Draft Genome Sequence of Rice Endophyte-Associated Isolate Kosakonia oryzae KO348.

Kosakonia oryzae KO348 is an endophytic and plant growth-promoting strain isolated from the roots of rice in Italy. Here, we report the draft genome sequence of Kosakonia oryzae KO348.

GENOME ANNOUNCEMENT

Created in 1960, the genus Enterobacter is one of the largest genera within the family Enterobacteriaceae (1). Recently, taxonomic studies have resulted in rearrangement of the Enterobacter genera (2). As a result, a new genus designated Kosakonia, which includes the species Kosakonia cowanii, Kosakonia radicincitans, Kosakonia oryzae, and Kosakonia arachidis (2), was proposed, and in 2014, the nitrogen-fixing bacterium Enterobacter sacchari was reclassified as Kosakonia sacchari (3). Kosakonia oryzae has been associated with rice and has been shown to possess plant growth-promoting properties, including the ability to fix atmospheric nitrogen (4).

Kosakonia oryzae KO348 was isolated from surface-sterilized roots of the Italian rice cultivar Vialone Nano. Phylogenetic analyses using 16s rRNA and multilocus sequence analysis based on gyrB, rpoB, infB, and atpD indicate that this novel isolate belongs to genus Kosakoni, and here we announce its draft genome sequence. Genomic DNA of K. oryzae KO348 was purified following the protocol of the Nextera XT DNA library preparation kit (Illumina) and then used to prepare a sequencing-ready library. Sequencing was performed on Illumina MiSeq platform using 150-bp paired-end reads. Total number of pairs of reads was 5,010,628, representing approximately 10-fold coverage of the genome. We performed the de novo assembly using SPAdes v3.0 (5), generating 68 contigs with a maximum length of 462 kbp. The total length of the contig assembly was 5.0 Mbp, and the N50 length was 172 kbp, assuming a genome size of 5.0 Mbp. The G+C content was 53.9%, similar to that of other Kosakonia sequenced genomes. Automated annotation of the K. oryzae KO348 draft genome sequence was performed using RAST (6) assigning a total of 4,763 candidate protein-coding genes with 1,045 (21.94%) annotated as hypothetical proteins. A total of 86 RNA coding sequences were also identified. The K. oryzae KO348 genome presents several genes related to plant colonization and plant growth promotion, including genes for exopolysaccharide production, flagellar motility, siderophore production, auxin biosynthesis, and the nif gene cluster. Furthermore, it contains genes involved in the biosynthesis of type II, IV, V, VI, VII, and VIII secretion systems.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JZLI00000000. The version described in this paper is version JZLI01000000.