References
- Aiyar A. The use of CLUSTAL W and CLUSTAL X for Multiple Sequence Alignment. Methods Mol Biol. 2000;132:221–241. https://doi.org/10.1385/1-59259-192-2:221
- Baker BA, Gutiérrez-Preciado A, Rodríguez Del Río Á, McCarthy CGP, López-García P, Huerta-Cepas J, Susko E, Roger AJ, Eme L, Moreira D. Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments. Nat Microbiol. 2024;9(4):964–975. https://doi.org/10.1038/s41564-024-01647-4
- Brown J, Pirrung M, McCue LA. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics. 2017;33(19):3137–3139. https://doi.org/10.1093/bioinformatics/btx373
- Chen S, Liu HC, Zhao D, Yang J, Zhou J, Xiang H. Halorubrum yunnanense sp. nov., isolated from a subterranean salt mine. Int J Syst Evol Microbiol. 2015;65(12):4526–4532. https://doi.org/10.1099/ijsem.0.000605
- Cline SW, Schalkwyk LC, Doolittle WF. Transformation of the archaebacterium Halobacterium volcanii with genomic DNA. J Bacteriol. 1989;171(9):4987–4991. https://doi.org/10.1128/jb.171.9.4987-4991.1989
- Cui HL, Gao X, Yang X, Xu XW. Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles. 2010;14(6):493–499. https://doi.org/10.1007/s00792-010-0329-0
- Cui HL, Hou J, Amoozegar MA, Dyall-Smith ML, de la Haba RR, Minegishi H, Montalvo-Rodriguez R, Oren A, Sanchez-Porro C, Ventosa A, et al. Proposed minimal standards for description of new taxa of the class Halobacteria. Int J Syst Evol Microbiol. 2024;74(3):006290. https://doi.org/10.1099/ijsem.0.006290
- Cui HL, Mou YZ, Yang X, Zhou YG, Liu HC, Zhou PJ. Halorubellus salinus gen. nov., sp. nov. and Halorubellus litoreus sp. nov., novel halophilic archaea isolated from a marine solar saltern. Syst Appl Microbiol. 2012;35(1):30–34. https://doi.org/10.1016/j.syapm.2011.08.001
- Ding Y, Ke J, Hong T, Zhang A, Wu X, Jiang X, Shao S, Gong M, Zhao S, Shen L, et al. Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes. BMC Microbiol. 2025;25(1):287. https://doi.org/10.1186/s12866-025-03997-3
- Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol. 1955;70(4):484–485. https://doi.org/10.1128/jb.70.4.484-485.1955
- Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57(Pt_1):81–91. https://doi.org/10.1099/ijs.0.64483-0
- Hall TA. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–98.
- Hao Y, Jin Y, Zhang A, Jiang X, Gong M, Lu C, Pan R, Chen S. Identification and biochemical characterization of a novel halolysin from Halorubellus sp. PRR65 with a relatively high temperature activity. World J Microbiol Biotechnol. 2024;40(11):340. https://doi.org/10.1007/s11274-024-04149-x
- Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64(Pt_2):346–351. https://doi.org/10.1099/ijs.0.059774-0
- Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–1874. https://doi.org/10.1093/molbev/msw054
- Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R, Hashimoto T. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B’ (rpoB’) gene. Int J Syst Evol Microbiol. 2010;60(Pt_10):2398–2408. https://doi.org/10.1099/ijs.0.017160-0
- Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043–1055. https://doi.org/10.1101/gr.186072.114
- Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics. 2020;70(1):e102. https://doi.org/10.1002/cpbi.102
- Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009;106(45):19126–19131. https://doi.org/10.1073/pnas.0906412106
- Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. https://doi.org/10.1093/bio-informatics/btu153
- Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT. Microbial diversity of hypersaline environments: A metagenomic approach. Curr Opin Microbiol. 2015;25:80–87. https://doi.org/10.1016/j.mib.2015.05.002
- Zhang DF, He W, Shao Z, Ahmed I, Zhang Y, Li WJ, Zhao Z. Easy-CGTree: A pipeline for prokaryotic phylogenomic analysis based on core gene sets. BMC Bioinformatics. 2023;24(1):390. https://doi.org/10.1186/s12859-023-05527-2
- Zhou Z, Charlesworth J, Achtman M. Accurate reconstruction of bacterial pan- and core genomes with PEPPAN. Genome Res. 2020;30(11):1667–1679. https://doi.org/10.1101/gr.260828.120