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

作　　者：Pan Zhang Biliang Zhang Yuan-Yuan Ji Jian Jiao Ziding Zhang Chang-Fu Tian 

机构地区：[1]State Key Laboratory of Plant Environmental Resilience,and College of Biological Sciences,China Agricultural University,Beijing,China [2]MOA Key Laboratory of Soil Microbiology,and Rhizobium Research Center,China Agricultural University,Beijing,China [3]Shenzhen Institute of Synthetic Biology,Shenzhen Institute of Advanced Technology,Chinese Academy of Sciences,Shenzhen,China [4]State Key Laboratory of Livestock and Poultry Biotechnology Breeding,and College of Biological Sciences,China Agricultural University,Beijing,China

出　　处：《mLife》2024年第2期277-290,共14页微生物（英文）

基　　金：supported by the National Key R&D Program of China(grant number 2022YFA0912100);the National Natural Science Foundation of China(grant number 32070078)to C.F.T.

摘　　要：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.

关 键 词：cofitnessnetwork pangenome Tn-seq 

分 类 号：Q93[生物学—微生物学]