Complete genome sequence of a plant growth-promoting Methylorubrum aminovorans MtTm-13

ABSTRACT

We report the complete genome of plant growth-promoting Methylorubrum aminovorans MtTm-13 (5,231,310 bp, 69% GC, 4,660 protein-coding genes) isolated from the tomato phyllosphere.

ANNOUNCEMENT

The genus Methylorubrum, formerly classified under Methylobacterium, is facultative methylotrophic Alphaproteobacteria (1). These are pink-pigmented, gram-negative, ubiquitous in nature and possess the ability to utilize single-carbon compounds or methyl groups as the sole carbon source (2). They exhibit plant growth-promoting traits, including hormone modulation, mineral solubilization, and the production of 1-aminocyclopropane-1-carboxylate deaminase and siderophores, which aid plant growth and reduce adverse effects of abiotic stress (3). Strain MtTm-13, a stress-tolerant plant growth-promoting bacterium (4, 5), was isolated from leaves of a tomato plant at the Tamil Nadu Agricultural University, Coimbatore (11.0069° N, 76.9309° E), India. The leaf sample was surface-sterilized with 2% sodium hypochlorite and rinsed with sterile distilled water three times. The sterilized leaf sections were then imprinted onto ammonia mineral salt (AMS) agar containing 0.5% methanol and cycloheximide (10 μg/mL) and incubated at 28 ± 2°C for 7 days, until a distinct pink colony appeared. Whole-genome sequencing was performed to elucidate the genetic basis of its plant growth-promoting potential.

Genomic DNA was isolated from a single purified colony, grown in AMS broth at 30°C for 7 days under shaking conditions, using the QIAGEN Genomic-tip 20/G kit (QIAGEN, Hilden, Germany), following the manufacturer’s instructions (6, 7). DNA quantity and integrity were evaluated using a Qubit 4 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and agarose gel electrophoresis. The purified DNA was then submitted to ONEOMICS Private Limited (Tiruchirappalli, India) for whole-genome sequencing. Illumina sequencing libraries were prepared with the TruSeq DNA PCR-Free Kit (Illumina, USA), following the manufacturer’s instructions. Briefly, genomic DNA was fragmented, end-repaired, A-tailed, size-selected, and ligated with indexed adapters. Library concentrations were quantified using a QuantStudio Real-Time PCR System (Applied Biosystems, USA), and fragment size profiles were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) (8). Sequencing was carried out on the Illumina NovaSeq X platform, generating 64,041,602 paired-end reads (2 × 150 bp). No modifications were made to the standard protocol.

Raw reads were quality-checked using FastQC v0.10.1 and trimmed with Trimmomatic v0.39 (9, 10). Genome assembly was produced using Shovill v1.4.2 (11), and the draft assembly was subsequently scaffolded with RagTag v2.1.0 (12) using reference genome OZ375356.1, selected based on 16S rRNA gene sequence analysis. Assembly quality was assessed using QUAST v5.3.0 (13). The genome spans 5,231,310 bp with a GC content of 69% and sequencing depth of 1,332.75× (Table 1). Genome completeness was estimated at 98.59%, using BUSCO v5 with the bacteria_odb10 data set (14, 15). Functional annotation using PGAP v6.10 (16) revealed genes associated with plant growth promotion and stress tolerance, including tryptophan synthase subunits (trpA and trpB) for IAA biosynthesis, phosphate transport genes (phoB and pstS), siderophore receptors (fhuF) for iron acquisition, and catalases and superoxide dismutases. Taxonomic classification was carried out using the GTDB-Tk v1.7.0 against GTDB reference set (17, 18). Unless noted, all software was used with default parameters.

TABLE 1.

Detailed information of draft genome

Feature	Value
Genome size	5,231,310 bp
Number of chromosomes	1
Contig N50	5,231,310 bp
Contig L50	1
GC content (%)	69
Genome coverage	1,332.75×
Assembly level	Chromosome
BUSCO completeness	98.59%
SRA	SRS27774344
GenBank Assembly	CM143384

DATA AVAILABILITY

The complete genome sequence of Methylorubrum aminovorans MtTm-13 has been deposited in GenBank under the accession number CM143384. The raw sequencing reads are available under BioProject accession number PRJNA1403065, and the BioSample accession number is SAMN54618850. All sequencing data produced in this study are accessible through the Sequence Read Archive (SRA) under accession SRS27774344. Additionally, the assembled genome sequence is available in GenBank under accession number GCA054962035.1.

ETHICS APPROVAL

Research does not report on or involve the use of any animal or human data or tissue.