The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens

Abstract

We report the draft genome sequence of Xanthomonas sp. strain Mitacek01, isolated from an indoor environment vending machine surface with frequent human use in Stillwater, Oklahoma, USA, as part of the Student-Initiated Microbial Discovery project. The genome has a total size of 3,617,426 bp and a contig N₅₀ of 1,906,967 bp.

GENOME ANNOUNCEMENT

Xanthomonas spp. infect over 300 host plants, including many important crops such as rice (1). Such infections can result in reduction in crop yields or outright crop failures and hence could have a major impact on economic development and global food supply (2). Genomic analysis of strains belonging to the genus Xanthomonas can contribute to understanding the molecular mechanisms of pathogenesis and subsequently reduce the occurrence and/or mitigate the severity of such infections (3, 4).

Xanthomonas sp. strain Mitacek01 was isolated from an indoor environment vending machine surface and was sequenced on the Illumina MiSeq platform at the University of Georgia Genomics Facility using 2 × 300 paired-end chemistry. Generated reads were quality filtered with standard Illumina filtering settings resulting in 1,511,702 (453.5 Mb) quality sequences. All quality-filtered reads were assembled using the short read de Brujin graph assembly (5) program Velvet (6). Velvet assembly run-time settings used were a k-mer value of 101 bp and a minimum contig coverage value of 7×. Gene models were created using the prokaryotic gene calling software package Prodigal (7). The Velvet assembly had a total size of 3,617,426 bp and an N₅₀ of 1,906,967 bp. The largest assembled contig was 1,906,967 bp, with a GC content of 68.5%. A total of 3,212 gene models were predicted. Translated protein sequences were functionally annotated using a combination of NCBI BLAST C++ homology search (8) and HMMER version 3.0 hmmscan (9) against the PFAM 26.0 database (10).

16S rRNA gene-based comparisons to Xanthomonas genomes publicly available in the GenBank database (n = 302,955,543, October 2015) revealed that strain Mitacek01 was closely related (97.0% similarity) to Xanthomonas oryzae pv. oryzicola strain YM15, a causative agent of bacterial leaf streak in rice (11), Xanthomonas campestris strain 17, a phytopathogen capable of infecting a wide range of plants (12), and 21 different strains of Xanthomonas citri, causative agents of citrus canker (13). Despite close 16S rRNA gene sequence similarity to multiple Xanthomonas strains, BLAST analysis identified 393 genes (12.2%) within the Mitacek01 genome with no sequence homology (e value <10⁻⁰⁵) to any of the genes in the Xanthomonas pan genome (genomes = 32; protein sequences = 298,975; October 2015). The majority of these genes were hypothetical (147/393, 37.4%) and conserved hypothetical (186/393, 47.3%) proteins. In addition, genes encoding β-lactamase, glucolactone synthesis, and phenol metabolism were identified, further expanding the pan-metabolic repertoire of the genus Xanthomonas.

To identify putative virulence factors we used signalP (14) to identify secreted proteins and compared gene models to the pathogen-host interactions (PHI) (15) database to identify genes that had been previously established to affect Xanthomonas pathogenesis. A total of 497 secreted genes were identified, and 29 genes in the genome were present in the PHI database.

In conclusion, this initial genomic analysis of strain Mitacek01 highlights a high level of intergenomic diversity within the genus Xanthomonas, supporting previous findings for this genus (16, 17) and contributing to the available genomic resources for the study of an economically relevant group of phytopathogens.

Nucleotide sequence accession number.

The draft genome of Xanthomonas sp. strain Mitacek01 has been deposited in GenBank under the accession number LKIT00000000.