Genomic evidence of genetic diversity and functional evolution in Flavobacterium columnare

Rui Han; Yuhao Hong; Ruilong Xu; Wenjie Guo; Mingshu Zhang; Zijun Lu; Qing Han; Zequan Mo; Xueming Dan; Yanwei Li

doi:10.3389/fmicb.2023.1240471

Genomic evidence of genetic diversity and functional evolution in Flavobacterium columnare

Front Microbiol. 2023 Sep 28:14:1240471. doi: 10.3389/fmicb.2023.1240471. eCollection 2023.

Authors

Rui Han^{1

2}, Yuhao Hong¹, Ruilong Xu¹, Wenjie Guo¹, Mingshu Zhang³, Zijun Lu¹, Qing Han⁴, Zequan Mo^{1

2}, Xueming Dan^{1

2}, Yanwei Li^{1

2}

Affiliations

¹ University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.
² Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China.
³ School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.
⁴ Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.

Abstract

Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish. Columnaris disease can cause heavy economic losses in aquaculture. In this study, whole-genome sequencing was used to characterize this pathogen. F. columnare isolate AH-01 had a circular chromosome and plasmid that encoded a total of 3,022 genes. Isolate GX-01 only had a circular chromosome and encoded 2,965 genes. Genomic islands, prophage regions, and CRISPR/Cas systems were identified in both genomes. Both genomes presented evidence of gene variation and horizontal transfer, both of which are the essential components of genetic diversity, genome plasticity, and functional evolution. Single-gene phylogeny and comparative genome analyses were performed to investigate the variation and evolution of this pathogen. Genetic analysis of 16S rRNA and housekeeping gene sequences significantly clustered 55 F. columnare isolates into four clades. The intragroup identity of the 16S rRNA gene exceeded 99%, while the intergroup identity was below the species delineation threshold. We discovered significant translocation, inversion, and rearrangement events that influenced local synteny within each group. Notably, the observed alignments varied considerably among all the studied groups. The core genomes of all strains with available sequences comprised 747 genes, corresponding to approximately 25% of the genome. Core genome multilocus sequence typing, genome-wide orthology and phylogenetic analyses, and average nucleotide identity suggested that the currently existing F. columnare was an assemblage of several distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. The present investigation provided genomic evidence of gene variation and horizontal transfer, which were the basis of genetic diversity, genome plasticity, and functional evolution. The findings supported a proposed new taxonomic perspective on F. columnare.

Keywords: Flavobacterium columnare; cgMLST; comparative genomics; genome-wide analysis (GWA); single-gene phylogeny.

Grants and funding

This study was supported by the Science and Technology Program of Guangzhou (2023B04J0172), the Guangdong Provincial Special Fund for Modern Agriculture Industry Technology Innovation Teams (2019KJ141), and the China Postdoctoral Science Foundation (2022M710836).