Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

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


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.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6


  1. Ali A, Naz A, Soares SC, Bakhtiar M, Tiwari S, Hassan SS, Hanan F, Ramos R, Pereira U, Barh D, Figueiredo HC, Ussery DW, Miyoshi A, Silva A, Azevedo V (2015) Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets. Biomed Res Int 2015:139580

  2. Avila-Calderon ED, Lopez-Merino A, Jain N, Peralta H, Lopez-Villegas EO, Sriranganathan N, Boyle SM, Witonsky S, Contreras-Rodriguez A (2012) Characterization of outer membrane vesicles from Brucella melitensis and protection induced in mice. Clin Dev Immunol 2012:352493

  3. Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJ (2012) Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways. BMC Genom 13:373

  4. Comerci DJ, Martinez-Lorenzo MJ, Sieira R, Gorvel JP, Ugalde RA (2001) Essential role of the VirB machinery in the maturation of the Brucella abortus-containing vacuole. Cell Microbiol 3:159–168

  5. De Maayer P, Chan WY, Rubagotti E, Venter SN, Toth IK, Birch PR, Coutinho TA (2014) Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts. BMC Genom 15:404

  6. DelVecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D’Souza M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O’Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R (2002) The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci USA 99:443–448

  7. Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575–1584

  8. Gao F, Luo H, Zhang CT, Zhang R (2015) Gene essentiality analysis based on DEG 10, an updated database of essential genes. Methods Mol Biol 1279:219–233

  9. Gogarten JP, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679–687

  10. Grazziotin AL, Vidal NM, Venancio TM (2015) Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. FEBS J

  11. Jain R, Rivera MC, Moore JE, Lake JA (2002) Horizontal gene transfer in microbial genome evolution. Theor Popul Biol 61:489–495

  12. Katoh K, Toh H (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26:1899–1900

  13. Kryazhimskiy S, Plotkin JB (2008) The population genetics of dN/dS. PLoS Genet 4:e1000304

  14. Lawrence JG (2005) Horizontal and vertical gene transfer: the life history of pathogens. Contrib Microbiol 12:255–271

  15. Lee JJ, Lim JJ, Kim DG, Simborio HL, Kim DH, Reyes AW, Min W, Lee HJ, Chang HH, Kim S (2014) Characterization of culture supernatant proteins from Brucella abortus and its protection effects against murine brucellosis. Comp Immunol Microbiol Infect Dis 37:221–228

  16. Lefebure T, Stanhope MJ (2007) Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8:R71

  17. Liu W, Fang L, Li M, Li S, Guo S, Luo R, Feng Z, Li B, Zhou Z, Shao G, Chen H, Xiao S (2012) Comparative genomics of mycoplasma: analysis of conserved essential genes and diversity of the pan-genome. PLoS One 7:e35698

  18. Lu Y, Deng J, Rhodes JC, Lu H, Lu LJ (2014) Predicting essential genes for identifying potential drug targets in Aspergillus fumigatus. Comput Biol Chem 50:29–40

  19. MacDonald KL, Beveridge TJ (2002) Bactericidal effect of gentamicin-induced membrane vesicles derived from Pseudomonas aeruginosa PAO1 on gram-positive bacteria. Can J Microbiol 48:810–820

  20. Mira A, Martin-Cuadrado AB, D’Auria G, Rodriguez-Valera F (2010) The bacterial pan-genome:a new paradigm in microbiology. Int Microbiol 13:45–57

  21. Muzzi A, Masignani V, Rappuoli R (2007) The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. Drug Discov Today 12:429–439

  22. Rocha EP, Smith JM, Hurst LD, Holden MT, Cooper JE, Smith NH, Feil EJ (2006) Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol 239:226–235

  23. Ronneau S, Moussa S, Barbier T, Conde-Álvarez R, Zuniga-Ripa A, Moriyon I, Letesson JJ (2014) Brucella, nitrogen and virulence. Crit Rev Microbiol: 1–19

  24. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 102:13950–13955

  25. Urbanczyk H, Ast JC, Kaeding AJ, Oliver JD, Dunlap PV (2008) Phylogenetic analysis of the incidence of lux gene horizontal transfer in Vibrionaceae. J Bacteriol 190:3494–3504

  26. Vernikos G, Medini D, Riley DR, Tettelin H (2015) Ten years of pan-genome analyses. Curr Opin Microbiol 23:148–154

  27. Wang F, Hu S, Gao Y, Qiao Z, Liu W, Bu Z (2011) Complete genome sequences of Brucella melitensis strains M28 and M5-90, with different virulence backgrounds. J Bacteriol 193:2904–2905

  28. Wang Y, Ke Y, Wang Z, Yuan X, Qiu Y, Zhen Q, Xu J, Li T, Wang D, Huang L, Chen Z (2012) Genome sequences of three live attenuated vaccine strains of Brucella species and implications for pathogenesis and differential diagnosis. J Bacteriol 194:6012–6013

  29. Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyon I, O’Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC (2012) Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. MBio 3:e00246–12

  30. Wattam AR, Foster JT, Mane SP, Beckstrom-Sternberg SM, Beckstrom-Sternberg JM, Dickerman AW, Keim P, Pearson T, Shukla M, Ward DV, Williams KP, Sobral BW, Tsolis RM, Whatmore AM, O’Callaghan D (2014) Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence. J Bacteriol 196:920–930

  31. Yu D, Hui Y, Zai X, Xu J, Liang L, Wang B, Yue J, Li S (2015) Comparative Genomic Analysis of Brucella abortus vaccine strain 104M reveals a set of candidate genes associated with its virulence attenuation. Virulence 6

  32. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J (2012) PGAP: pan-genomes analysis pipeline. Bioinformatics 28:416–418

Download references


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).

Author information

Correspondence to Yanli Lu or Qingmin Wu.

Ethics declarations

Ethical approval

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

Additional information

Communicated by D. Ussery.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Yang, X., Li, Y., Zang, J. et al. Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.. Mol Genet Genomics 291, 905–912 (2016).

Download citation


  • Brucella
  • Pan-genome
  • Core genome
  • Positive selection
  • Essential genes