Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2

• Published in: Gene 2023-03, Vol.855, p.147118, Article 147118
• Main Authors: Wang, Yongqiang, Cai, Xunhui, Hu, Shengnan, Qin, Sidong, Wang, Ziqi, Cao, Yixiang, Hou, Chaoliang, Yang, Jiangshan, Zhou, Wei
• Format: Article
• Language: English
• Subjects: Bacterial Typing Techniques; Comparative genomic analysis; Complete genome sequencing; DNA, Bacterial - genetics; Evolution; Fatty Acids; Genomics; Phylogeny; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; Species classification; Sphingobacterium - genetics; Sphingobacterium sp. CZ-2
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2022.147118

•The strain CZ-2 was identified as a novel species of the genus Sphingobacterium.•Three specific genes contribute to the environmental adaptability of strain CZ-2.•Gene family contraction may be a major process in the evolution of strain genome.•Gene structural changes as a potential mechanism for adaptive evolution of strain.•The strain CZ-2 has the potential to degrade aminobenzoates. Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.