Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots

Abstract

Objectives

This study aims to generate a de novo complete whole-genome assembly of Pseudomonas sp. strain HOU2, which is an endophytic bacterium isolated from dangshen roots that shows to improve the growth of in vitro dangshen plants. Further investigation of the whole genome of Pseudomonas sp. strain HOU2 will help identify potential genes or pathways that could be involved in the plant growth-promoting effects on in vitro dangshen plants, providing valuable information for future applications.

Data description

The genomic DNA of Pseudomonas sp. strain HOU2 was sequenced using Oxford Nanopore’s PromethION sequencer with an R10.4.1 flow cell (Table 1, Data file 1). The assembly of the Pseudomonas sp. strain HOU2 genome was conducted using Flye version 2.9, resulting in a single circular chromosome of 6,047,544 bp with a mean coverage of 488 (Table 1, Data file 2). The annotation of genes, proteins, and features of the HOU2 genome were performed by the RAST server (Rapid Annotation using Subsystem Technology) (https://rast.nmpdr.org/) (Table 1, Data file 3, 4, 5) [6, 7]. The Pseudomonas sp. strain HOU2 genome was determined to be most similar to that of Pseudomonas koreensis using the Type Strain Genome Server (https://tygs.dsmz.de/, version v391) [8].

Objective

The study of plant growth-promoting bacteria can provide important information for the application of beneficial bacteria in sustainable crop production. Endophytic bacterial inoculation increased stalk length, root number, fresh mass and dry mass [1]. Endophytic bacteria play crucial roles in the health and development of medicinal plants. They promote plant growth and increase resistance against pathogens and environmental stresses. Moreover, endophytes also regulate the synthesis of secondary metabolites of host plants or produce bioactive metabolites on their own without interacting with the host [2,3,4].

Dangshen (Codonopsis javanica) has been used as a medicinal herbal plant to treat diabetes and other diseases [5]. In Vietnam, dangshen has been cultivated in many provinces, such as Lai Chau, Dien Bien, and Lao Cai. The use of beneficial microorganisms in the production of dangshen is suitable for sustainable medicinal plant value chain development. Therefore, the isolation, characterization and study of the whole genome of bacterial endophytes may help improve the yield and quality of medicinal plants.

We isolated and characterized the plant growth-promoting effects of several endophytic bacteria isolated from C. javanica roots, of which the Pseudomonas sp. strain HOU2 improved the growth of in vitro C. javanica plants and was selected for whole-genome sequencing investigation. Here, we present the complete whole genome and gene annotation predicted by the RAST server, [6,7,8] for Pseudomonas sp. strain HOU2, which could serve as a resource and dataset for investigating genes and pathways associated with plant growth-promoting effects.

Data description

Roots from healthy Codonopsis javanica plants were subjected to surface sterilization with 0.5% NaOCl for 20 min. One hundred microliters of the third rinse water were placed on Luria broth (LB) medium and incubated at 27 °C for 3 days to check for surviving colonies. The surface-disinfected roots were smashed in a sterilized Petri dish, diluted in liquid LB, and then spread on LB media. Pure culture isolation was achieved by re-streaking twice on LB agar medium [1].

A single colony of the HOU2 bacteria was grown overnight in liquid LB media in a shaker (27 °C, 200 rpm). Genomic DNA extraction was conducted using a modified protocol [9]. The integrity of the HOU2 genomic DNA was verified on 1% agarose gel electrophoresis. DNA quantity and quality were evaluated using the Qubit dsDNA Broad Range assay kit (Thermo Fisher Scientific) and NanoDropND 1000 (v.3.5.2, Thermo Fisher Scientific). The genomic DNA was sequenced with an Oxford Nanopore’s PromethION sequencer using R10.4.1 flow cell.

The extracted DNA sample was prepared using the Native Barcoding Kit 24 V14 protocol (SQK-NBD114.24) from Oxford Nanopore Technologies (Oxford, United Kingdom). The library was prepared according to the manufacturer’s instructions, with the exception of increasing the incubation time to 30 min for both the end-repair and ligation steps. To avoid or reduce DNA shearing, bore tips and gentle sample flicking (without vortexing) were used. Raw signal files (FAST5) were used for base calling with Guppy v6.4.6 in super accuracy mode, resulting in over 3.9 million reads (Q score ≥ 10) with an average read length of 7.4 kb. Reads under 5000 bp and with a Q score ≤ 20 were removed by Chopper version 0.5, resulting in over 262 thousand reads with a read length N50 of 12.8 kb [10].

The pre-processed reads were de novo assembled using Flye v. 2.9-b1768 with the parameters --nano-hq and --read-error 0.03 for the Nanopore super accuracy base call file [11] to obtain the complete whole genome of Pseudomonas sp. strain HOU2. The quality and completeness of the assembly were assessed using BUSCO v5.4.5 [12] in prok_genome mode (the lineage dataset is bacteria_odb10, creation date: 2020-03-06, number of genomes: 4085, number of BUSCOs: 124), which indicated that the whole genome of the HOU2 sequence is > 99.2% complete (Table 1, Data set 2). In addition, the genome was also evaluated by NCBI, using the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Pseudomonas CheckM marker set (v1.2.3) [13], resulting in a completeness of 99.68% (100th percentile) and contamination of 0.08% (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_040729435.1/).

The HOU2 genome was most similar to that of Pseudomonas koreensis strain FP1691, accession number: GCA_026314355.1, with an original ANI score of 93.68 and an OrthoANI score of 94.01%, as determined by CJ Bioscience’s Orthologous Average Nucleotide Identity Tool (OAT) [8, 14].

Table 1 Overview of data files/ sets

Limitations

Here, we used Nanopore long-read sequencing to produce a complete, high-quality single circular genome of Pseudomonas sp. HOU2. The main limitation of this data note is the genome assembly completeness of the HOU2 strain was > 99.2%, which was not yet fully covered. In addition, this data note was limited to the description of how the datasets were generated. Further data analysis of the biosynthesis-related gene clusters associated with plant growth-promoting effects should be performed to explain why and how Pseudomonas sp. HOU2 improves Codonopsis javanica growth performance.