Genome Sequence of Methylobacterium sp. Strain GXF4, a Xylem-Associated Bacterium Isolated from Vitis vinifera L. Grapevine

Abstract

Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium.

GENOME ANNOUNCEMENT

The soil and insect feeding on plants are important reservoirs of microbes that may be selected and propagated within host plants. Microorganisms that predominantly inhabit xylem systems are called xylem limited and generally rely on insect vectors or wounding for dissemination (1). Important examples of pathogenic xylem-limited bacteria are strains of Xylella fastidiosa that are vectored by sap-feeding insects of the Cicadellidae family (1, 9). X. fastidiosa causes economically important diseases in a wide variety of plants, including grape, citrus, plum, peach, coffee, and others (1, 9).

This sequenced strain was isolated from xylem fluids of Riesling grapevines grafted onto rootstock Courderc 3309 from a Cornell University vineyard located at the New York State Agricultural Experiment Station, Geneva, NY. It has been previously identified by sequencing of the full-length 16S rRNA gene, is related to bacteria of the genus Methylobacterium, and was designated GXF4 (4). Few studies have characterized bacteria from xylem fluids of grapevines. Strain GXF4 was shown to produce bacterial cell-to-cell communication signals of the acyl-homoserine lactone (AHL) family that may influence communication and colonization outcomes within the xylem at the bacterial community level (4). Such interactions may have implications for both biotic and abiotic disease management of vineyards (1, 9). In this study, the genome sequence of Methylobacterium sp. strain GXF4, an endophyte from grapevine xylem, was determined to provide novel insight into the molecular principles of xylem endophytes. This work has the potential to enhance the development of novel approaches to improve disease resistance to xylem-limited plant pathogens (1, 9).

The genome sequencing of Methylobacterium sp. strain GXF4 was performed with the Illumina Genome Analyzer IIx with 100-bp paired-end reads. The paired-end reads were trimmed and assembled using CLC Genomics Workbench 4.8 (CLC Bio, Aarhus, Denmark). The prediction of open reading frames (ORFs), tRNAs, and rRNAs was performed by using Prodigal 2.50, tRNAscan-SE 1.3, and RNAmmer 1.2 (5, 6, 8), respectively. Subsequent genome annotation was done using Blast2GO 2.5.0 (3). The de novo assembly yielded 123 contigs with an accumulated length of 6,116,340 bp (97× coverage) and an average GC content of 69.64%. The contig N50 was 113 kb, and the largest assembled contig was approximately 373 kb. The draft genome contains 5,933 ORFs, 46 tRNAs, and 3 rRNAs.

Similar to Methylobacterium extorquens AM1, strain GXF4 contains the complete gene set for methanol oxidation, which is located at contigs 54 (mxcQE), 66 (mxbMD and pqqABCDE), 78 (mxaKLDEHB), and 124 (mxaFJGIRSAC) (2). Consistent with its AHL-producing phenotype, two putative AHL synthase genes were identified in the genome of strain GXF4. Interestingly, strain GXF4 contains a gene that codes for β-galactosidase that, to the best of our knowledge, has not been reported in the genomes of the genus Methylobacterium. β-Galactosidase catalyzes the hydrolysis of galactan, a common polysaccharide component of the plant cell wall (7). On the basis of the isolation source of strain GXF4, it is reasonable to suggest that this gene endows strain GXF4 with the ability to modify the xylem cell wall structure.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. AKFK00000000. The version described in this paper is the first version, AKFK01000000.