe this decay is brought about by the process of host adaptation and narrow host range (Table 1). This large number of pseudogenes is an indicator of L. xyli subsp.…”

“…Based on its xylem habitat, restricted host range (Rao et al 1990), close relationship with another grass endophyte (Leifsonia xyli subsp. cynodontis) and certain genomic features (Monteiro-Vitorello et al 2004), the bacterium appears to have had a long association with grasses. Interestingly, clones of the wild cane, Saccharum spontaneum, support >10 times the bacterial titres of L. xyli subsp.…”