Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
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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)
  • Received : 2015.11.30
  • Accepted : 2015.12.14
  • Published : 2015.12.31
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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.

Nitrosomonadales 목에서 속하는 균주 중 현재 유전체 서열이 알려진 모든 유전체(N=10)를 이용하여 범유전체 및 핵심유전체 분석을 수행한 결과, 각각 9,808개와 908개 유전자클러스터를 포함하는 것을 확인하였다. Betaproteobacteria의 다른 목의 참조군들과 비교를 통하여 범유전체와 핵심유전체의 크기에 유전체의 수와 집단 내의 유전체들의 차이가 영향을 미치는 것을 확인하였다. Nitrosomonas 속과 Nitrosospira 속의 범유전체는 7,180개와 4,586개, 핵심유전체는 1,092개와 1,600로로 각각 측정되어 Nitrosospira 속의 동질성이 더 높은 것을 확인하였다. Nitrosomonadales 목의 범유전체와 핵심유전체의 크기에 Nitrosomonas 속이 대부분의 영향을 미치는 것을 확인하였다. COG 분석을 통하여 핵심유전체의 크기에는 J (translation, ribosomal structure and biogenesis) 범주가 가장 큰 비율(9.7-21.0%)을 차지하며, 유전체 사이의 유전적 거리가 먼 집단일수록 그 비율이 높아지는 것을 확인하였다. 범유전체의 크기에는 "-" (unclassified) 범주가 34-51%의 높은 비율을 차지하고 있을 정도로 큰 영향을 미치는 것을 확인하였다. 총 97개의 유전자 클러스터가 참조군에는 없고 Nitrosomonadales에만 존재하는 것을 확인하였다. 이들 클러스터들은 Nitrosomonadales을 특징 지우는 유전자들인 ammonia monooxygenase의 유전자인 amoA와 amoB와 그와 관련 있는 amoE와 amoD들을 포함하는 반면에 unclassified 유전자들도 상당량(16-45%)을 포함하고 있다. 이러한 유전자 클러스터는 Nitrosomonadales의 유전적 특이성을 밝히는 데 중요한 역할을 할 것이다.

Keywords

References

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