Genome Sequence of the Rice-Pathogenic Bacterium Acidovorax avenae subsp. avenae RS-1

Abstract

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...

Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae

“…The Aaa bacteria possesses four types of secretion system (types I, II, III, IV) in its genome [11,13]. The type III secretion system (T3SS) is involved with virulence capacity and the injected effectors into the plant cell and can be recognized by NBS-LRR genes (R genes), triggering the ETI [144].…”

“…The complete genome of Aaa (strain RS-1 which infects rice) reveals many genes involved in pathogenicity [11]. Subsequently, it was shown that mutations in the pilP gene, which encodes one of the proteins that form the Type IV (pili hair-like appendages involved in several bacterial activities), affects the ability to initiate the disease in rice [12].…”

Genome Sequence of the Plant Pathogen Pseudomonas syringae pv. panici LMG 2367

“…The pathogen can also attack young, unfolded leaves, resulting in the stunting or death of seedlings (3,5,6), which is similar to the symptoms caused by Acidovorax avenae subsp. avenae (10). The disease is more severe in the years after floods.…”

Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1

“…The sequenced genomes of Acidovorax members can be further separated into two groups, four environmental species, including those from soil and water habitats (NZ_ ACQT00000000) (4, 6, 7), and three plant pathogens that cause fruit blotch or brown stripe (ADCB01000000) (3,15), which makes the Acidovorax genus a good candidate for genome comparison to explore its different physiological and ecological roles.…”