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Open Access Research article

Comparative genomics of Riemerella anatipestifer reveals genetic diversity

Xiaojia Wang13, Wenbin Liu2, Dekang Zhu14, LinFeng Yang2, MaFeng Liu134, Sanjun Yin2, MingShu Wang134*, RenYong Jia134, Shun Chen134, KunFeng Sun134, Anchun Cheng134* and Xiaoyue Chen14

Author Affiliations

1 Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, 46# Xinkang Road, Ya’an, Sichuan 625014, P.R. China

2 BGI-Shenzhen, Shenzhen 518083, China

3 Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China

4 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, P. R. China

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BMC Genomics 2014, 15:479  doi:10.1186/1471-2164-15-479

Published: 17 June 2014

Abstract

Background

Riemerella anatipestifer is one of the most important pathogens of ducks. However, the molecular mechanisms of R. anatipestifer infection are poorly understood. In particular, the lack of genomic information from a variety of R. anatipestifer strains has proved severely limiting.

Results

In this study, we present the complete genomes of two R. anatipestifer strains, RA-CH-1 (2,309,519 bp, Genbank accession CP003787) and RA-CH-2 (2,166,321 bp, Genbank accession CP004020). Both strains are from isolates taken from two different sick ducks in the SiChuang province of China. A comparative genomics approach was used to identify similarities and key differences between RA-CH-1 and RA-CH-2 and the previously sequenced strain RA-GD, a clinical isolate from GuangDong, China, and ATCC11845.

Conclusion

The genomes of RA-CH-2 and RA-GD were extremely similar, while RA-CH-1 was significantly different than ATCC11845. RA-CH-1 is 140,000 bp larger than the three other strains and has 16 unique gene families. Evolutionary analysis shows that RA-CH-1 and RA-CH-2 are closed and in a branch with ATCC11845, while RA-GD is located in another branch. Additionally, the detection of several iron/heme-transport related proteins and motility mechanisms will be useful in elucidating factors important in pathogenicity. This information will allow a better understanding of the phenotype of different R. anatipestifer strains and molecular mechanisms of infection.

Keywords:
Riemerella anatipestifer; Comparative genomics; Structural variation