title: Essentiality drives the orientation bias of bacterial genes in a continuous manner.
abstract: Studies had found that bacterial genes are preferentially located on the leading strands. Subsequently, the preferences of essential genes and highly expressed genes were compared by classifying all genes into four groups, which showed that the former has an exclusive influence on orientation. However, only some functional classes of essential genes have this orientation bias. Nevertheless, previous studies only performed comparative analyzes by differentiating the orientation bias extent of two types of genes. Thus, it is unclear whether the influence of essentiality on strand bias works continuously. Herein, we found a significant correlation between essentiality and orientation bias extent in 19 of 21 analyzed bacterial genomes, based on quantitative measurement of gene essentiality (or fitness). The correlation coefficient was much higher than that derived from binary essentiality measures (essential or non-essential). This suggested that genes with relatively lower essentiality, i.e., conditionally essential genes, also have some orientation bias, although it is weaker than that of absolutely essential genes. The results demonstrated the continuous influence of essentiality on orientation bias and provided details on this visible structural feature of bacterial genomes. It also proved that Geptop and IFIM could serve as useful resources of bacterial gene essentiality, particularly for quantitative analysis.
authors.affiliation: School of Biomedical Engineering, Capital Medical University, Beijing 100069, China.|Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing 100069, China.
authors.forename: Wen-Xin
authors.initials: WX
authors.lastname: Zheng
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Key Laboratory for Neuro Information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Cheng-Si
authors.initials: CS
authors.lastname: Luo
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Key Laboratory for Neuro Information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Yan-Yan
authors.initials: YY
authors.lastname: Deng
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Key Laboratory for Neuro Information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
mesh_terms: D002876:Chromosomes, Bacterial; D015870:Gene Expression; D023061:Gene Order; D005798:Genes, Bacterial; D020043:Genes, Essential; D056084:Genetic Fitness; D016680:Genome, Bacterial