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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

Abstract

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.

Keywords

Nitrosomonadales;comparative genomics;core genome;pan-genome

Acknowledgement

Supported by : 부경대학교

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