Whole-genome sequencing of a biocontrol Myxococcus xanthus R31 isolate and comparative genomic analysis

Honghong Dong; Ruixiang Gao; Yijie Dong; Qing Yao; Honghui Zhu

doi:10.1016/j.gene.2023.147286

Whole-genome sequencing of a biocontrol Myxococcus xanthus R31 isolate and comparative genomic analysis

Gene. 2023 May 5:863:147286. doi: 10.1016/j.gene.2023.147286. Epub 2023 Feb 17.

Authors

Honghong Dong¹, Ruixiang Gao², Yijie Dong¹, Qing Yao³, Honghui Zhu⁴

Affiliations

¹ Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
² Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; College of Plant Protection, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou 510642, China.
³ College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou 510642, China.
⁴ Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China. Electronic address: zhuhh_gdim@163.com.

PMID: 36804855
DOI: 10.1016/j.gene.2023.147286

Abstract

Tomato bacterial wilt (TBW) caused by Ralstonia solanacearum is one of the most destructive soil-borne diseases. Myxococcus xanthus R31, isolated from healthy tomato rhizosphere soil using the R. solanacearum baiting method, exhibiting good biocontrol efficacy against TBW. However, the genomic information and evolutionary features of R31 are largely unclear. Here, the high-quality genome assembly of R31 was presented. Using Nanopore sequencing technology, we assembled the 9.25 Mb complete genome of R31 and identified several extracellular enzyme proteins, including carbohydrate-active enzymes (CAZymes) and peptidases. We also performed a comparative genome analysis of R31 and 17 other strains of M. xanthus with genome sequences in the NCBI database to gain insights into myxobacteria predation and genome size expansion. Average nucleotide identity and digital DNA-DNA hybridization calculation and phylogenetic analysis indicated that R31 was closely related to the species M. xanthus. Further comparative genomics analysis suggested that, in addition to characteristics of predatory microorganisms, R31 contains many strain-specific genes, which may provide a genetic basis for its proficient predatory ability. This study provides new insights into R31 and other closely related species and facilitates studies using genetic approaches to further elucidate the predation mechanism of myxobacteria.

Keywords: Biocontrol; Comparative genomics analysis; Extracellular enzyme; Myxobacteria; Predation; Whole-genome sequencing.

MeSH terms

DNA / metabolism
Genomics
Myxococcus xanthus* / genetics
Myxococcus xanthus* / metabolism
Phylogeny
Soil

Substances

Soil
DNA