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Journal of Bacteriology logoLink to Journal of Bacteriology
. 2012 Dec;194(23):6666–6667. doi: 10.1128/JB.01468-12

Genome Sequence of the Biocontrol Agent Microbacterium barkeri Strain 2011-R4

Jian Liu a,b,c, Qing Zhou a,c, Muhammad Ibrahim a,c, He Liu a,c, Gulei Jin d, Bo Zhu a,c,, Guanlin Xie a,c,
PMCID: PMC3497549  PMID: 23144410

Abstract

Microbacterium barkeri strain 2011-R4 is a Gram-positive epiphyte which has been confirmed as a biocontrol agent against several plant pathogens in our previous studies. Here, we present the draft genome sequence of this strain, which was isolated from the rice rhizosphere in Tonglu city, Zhejiang province, China.

GENOME ANNOUNCEMENT

Microbacterium barkeri is one of the species in the genus Microbacterium, which belongs to the high-GC-content phylum Actinobacteria (13). It has been reported that Microbacterium strains can cause human, animal, and plant diseases (1, 7, 9). However, Microbacterium spp. have frequently been isolated from the soil and used as biocontrol agents (2, 16, 18). Some reports have demonstrated that Microbacterium barkeri strains are strong in plant colonization (17) and play a very important role in biocontrol. Cottyn et al. isolated several Microbacterium barkeri strains with potential biocontrol ability from rice seeds (5, 6). These results suggested that Microbacterium barkeri may be useful to further explore the commercial potential for biocontrol in rice fields, and genome-wide sequence analysis could play an important role for genetic studies of this bacterium.

In this research, we sequenced and annotated the draft genome of Microbacterium barkeri 2011-R4 isolated as an epiphyte from the rice rhizosphere of Tonglu city, Zhejiang province. The bacterial genomic DNA, isolated using a QIAamp DNA minikit (Qiagen, Germany), was paired-end whole-genome shotgun sequenced using Illumina HiSeq 2000 with a 500-bp inserted library. This resulted in 20,513,376 high-quality filtered reads with a 95-bp average read length and coverage equivalent to about 1,000×. Paired-end reads were assembled in silico with IDBA-UD 1.0.9 (15). Assembled contigs were scaffolded using SSPACE Basic 2.0 (3). Based on the reference genome of Microbacterium testaceum StLB037 (13), a draft genome of 2011-R4 was completed. By subsequent PCR and resequencing, 35 genome gaps were closed but 142 contigs remained.

The draft genome sequence of strain Microbacterium barkeri 2011-R4 comprises 3,637,250 bases representing approximately >99.9% of the estimated genome size of 2011-R4. The genome of this strain has a high G+C content of 69.1%. A total of 3,817 coding sequences (CDSs) were predicted using Prodigal v2.6 with default parameters (8). The functions of encoding genes were automatically identified by the GenDB annotation engine (12). The chromosome has eight rRNA operons and 47 tRNAs predicted by RNAmmer and tRNAscan (10, 11). Furthermore, 68.2% of the open reading frames (ORFs) have orthologs in the reference strain M. testaceum StLB037 (BLASTP, <1e−5), but 1,213 ORFs were not found in the released genomes of the Microbacterium genus. Of these previously unreported ORFs, 1,057 ORFs did not generate hits in current public databases (NCBInr database).

The Microbacterium barkeri 2011-R4 genome contains a repertoire of antimicrobial-, antibiotic-, and metabolism-associated pathways and epiphytic fitness genes which were identified by KEGG databases (14). Until now, only two Microbacterium genome sequences have been released (4, 13); therefore, it is very hard to predict the potential biocontrol functions of many genes in our strain. Overall, the genome sequence of S. maltophilia RR-10 provides a foundation not only for plant disease control research but also for Microbacterium genomics and comparative genomics research.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AKVP00000000. The version described in this paper is the first version, AKVP01000000.

ACKNOWLEDGMENTS

This work was supported by the China Postdoctoral Foundation (317000-X91102), the Special Fund for Agro-scientific Research in the Public Interest (201003029, 201003066), the National Natural Science Foundation of China (30871655, 30900074), the Zhejiang Natural Science Foundation of China (LY12C14007), and the Zhejiang Agriculture Department (Ji-fa 2008-97).

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