Abstract
Pantoea sp. strain A4 is a Gram-negative bacterium isolated from the Rafflesia flower. We present here, for the first time, the genome sequence of Rafflesia-associated Pantoea sp. strain A4, which exhibited quorum-sensing activity.
GENOME ANNOUNCEMENT
Rafflesia is an endophytic holoparasite flowering plant found mostly in Southeast Asia, and it is one of the world's largest flowers (1, 2). A member of the genus Pantoea has been reported to synthesize quorum-sensing signaling molecules, i.e., N-acylhomoserine lactones (AHLs) (9), that regulate several phenotypes, such as virulence factor production, cell aggregation (8), and biofilm formation (7). Here we present the genome sequence of Pantoea sp. strain A4, an AHL-producing bacterium isolated from Rafflesia cantleyi in the tropical rain forest of Peninsular Malaysia. We sequenced the complete genome of Pantoea sp. strain A4 as a step toward understanding the molecular regulation of the quorum-sensing system in this bacterium.
The total genomic DNA of Pantoea sp. strain A4 was isolated using the QIAamp DNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. The quality of the DNA was examined using a Nanodrop spectrophotometer (Thermo Scientific) and a Qubit 2.0 fluorometer (Life Technologies). Whole-genome sequencing of Pantoea sp. strain A4 was performed using the Illumina HiSeq 2000 (Illumina, Inc.) platform. This resulted in 577,857,447 filtered reads with an average read length of 77.94 bp and approximately 108.25-fold coverage. The filtered reads were de novo assembled with CLC Genomic Workbench version 5.1, generating 72 contigs (N50, 224,734.58). The genome contains a total of 5,331,108 bp with a G+C content of 52.91%. Gene prediction was performed using Prodigal (version 2.60), and a total of 4,793 open reading frames were predicted (4) and annotated by comparison with the NCBI nonredundant database (3). A total of 43 tRNAs were predicted using tRNAscan-SE (v.1.21) (6), and the rRNAs were predicted using the RNAmmer 1.2 server (5).
From the BLAST results, Pantoea sp. strain A4 possesses two AHL synthase genes, of which the first is similar to eanI of Pantoea ananatis (identity score of 74%) and the other is similar to phzI of Pantoea sp. (identity score of 79%). The genome sequence of Pantoea sp. strain A4 may provide novel insight into the quorum-sensing regulation mechanism of this bacterium.
Nucleotide sequence accession numbers.
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. ALXE00000000. The version described in this paper is the first version, ALXE01000000.
ACKNOWLEDGMENTS
K.-G. Chan thanks the University of Malaya for the financial support awarded (High Impact Research Grant A000001-50001).
We thank Sonny Wong (Malaysian Nature Society) for his assistance during the field sampling of the Rafflesia flower.
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