Abstract
The complete genome sequence of the endophytic diazotroph Kosakonia sacchari, isolated from a sweet potato, was analyzed. The 4,902,106-bp genome with 53.7% G+C content comprises 4,638 open reading frames, including nif genes, 84 tRNAs, and seven complete rRNAs in a circular chromosome.
GENOME ANNOUNCEMENT
The endophytic bacterial strain BO-1 was originally isolated from the surface-sterilized stem of a sweet potato (Ipomoea batatas, cultivar “Beniotome”) from Miyakonojo, Miyazaki, Japan, and identified as Klebsiella oxytoca based on a partial sequence of the 16s rRNA (1). The strain grew diazotrophically in a free-living state under nitrogen-deficient conditions and showed a positive reaction in the acetylene reduction activity test (1). Whole-genome sequencing analysis revealed that the genome of strain BO-1 is most similar to Kosakonia sacchari strain SP1, isolated from sugarcane (2); therefore, this strain likely belongs to Kosakonia sacchari, which is a Gram-negative, aerobic, non-spore-forming, motile rod-shaped species, recently reclassified from Enterobacter sacchari (3).
The bacterial strain BO-1 (MAFF 211344) was obtained from the National Institute of Agrobiological Science (NIAS, Japan). Genomic DNA was extracted using a genomic DNA purification kit (Promega, USA). Paired-end DNA libraries were prepared for sequencing with an Illumina MiSeq platform. A total of 12,874,059 high-quality paired-end reads were generated, with 788-fold coverage. De novo assembly was performed using SPAdes genome assembler version 3.6.2 (4). Removal of short contigs resulted in 916 contigs with an N50 of 828,908 bp. Gaps were closed by PCR amplification and Sanger sequencing of the PCR products. The genome of K. sacchari BO-1 consists of a circular chromosome (4,902,106 bp; 53.7% G+C content).
The strain BO-1 is most closely related to K. sacchari strain SP1, with which it shares 98.67% average nucleotide identity (ANI) (5). Since two genomes with an ANI >95% are considered to be from the same species, the strain BO-1 is reidentified as Kosakonia sacchari. The chromosome of K. sacchari strain SP1 had the highest sequence similarities to the chromosome of Enterobacter sp. strain R4-368, an endophytic nitrogen-fixing bacterium isolated from Jatropha curcas (2, 6). The ANIs of Enterobacter sp. strain R4-368 with K. sacchari strain BO-1 and strain SP1 were 94.06% and 94.01%, respectively.
The genomic sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok). The chromosome has 4,448 coding sequences, seven sets of rRNA genes, and 84 tRNA genes. The genome annotation also confirmed the presence of the nif gene locus for nitrogen fixation.
Accession number(s).
The genome sequence of K. sacchari strain BO-1 was deposited in DDBJ/EMBL/GenBank under the accession number CP016337.
ACKNOWLEDGMENTS
We thank Katsuki Adachi (Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Japan), Motohiko Kondo (Nagoya University, Japan), and Joyce Cartagena (Nagoya University, Japan) for comments on the manuscript. We also thank Hiroyuki Sawada (Genetic Resources Center, National Agriculture and Food Research Organization, Japan) for advice on classifying bacterial strains.
Footnotes
Citation Shinjo R, Uesaka K, Ihara K, Loshakova K, Mizuno Y, Yano K, Tanaka A. 2016. Complete genome sequence of Kosakonia sacchari strain BO-1, an endophytic diazotroph isolated from a sweet potato. Genome Announc 4(5):e00868-16. doi:10.1128/genomeA.00868-16.
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