This study, published in mLife, was led by Profs. Chang‐Fu Tian and Ziding Zhang (College of Biological Sciences, China Agricultural University).

sinor

Source: Ninjatacoshell

The root nodules of a 4-week-old Medicago truncatula A20 inoculated with Sinorhizobium meliloti.

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).

Low-Res_图片 1 (2)

Source: Chang‐Fu Tian, College of Biological Sciences, China Agricultural University

(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).

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.

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