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Molecular Genetics and Genomics

, Volume 291, Issue 2, pp 905–912 | Cite as

Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.

  • Xiaowen Yang
  • Yajie Li
  • Juan Zang
  • Yexia Li
  • Pengfei Bie
  • Yanli Lu
  • Qingmin Wu
Original Article

Abstract

Brucella spp. are facultative intracellular pathogens, that cause a contagious zoonotic disease, that can result in such outcomes as abortion or sterility in susceptible animal hosts and grave, debilitating illness in humans. For deciphering the survival mechanism of Brucella spp. in vivo, 42 Brucella complete genomes from NCBI were analyzed for the pan-genome and core genome by identification of their composition and function of Brucella genomes. The results showed that the total 132,143 protein-coding genes in these genomes were divided into 5369 clusters. Among these, 1710 clusters were associated with the core genome, 1182 clusters with strain-specific genes and 2477 clusters with dispensable genomes. COG analysis indicated that 44 % of the core genes were devoted to metabolism, which were mainly responsible for energy production and conversion (COG category C), and amino acid transport and metabolism (COG category E). Meanwhile, approximately 35 % of the core genes were in positive selection. In addition, 1252 potential essential genes were predicted in the core genome by comparison with a prokaryote database of essential genes. The results suggested that the core genes in Brucella genomes are relatively conservation, and the energy and amino acid metabolism play a more important role in the process of growth and reproduction in Brucella spp. This study might help us to better understand the mechanisms of Brucella persistent infection and provide some clues for further exploring the gene modules of the intracellular survival in Brucella spp.

Keywords

Brucella Pan-genome Core genome Positive selection Essential genes 

Notes

Acknowledgments

This work was funded by the National Natural Science Foundation of China (No. 31372446) and National Special Foundation for Science and Technology Basic Research (No. 2012FY111000).

Compliance with ethical standards

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary material 1 (DOCX 50 kb)
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Supplementary material 2 (XLSX 126 kb)
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Supplementary material 3 (XLSX 178 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary MedicineChina Agricultural UniversityBeijingPeople’s Republic of China

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