BackgroundThe domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs.ResultsTen candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori.ConclusionsResults from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes.

Acidovorax avenae subsp. avenae is a phytobacterium which is the causative agent of several plant diseases with economic significance. Here, we present the draft genome sequence of strain RS-1, which was isolated from rice shoots in a rice field in China. This strain can cause bacterial stripe of rice.Acidovorax avenae subsp. avenae, formerly Pseudomonas avenae (10), can cause diseases in many plants with economic importance, including rice, corn, oats, sugarcane, millet, and foxtail (9). In rice, this pathogen can cause bacterial brown stripe and has been reported in many countries in Asia, Africa, the Americas, and Europe (11). The symptoms start as brown stripes on the bottom of stems 5 days after emergence and frequently extend into the sheaths, spreading along the leaf midrib and throughout the seedling at the one-leaf stage (3). As A. avenae subsp. avenae is a widely distributed seed-borne pathogen of rice (8-9), the rice seeds contaminated with this pathogen are important sources of the primary inoculum and a means of dissemination of the pathogen to new areas (1, 8). Therefore, this pathogen has been gaining increasing attention in China.We sequenced and annotated the draft genome of A. avenae subsp. avenae strain RS-1, a strain isolated from a diseased rice sheet in Zhejiang province in 2010 (3). The genomic DNA, isolated with a Wizard genomic DNA purification kit (Promega, Madison, WI), was whole-genome sequenced by using an Illumina HiSeq 2000 sequencing system. This resulted in 17,300,242 high-quality filtered reads with an average read length of 96 bp and coverage equivalent to about 200ϫ. Quality filtered reads were assembled in silico with SOAPdenovo and the GapCloser program (4). Based on the reference genome of A. avenae subsp. avenae ATCC 19860 (sequenced by JGI; isolated from maize leaf), a draft genome of RS-1 was completed. By subsequent PCR and resequencing, 62 genome gaps were closed, but 156 contigs remained.The draft genome sequence of strain RS-1 comprises 5,522,282 bases, representing approximately more than 99.9% of the estimated genome of RS-1. The genome of this strain has a high GϩC content, 68.7%. A total of 5,043 coding sequences (CDSs) were predicted using GLIMMER (7). Putative functions of encoding genes were automatically identified using the GenDB annotation engine (6). The chromosome has three rRNA operons and 43 tRNAs predicted by RNAmmer and tRNAscan (2, 5). Furthermore, 90.4% of the open reading frames (ORFs) have orthologs in the reference strain A. avenae subsp. avenae ATCC 19860 (BLASTP value Ͻ 1e-5), but 301 ORFs were not found in the released genomes of members of the genus Acidovorax. Interestingly, many of these ORFs are clustered together. The result suggested that these regions may be genomic islands in A. avenae subsp. avenae RS-1.Pathogenicity-related genes (such as those involved in hypersensitive response and the type III secretion system-related proteins), which are essential for many plant-pathogenic bacteria, are found in RS-1. Meanwhile, several loci enco...

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Aims:  To investigate the inhibition potential of leaf‐associated bacteria against the pathogen of bacterial leaf spot of Euphorbia pulcherrima. Methods and Results:  Seven out of 200 bacterial strains were effective antagonists by in vitro screening and the two strains PAB241 and PAB242 significantly reduced the disease incidence and severity as foliar treatments of E. pulcherrima. The two effective strains, PAB241 and PAB242, were both identified as Bacillus amyloliquefaciens by a polyphasic approach including phenotypic feature, carbon source utilization profile, fatty acid methyl esters and analysis of 16S rRNA gene sequence. In addition, the suspensions of B. amyloliquefaciens PAB241 and PAB242 showed antibacterial activities against the pathogen of bacterial leaf spot of E. pulcherrima under different treatments. Conclusions:  The leaf‐associated bacteria, B. amyloliquefaciens PAB241 and PAB242, markedly inhibited the growth of X. axonopodis pv. poinsettiicola under different treatments and protected E. pulcherrima from pathogen infection in growth chamber conditions. Significance and Impact of the Study:  This is the first study that showed B. amyloliquefaciens from plant leaves was a potential bactericide against bacterial leaf spot of E. pulcherrima.

Two isolates of mulberry-pathogenic bacteria isolated from diseased mulberry roots were investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strains R18-2(T) and R3-3 to the genus Enterobacter, with Enterobacter asburiae, E. amnigenus, E. cancerogenus, E. cloacae subsp. cloacae, E. cloacae subsp. dissolvens and E. nimipressuralis as their closest relatives. Cells of the isolates were Gram-negative, facultatively anaerobic rods, 0.3-1.0 µm wide and 0.8-2.0 µm long, with peritrichous flagella, showing a DNA G+C content of 55.1 ± 0.5 mol%. Calculation of a similarity index based on phenotypic features and fatty acid methyl ester (FAME) analysis suggested that these isolates are members of E. cancerogenus or E. asburiae or a closely related species. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by the presence of lysine decarboxylase activity and their ability to utilize d-arabitol. DNA-DNA relatedness also distinguished the two isolates from phylogenetically closely related Enterobacter strains. Based on these data, it is proposed that the isolates represent a novel species of the genus Enterobacter, named Enterobacter mori sp. nov. The type strain is R18-2(T) ( = CGMCC 1.10322(T) = LMG 25706(T)).

The effect of rhizobacterium Burkholderia sp. strain R456 on the inhibition of Rhizoctonia solani, sheath blight of rice was examined. Results from this study indicated that strain R456 not only suppressed the in vitro mycelial growth of R. solani, but also reduced the incidence and severity of rice sheath blight under greenhouse conditions. However, similar to plant pathogenic strain LMG 1222 T of Burkholderia cepacia, the type species of the genus, infiltration of tobacco leaves with cell suspension of strain R456 resulted in typical hypersensitivity reactions while the two bacterial strains were unable to cause disease symptoms on rice seedlings. The fatty acid methyl ester profile, sole carbon source utilization, and biochemical tests confirmed that the antagonistic rhizobacterium R456 is a member of the genus Burkholderia. Furthermore, strain R456 was differentiated from B. cepacia LMG 1222 T and was identified as Burkholderia seminalis based on recA gene sequence analysis and multilocus sequence typing. In addition, this rhizobacterium had a lower proteolytic activity compared with that of the pathogenic B. cepacia LMG 1222 T while no cblA and esmR marker genes were detected for the two bacterial strains. Overall, this is the first characterization of rhizobacterium B. seminalis that protected rice seedlings from infection by R. solani.

A survey of Burkholderia cepacia complex (Bcc) species was conducted in water bodies of West Lake in China. A total of 670 bacterial isolates were recovered on selective media. Out of them, 39.6% (265 isolates) were assigned to the following species: Burkholderia multivorans, Burkholderia cenocepacia recA lineage IIIA, IIIB, Burkholderia stabilis, Burkholderia vietnamiensis, and Burkholderia seminalis while B. cenocepacia is documented as a dominant Bcc species in water of West Lake. In addition, all Bcc isolates tested were PCR negative for the cblA and esmR transmissibility marker genes except B. cenocepacia IIIB A8 which was positive for esmR genelater. The present study raises great concerns on the role of West Lake as a "reservoir" for potential Bcc pathogenic strains.