Abstract
The group Nitriliruptoria, recently classified as a separate class of phylum Actinobacteria, has five members at present, which belong to halophilic or halotolerant Actinobacteria. Here, we sequenced the genomes of Egicoccus halophilus EGI 80432T and Egibacter rhizosphaerae EGI 80759T, and performed a comparative genomics approach to analyze the genomic differences and salt adaptation mechanisms in Nitriliruptoria. Phylogenetic analysis suggested that Euzebya tangerina F10T has a closer phylogenetic relationship to Euzebya rosea DSW09T, while genomic analysis revealed highest genomic similarity with Nitriliruptor alkaliphilus ANL-iso2T and E. halophilus EGI 80432T. Genomic differences of Nitriliruptoria were mainly observed in genome size, gene contents, and the amounts of gene in per functional categories. Furthermore, our analysis also revealed that Nitriliruptoria possess similar synthesis systems of solutes, such as trehalose, glutamine, glutamate, and proline. On the other hand, each member of Nitriliruptoria species possesses specific mechanisms, K+ influx and efflux, betaine and ectoine synthesis, and compatible solutes transport to survive in various high-salt environments.
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Abbreviations
- NCBI:
-
National center for biotechnology information
- BLASR:
-
Basic local alignment with successive refinement
- BLAST:
-
Basic local alignment search tool
- CDS:
-
Coding sequence
- ORF:
-
Open reading framed
- COG:
-
Cluster of orthologous group
- GO:
-
Gene ontology
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- dDDH:
-
Digital DNA–DNA hybridization
- gANI:
-
Genome-aggregate average nucleotide identity
- gAAI:
-
Genome-aggregate average amino acid identity
- RAST:
-
Rapid annotation using subsystems technology
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Acknowledgements
This research was supported by National Natural Science Foundation of China (91751206), Xinjiang Uygur Autonomous Region regional coordinated innovation project (Shanghai cooperation organization science and technology partnership program) (No. 512 2017E01031), China Postdoctoral Science Foundation (No. 2019M662952) and China Biodiversity Observation Networks (Sino BON).
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Supplementary Fig. S1 Functional annotations of genes in E. halophilus EGI 80432T and E. rhizosphaerae EGI 80759T genomes. (a) Functional categories of genes were based on the COG database. (b) Functional categories of genes were based on the KEGG database. (PPT 322 kb)
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Chen, DD., Tian, Y., Jiao, JY. et al. Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies. Extremophiles 24, 249–264 (2020). https://doi.org/10.1007/s00792-019-01150-3
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DOI: https://doi.org/10.1007/s00792-019-01150-3