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KMID : 0364820150510040329
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Korean Journal of Microbiology
2015 Volume.51 No. 4 p.329 ~ p.337
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Comparative analysis of core and pan-genomes of order Nitrosomonadales
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Lee Jin-Hwan
Kim Kyoung-Ho
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Abstract
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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.
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KEYWORD
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Nitrosomonadales, comparative genomics, core genome, pan?genome
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