Abstract
The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.
Highlights
The genus Paenibacillus was designated in 1993 and was composed of 11 species originally belonging to the genus Bacillus[1]
The genomic features of SSG-1 are shown in Fig. 1 and Table 1, and those of other genus members are shown in Dataset S1
We proposed that the agarase gene Aga[1] together with surrounding genes in SSG-1 were acquired through horizontal gene transfer (HGT), but the evidences obtained in the previous study were limited[26]
Summary
The genus Paenibacillus was designated in 1993 and was composed of 11 species originally belonging to the genus Bacillus[1]. Comparative genomics revealed that the diversity of the gene repertoires endows these microorganisms with various metabolic activities and extensive adaptabilities to the environment[14,15,16,17,18]. In this context, the key unit of microbial evolution is not the genome of an individual bacterium but, rather, the pan-genome of a prokaryote species. The present study examined the effects of genome dynamics on the adaptability of Paenibacillus species to disclose the evolution pattern of the genus Paenibacillus. SSG-1 with the agar-degrading trait was further investigated
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