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Open AccessArticle

Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes

by Hai-Long Zhao 1,2,†, Zhong-Kui Xia 1,2,†, Fa-Zhan Zhang 1,2, Yuan-Nong Ye 1,2,* and Feng-Biao Guo 1,2,*
1
Center of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
2
Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Patrick C. Y. Woo
Int. J. Mol. Sci. 2015, 16(9), 23111-23126; https://doi.org/10.3390/ijms160923111
Received: 27 July 2015 / Revised: 18 August 2015 / Accepted: 18 September 2015 / Published: 23 September 2015
(This article belongs to the Special Issue Microbial Genomics and Metabolomics)
Composition bias from Chargaff’s second parity rule (PR2) has long been found in sequenced genomes, and is believed to relate strongly with the replication process in microbial genomes. However, some disagreement on the underlying reason for strand composition bias remains. We performed an integrative analysis of various genomic features that might influence composition bias using a large-scale dataset of 1111 genomes. Our results indicate (1) the bias was stronger in obligate intracellular bacteria than in other free-living species (p-value = 0.0305); (2) Fusobacteria and Firmicutes had the highest average bias among the 24 microbial phyla analyzed; (3) the strength of selected codon usage bias and generation times were not observably related to strand composition bias (p-value = 0.3247); (4) significant negative relationships were found between GC content, genome size, rearrangement frequency, Clusters of Orthologous Groups (COG) functional subcategories A, C, I, Q, and composition bias (p-values < 1.0 × 10−8); (5) gene density and COG functional subcategories D, F, J, L, and V were positively related with composition bias (p-value < 2.2 × 10−16); and (6) gene density made the most important contribution to composition bias, indicating transcriptional bias was associated strongly with strand composition bias. Therefore, strand composition bias was found to be influenced by multiple factors with varying weights. View Full-Text
Keywords: strand composition bias; multiple factors; gene density; genomic features; COG functional category; obligate intracellular bacteria strand composition bias; multiple factors; gene density; genomic features; COG functional category; obligate intracellular bacteria
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Zhao, H.-L.; Xia, Z.-K.; Zhang, F.-Z.; Ye, Y.-N.; Guo, F.-B. Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes. Int. J. Mol. Sci. 2015, 16, 23111-23126.

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