title: Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.
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.
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Yang
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
authors.forename: Yajie
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
authors.forename: Juan
authors.initials: J
authors.lastname: Zang
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
authors.forename: Yexia
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Bie
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China. luyanli@cau.edu.cn.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China. wuqm@cau.edu.cn.
authors.forename: Qingmin
authors.identifier: http://orcid.org/0000-0001-5685-0766
authors.initials: Q
authors.lastname: Wu
mesh_terms: D000818:Animals; D002002:Brucella / Q000235:genetics* / Q000472:pathogenicity; D019295:Computational Biology; D004734:Energy Metabolism / Q000235:genetics*; D020043:Genes, Essential; D016680:Genome, Bacterial; D006801:Humans; D015047:Zoonoses / Q000235:genetics* / Q000382:microbiology
keywords: Brucella; Core genome; Essential genes; Pan-genome; Positive selection