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Original Research | Open Access

Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome

Pan Zhang1,2,3,#,, Biliang Zhang2,4,#, Yuan-Yuan Ji1,2, Jian Jiao1,2, Ziding Zhang4( ), Chang-Fu Tian1,2 ( )
State Key Laboratory of Plant Environmental Resilience, and College of Biological Sciences, China Agricultural University, Beijing, China
MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
State Key Laboratory of Livestock and Poultry Biotechnology Breeding, and College of Biological Sciences, China Agricultural University, Beijing, China

#Pan Zhang and Biliang Zhang contributed equally to this study.

Editor: Fangqing Zhao, Beijing Institutes of Life Science, Chinese Academy of Sciences, China

Show Author Information

Abstract

Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open pangenome. To evaluate the robustness of fitness category assignment, Tn-seq data for three independent mutant libraries per strain were analyzed by three methods, which indicates that the Hidden Markov Model (HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size, outperforming the Bayesian and Monte Carlo simulation-based methods. Consequently, the HMM method was used to classify the fitness category. Fitness genes, categorized as essential (ES), advantage (GA), and disadvantage (GD) genes for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Accessory ES/GA genes showed a lower fitness effect than core ES/GA genes. Connectivity degrees in the cofitness network decrease in the order of ES, GD, and GA/NE. In addition to accessory genes, 1599 out of 3284 core genes display differential essentiality across test strains. Within the pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.

Keywords

cofitness networkpangenomeTn-seq

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mLife
Volume 3 Issue 2,
June 2024
Pages 277-290
DOI: 10.1002/mlf2.12132
Cite this article:
Zhang P, Zhang B, Ji Y-Y, et al. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. mLife, 2024, 3(2): 277-290. https://doi.org/10.1002/mlf2.12132

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Received: 07 November 2023
Accepted: 24 April 2024
Published: 28 June 2024
© 2024 The Author(s). mLife published by John Wiley & Sons Australia, Ltd on behalf of Institute of Microbiology, Chinese Academy of Sciences.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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