image: (A) Strain-dependent gene essentiality of genes shared by five strains. The Maximum Likelihood phylogenetic tree based on 3284 core genes of five test strains is shown and all branches have 100% bootstrap support. (B, C) COG enrichment analysis of shared (quasi-)essential genes (341 essential and growth-advantage genes) (B), and core genes showing strain-dependent requirement for growth (C). Red in (B, C), p < 0.05 in Fisher's exact test. The proportion of each COG category and its abundance order among 27,724 genes with COG annotations in the pangenome of five test strains are shown in (B).
Credit: Chang‐Fu Tian, College of Biological Sciences, China Agricultural University
This study was led by Profs. Chang‐Fu Tian and Ziding Zhang (College of Biological Sciences, China Agricultural University). Based on a robust Tn-seq analysis of independent mariner transposon insertion libraries of Sinorhizobium strains, pangenomic and network-based analyses allowed identification of a strain-dependent variation in the fitness network (harboring ES, GA, GD, and NE genes) of Sinorhizobium pangenome under a nutrient-rich condition. This fitness network is characterized by a highly connected ES subnetwork, and beneficial (GA) and deleterious (GD) subnetworks of lower connectivity. Genus core genes belonging to both the shared and strain-dependent essential zones of this fitness network exhibited a similar profile of functional categories, e.g., cell envelop biogenesis (Figure 1). The network-based analyses of the fuzzy essential zone of Sinorhizobium pangenome developed in this work can be used for any prokaryotes for which a robust Tn-seq procedure can be established. These efforts are significant for fully understanding the evolution of prokaryote pangenome, the in silico bipartition of which into essential core and non-essential accessory subsets is oversimplified.
How to cite this article:
Zhang P, Zhang B, Ji YY, Jiao J, Zhang Z, Tian C‐F. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. mLife.2024;3:277–290.
https://doi.org/10.1002/mlf2.12132
Journal
mLife
Article Title
Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome
Article Publication Date
28-Jun-2024