Genome Sequence of the Enterobacter mori Type Strain, LMG 25706, a Pathogenic Bacterium of Morus alba L.

Abstract

Enterobacter mori is a plant-pathogenic enterobacterium responsible for the bacterial wilt of Morus alba L. Here we present the draft genome sequence of the type strain, LMG 25706. To the best of our knowledge, this is the first genome sequence of a plant-pathogenic bacterium in the genus Enterobacter.

GENOME ANNOUNCEMENT

Mulberry (Morus alba L.) is an important economic plant widely grown in Asia, Africa, and Europe. Mulberry leaves are ecologically important as the sole nutrition resource of the silkworm Bombyx mori, the cocoon of which is used to make silk. China produces about 75% of the world's raw silk, which is valued at nearly $2 billion (2). In the summer of 2006, a severe bacterial wilt was noted in mulberry orchards in Hangzhou, Zhejiang Province, China. Our laboratory isolated the pathogen and identified it as an Enterobacter species (6–7, 10). Later, DNA-DNA hybridization, fatty acid analysis, and phylogenetic analysis suggested that it was a new species in the genus Enterobacter (9). We nominated it as Enterobacter mori (named after the mulberry genus Morus) and deposited the reference strain, R18-2, at the Belgian Co-Ordinated Collections of Microorganisms (BCCM) as the type strain LMG 25706 (9).

The genomic DNA, isolated using the Wizard genomic DNA purification kit (Promega, Madison, WI), was subjected to whole-genome sequencing by using Illumina GA (Solexa). This resulted in 15,593,018 high-quality filtered reads of an average read length of 80 bp and coverage equivalent to about 200 times. Quality filtered reads were assembled in silico with the Velvet program (8). Based on the reference genome of Enterobacter cloacae subsp. cloacae ATCC 13047^T (4), a draft genome of LMG 25706^T was completed. By subsequent PCR and resequencing, 84 genome gaps were closed, but the remaining 23 scaffolds (N₅₀ of approximately 280 kb, with the largest scaffold size being 982.8 kb).

The E. mori LMG 25706^T genome has a 4,960,223-base circular chromosome. A total of 4,732 coding sequences (CDSs) were predicted using GLIMMER (5). The putative functions of the encoding genes were automatically identified using the GenDB annotation engine (3). The chromosome has three rRNA operons and 63 tRNAs. Furthermore, 89.3% of the open reading frames (ORFs) have orthologs in the reference strain E. cloacae subsp. cloacae ATCC 13047 (BLASTP < 1e−5), but 457 ORFs were not found in the released genomes of species of the genus Enterobacter; of these, 124 ORFs did not give hits in current public databases.

Although the genome of E. mori LMG 25706^T lacks the type III secretion system (TTSS), which has been proved to be an important virulence-associated system in Gram-negative pathogenic bacteria (1), it still possesses virulence properties recognized to be important in infection. At least 66 genes were found to be potentially involved in different secretion systems (type I, type II, type VI, Sec-SRP, and TaT). They form diverse gene clusters with a high degree of synteny to the reference genome. Interestingly, several genes which were not found in the reference genome have high-similarity orthologs in Erwinia amylovora, an important phytobacterium. The results suggest the differences between E. mori and E. cloacae subsp. cloacae. Overall, the genome sequence of E. mori LMG 25706^T provides a foundation for both basic and agriculturally applied research.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AEXB00000000. The version described in this paper is the first version, deposited under accession number AEXB01000000.