Complete genome sequences of biocontrol agents Serratia rubidaea strains SY163 and SY183 effective against tomato gray mold

TL;DR

This paper presents the full genome sequences of two Serratia rubidaea strains that can fight tomato gray mold.

Contribution

The novel contribution is the complete genome sequences of SY163 and SY183, biocontrol agents effective against Botrytis cinerea.

Findings

SY163 and SY183 have circular chromosomes of 4,915,045 and 4,978,521 bp respectively.

Both strains have a G + C content of 59.1%.

The strains were isolated from tomato leaves using methanol as the sole carbon source.

Abstract

We report the genome sequences of Serratia rubidaea strains SY163 and SY183, isolated from tomato leaves using methanol as the sole carbon source. These strains are known to inhibit the gray mold pathogen, Botrytis cinerea. PacBio Sequel IIe sequencing yielded circular chromosomes of 4,915,045 and 4,978,521 bp, both with 59.1% G + C content.

Full text

ANNOUNCEMENT

Gray mold, caused by Botrytis cinerea, poses a significant threat to tomato production worldwide, with resistant strains diminishing the effectiveness of traditional chemical control methods (1). Plant-associated symbiotic bacteria residing on leaves show promise as biocontrol agents because of their ability to produce antifungal compounds (2). In our previous study, Serratia rubidaea strains SY163 and SY183, isolated from tomato leaves using methanol as the sole carbon source, demonstrated substantial antifungal activity against B. cinerea (3). Herein, we present the complete genome sequences of these strains to facilitate further research into their biocontrol mechanisms.

Microbial samples were collected from tomato leaves grown in plastic greenhouses (130°38′21.68″E, 32°43′42.599″N, Kumamoto, Japan) on 1 July 2020. Cells of strains SY163 and SY183, stored as glycerol stocks in the laboratory of Sojo University, were cultured overnight at 30°C in Luria-Bertani medium under aerobic conditions. Genomic DNA was extracted using the NucleoBond HMW DNA Kit (Macherey-Nagel, Düren, Germany) and purified using the DNeasy PowerClean Pro Cleanup Kit (Qiagen, Venlo, the Netherlands). Short DNA fragments were removed using the Short Read Eliminator XS Kit (PacBio, CA, USA). DNA fragments were then sheared to approximately 10–20 kb using a g-TUBE (Covaris, MA, USA). SMRTbell libraries were prepared using the SMRTbell Express Template Prep Kit version 2.0 (PacBio), and polymerase complexes were formed using the Binding Kit 2.2 (PacBio). Sequencing was performed on a PacBio Sequel IIe system. Subreads were generated by removing adapter sequences with SMRT Link version 11.0.0.146107 using default parameters. High-fidelity (HiFi) reads with quality scores of >20 were obtained for SY163 (20,110 reads) and SY183 (20,304 reads). Reads shorter than 1,000 bp were filtered out using Filtlong version 0.2.1 (4), resulting in 17,853 and 17,850 HiFi reads for SY163 and SY183, respectively. De novo assembly was performed with Flye version 2.9.1-b1780 using default settings (5), resulting in single circular chromosomes for both strains. Genome coverages were 51.0× for SY163 and 49.8× for SY183, with N50 values corresponding to the full chromosome lengths. The completeness of the genome assemblies was evaluated using CheckM version 1.2.2 with Enterobacterales-specific marker sets, achieving 99.9% completeness rates for both strains (6). Annotation was performed using DFAST version 1.3.3 with the rotate option to place the dnaA gene first (7), employing MetaGeneAnnotator v2008/08/19 for coding sequences (8), Barrnap version 0.8 for rRNA genes (9), and ARAGORN version 1.2.38 for tRNA genes (10). Default parameters were used for all software.

The genome of strain SY163 consists of 4,915,045 bp with a G + C content of 59.1%, encoding 4,431 protein-coding genes, 22 rRNA genes (5S, 16S, and 23S), and 87 tRNA genes. Strain SY183 has a genome size of 4,978,521 bp with a G + C content of 59.1%, containing 4,476 protein-coding genes, 22 rRNA genes, and 89 tRNA genes.

Average nucleotide identity analysis using Pyani version 0.2.12 (ANIm) (11) revealed that SY163 and SY183 were 98.6% and 99.1% identical, respectively, to the type strain of Serratia rubidaea, FDAARGOS_926 (GCA_016026735.1). These findings support future studies to identify antifungal genes and develop biocontrol methods using antifungal bacteria symbiotic with plants.