title: Comprehensive transcriptome and improved genome annotation of Bacillus licheniformis WX-02.
abstract: The updated genome of Bacillus licheniformis WX-02 comprises a circular chromosome of 4286821 base-pairs containing 4512 protein-coding genes. We applied strand-specific RNA-sequencing to explore the transcriptome profiles of B. licheniformis WX-02 under normal and high-salt conditions (NaCl 6%). We identified 2381 co-expressed gene pairs constituting 871 operon structures. In addition, 1169 antisense transcripts and 90 small RNAs were detected. Systematic comparison of differentially expressed genes under different conditions revealed that genes involved in multiple functions were significantly repressed in long-term high salt adaptation process. Genes related to promotion of glutamic acid synthesis were activated by 6% NaCl, potentially explaining the high yield of γ-PGA under salt condition. This study will be useful for the optimization of crucial metabolic activities in this bacterium.
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: College of Life Science, South-Central University for Nationalities, Wuhan 430070, PR China.
authors.forename: Gang
authors.initials: G
authors.lastname: Cheng
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Xiang-Yong
authors.initials: XY
authors.lastname: Gou
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Feng
authors.initials: F
authors.lastname: Xing
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Sen
authors.initials: S
authors.lastname: Li
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Yi-Chao
authors.initials: YC
authors.lastname: Han
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Long
authors.initials: L
authors.lastname: Wang
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Song
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Cheng-Cheng
authors.initials: CC
authors.lastname: Shu
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan 430062, PR China. Electronic address: chenshouwen@mail.hzau.edu.cn.
authors.forename: Shou-Wen
authors.initials: SW
authors.lastname: Chen
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: llchen@mail.hzau.edu.cn.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
mesh_terms: D001407:Bacillus / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D021901:DNA, Intergenic / Q000235:genetics; D020869:Gene Expression Profiling; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics; D058977:Molecular Sequence Annotation; D011099:Polyglutamic Acid / Q000031:analogs & derivatives / Q000096:biosynthesis; D016372:RNA, Antisense / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012492:Salts / Q000494:pharmacology; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012492:Salts; C511775:poly(gamma-glutamic acid); D011099:Polyglutamic Acid
keywords: Bacillus licheniformis WX-02; Differentially expressed gene; Genome; Strand-specific RNA-seq; Transcriptome