Complete Genome Sequence of Riemerella anatipestifer Reference Strain

Abstract

Riemerella anatipestifer is an infectious pathogen causing serositis in ducks. We had the genome of the R. anatipestifer reference strain ATCC 11845 sequenced. The completed draft genome consists of one circular chromosome with 2,164,087 bp. There are 2,101 genes in the draft, and its GC content is 35.01%.

GENOME ANNOUNCEMENT

Riemerella anatipestifer is a Gram-negative, rod-shaped bacterium. It can cause septicemic and exudative diseases in domestic ducks and turkeys and various other birds. Segers et al. believed that R. anatipestifer should belong to the Riemerella genus (13). To date, more than 21 serotypes have been reported for R. anatipestifer, but there is no cross-protection among them (3, 10). R. anatipestifer has a very wide drug resistance spectrum and is resistant to most antibiotics (2, 17).

A standard R. anatipestifer strain, ATCC 11845, was sent to BGI for sequencing and was sequenced using Illumina high-throughput sequencing. By using a single-molecule array test for genotyping, the genome sequence was interpreted to be about 100 to 200 bp and was amplified by PCR into the library. SOAPdenovo assembly software (7), developed by BGI, read the data assembled using the mapping information, and the gap was complemented by results of software assembly and single-base proofreading. The potential of each connection relationship between the scaffolds was analyzed. A total of 66 contigs were formed by assembling 30 scaffolds. Gaps were closed by PCR amplification and paired-end sequencing. Sequencing depth was 140×, CG content was 35.01%, and genome coverage was 99.6%.

We used Glimmer software to predict open reading frames (ORF) and used KEGG, COG, Swiss-Prot, TrEMBL, and NR protein databases for alignment (4, 9, 12). The completed genome consists of one circular chromosome with 2,164,087 bp, and its GC content is 35.01%. We used the tRNAscan software, the rRNAmmer software, and the Rfam software to predict rRNA, tRNA, microRNA (miRNA), sRNA, and snRNA (5, 6, 8). RepeatMasker software (Repbase database) and RepeatProteinMasker software (the RepeatMasker library that comes with the transposon protein) were used to predict the transposon, and the Tandem Repeat Finder software was used to predict the tandem repeat (1, 14). The results indicate that the genome has 2,101 genes, 2,055 protein-coding genes, 36 tRNA genes, 9 rRNA genes, 1 miRNA gene, and 4 types of transposons (0.67%).

In the R. anatipestifer standard reference strain ATCC 11845, we found 34 proteins which are related to absorption and utilization of Fe. Five types of cell division proteins were also discovered, of which FtsZ is the key protein of bacterial cell division (11). However, by multiple alignments with other FtsZ sequences from R. anatipestifer strains in the database, we confirmed that the FtsZ protein of the reference stain has two amino acid site changes, and these may be considered in the development of new antibiotics. Most bacterial pathogens have active efflux systems (AEs) which are related to antibiotic resistance. To date, four families of AEs have been elucidated (15, 16). In our test strain, two families, the small multidrug resistance protein (SMR) family and the major facilitator superfamily (MFS), were found. In addition to genes for the two above-described AEs, we found several other resistance-associated genes: vanZ, a vancomycin resistance gene; a penicillinase repressor gene; an acriflavin resistance gene; and crcB, a camphor resistance gene. In general, R. anatipestifer has many drug resistance genes, which is probably why it has a wide range of drug resistance.

Nucleotide sequence accession number.

The sequence of the R. anatipestifer reference strain ATCC 11845 has been deposited in GenBank under accession no. CP003388.