Comparative analysis of core and pan-genomes of order Nitrosomonadales

Nitrosomonadales 목의 핵심유전체(core genome)와 범유전체(pan-genome)의 비교유전체학적 연구

  • Lee, Jinhwan (Aquaculture Division, National Institute of Fisheries Science) ;
  • Kim, Kyoung-Ho (Department of Microbiology, Pukyong National University)
  • 이진환 (국립수산과학원 양식관리과) ;
  • 김경호 (부경대학교 미생물학과)
  • Received : 2015.11.30
  • Accepted : 2015.12.14
  • Published : 2015.12.31


All known genomes (N=10) in the order Nitrosomonadales were analyzed to contain 9,808 and 908 gene clusters in their pan-genome and core genome, respectively. Analyses with reference genomes belonging to other orders in Betaproteobacteria revealed that sizes of pan-genome and core genome were dependent on the number of genomes compared and the differences of genomes within a group. The sizes of pan-genomes of the genera Nitrosomonas and Nitrosospira were 7,180 and 4,586 and core genomes, 1,092 and 1,600, respectively, which implied that similarity of genomes in Nitrosospira were higher than Nitrosomonas. The genomes of Nitrosomonas contributed mostly to the size of the pan-genome and core genomes of Nitrosomonadales. COG analysis of gene clusters showed that the J (translation, ribosomal structure and biogenesis) category occupied the biggest proportions (9.7-21.0%) among COG categories in core genomes and its proportion increased in the group which genetic distances among members were high. The unclassified category (-) occupied very high proportions (34-51%) in pan-genomes. Ninety seven gene clusters existed only in Nitrosomonadales and not in reference genomes. The gene clusters contained ammonia monooxygenase (amoA and amoB) and -related genes (amoE and amoD) which were typical genes characterizing the order Nitrosomonadales while they contained significant amount (16-45%) of unclassified genes. Thus, these exclusively-conserved gene clusters might play an important role to reveal genetic specificity of the order Nitrosomonadales.


Nitrosomonadales;comparative genomics;core genome;pan-genome


Supported by : 부경대학교


  1. Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. 2004. UniProt: the Universal Protein knowledge base. Nucleic Acids Res. 32, D115-119.
  2. Arp, D.J., Sayavedra-Soto, L.A., and Hommes, N.G. 2002. Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch. Microbiol. 178, 250-255.
  3. Bollmann, A., Sedlacek, C.J., Norton, J., Laanbroek, H.J., Suwa, Y., Stein, L.Y., Klotz, M.G., Arp, D., Sayavedra-Soto, L., Lu, M., et al. 2013. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations. Stand. Genomic Sci. 7, 469-482.
  4. Chain, P., Lamerdin, J., Larimer, F., Regala, W., Lao, V., Land, M., Hauser, L., Hooper, A., Klotz, M., Norton, J., et al. 2003. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185, 2759-2773.
  5. El Sheikh, A.F., Poret-Peterson, A.T., and Klotz, M.G. 2008. Characterization of two new genes, amoR and amoD, in the amo operon of the marine ammonia oxidizer Nitrosococcus oceani ATCC 19707. Appl. Environ. Microbiol. 74, 312-318.
  6. Foesel, B.U., Gieseke, A., Schwermer, C., Stief, P., Koch, L., Cytryn, E., de la Torre, J.R., van Rijn, J., Minz, D., Drake, H.L., et al. 2008. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm. FEMS Microbiol. Ecol. 63, 192-204.
  7. Head, I.M., Hiorns, W.D., Embley, T.M., McCarthy, A.J., and Saunders, J.R. 1993. The phylogeny of autotrophic ammoniaoxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J. Gen. Microbiol. 139 Pt 6, 1147-1153.
  8. Itoi, S., Niki, A., and Sugita, H. 2006. Changes in microbial communities associated with the conditioning of filter material in recirculating aquaculture systems of the pufferfish Takifugu rubripes. Aquaculture 256, 287-295.
  9. Kim, J.N., Kim, Y., Jeong, Y., Roe, J.H., Kim, B.G., and Cho, B.K. 2015. Comparative genomics reveals the core and accessory genomes of Streptomyces species. J. Microbiol. Biotechnol. 25, 1599-1605.
  10. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
  11. Klotz, M.G. and Stein, L.Y. 2011. Genomics of ammonica-oxidizing bacteria and insights into their evolution. Nitrification, American Society of Microbiology.
  12. Medini, D., Donati, C., Tettelin, H., Masignani, V., and Rappuoli, R. 2005. The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589-594.
  13. Mitchell, A., Chang, H.Y., Daugherty, L., Fraser, M., Hunter, S., Lopez, R., McAnulla, C., McMenamin, C., Nuka, G., Pesseat, S., et al. 2015. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43, D213-221.
  14. Norton, J.M., Klotz, M.G., Stein, L.Y., Arp, D.J., Bottomley, P.J., Chain, P.S., Hauser, L.J., Land, M.L., Larimer, F.W., Shin, M.W., et al. 2008. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl. Environ. Microbiol. 74, 3559-3572.
  15. Purkhold, U., Wagner, M., Timmermann, G., Pommerening-Roser, A., and Koops, H.P. 2003. 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int. J. Syst. Evol. Microbiol. 53, 1485-1494.
  16. Squizzato, S., Park, Y.M., Buso, N., Gur, T., Cowley, A., Li, W., Uludag, M., Pundir, S., Cham, J.A., McWilliam, H., et al. 2015. The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. Nucleic Acids Res. 43, W585-588.
  17. Stein, L.Y., Arp, D.J., Berube, P.M., Chain, P.S., Hauser, L., Jetten, M.S., Klotz, M.G., Larimer, F.W., Norton, J.M., Op den Camp, H.J., et al. 2007. Whole-genome analysis of the ammoniaoxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ. Microbiol. 9, 2993-3007.
  18. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725-2729.
  19. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278, 631-637.
  20. Teske, A., Alm, E., Regan, J.M., Toze, S., Rittmann, B.E., and Stahl, D.A. 1994. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J. Bacteriol. 176, 6623-6630.
  21. Tettelin, H., Masignani, V., Cieslewicz, M.J., Donati, C., Medini, D., Ward, N.L., Angiuoli, S.V., Crabtree, J., Jones, A.L., Durkin, A.S., et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc. Natl. Acad. Sci. USA 102, 13950-13955.
  22. Utaker, J.B., Bakken, L., Jiang, Q.Q., and Nes, I.F. 1995. Phylogenetic analysis of seven new isolates of ammonia-oxidizing bacteria based on 16S rRNA gene sequences. Syst. Appl. Microbiol. 18, 549-559.
  23. Vernikos, G., Medini, D., Riley, D.R., and Tettelin, H. 2015. Ten years of pan-genome analyses. Curr. Opin. Microbiol. 23, 148-154.
  24. Xia, F., Zou, B., Shen, C., Zhu, T., Gao, X.H., and Quan, Z.X. 2015. Complete genome sequence of Methylophilus sp. TWE2 isolated from methane oxidation enrichment culture of tap-water. J. Biotechnol. 211, 121-122.
  25. Xiong, X.H., Zhi, J.J., Yang, L., Wang, J.H., Zhao, Y., Wang, X., Cui, Y.J., Dong, F., Li, M.X., Yang, Y.X., et al. 2011. Complete genome sequence of the bacterium Methylovorus sp. strain MP688, a high-level producer of pyrroloquinolone quinone. J. Bacteriol. 193, 1012-1013.
  26. Zhao, Y., Wu, J., Yang, J., Sun, S., Xiao, J., and Yu, J. 2012. PGAP: pan-genomes analysis pipeline. Bioinformatics 28, 416-418.

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