Dataset for transcriptome analysis of abscisic acid degrading bacterium Novosphingobium sp. P6W

Plant growth-promoting rhizobacteria (PGPR) improve plant productivity and stress resistance. The mechanisms involved in plant-microbe interactions include the modulation of plant hormone status. The Novosphingobium sp. strain P6W was previously described as the bacterium capable of abscisic acid (ABA) degradation, and its inoculation decreased ABA concentrations in planta. The metabolic pathway for the ABA degradation in bacteria is still unknown. Here we present transcriptome data of Novosphingobium sp. P6W grown in the medium supplemented with ABA or fructose as the carbon source. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP189498) and have been assigned BioProject accession PRJNA529223.

Plant growth-promoting rhizobacteria (PGPR) improve plant productivity and stress resistance. The mechanisms involved in plantmicrobe interactions include the modulation of plant hormone status. The Novosphingobium sp. strain P6W was previously described as the bacterium capable of abscisic acid (ABA) degradation, and its inoculation decreased ABA concentrations in planta. The metabolic pathway for the ABA degradation in bacteria is still unknown. Here we present transcriptome data of Novosphingobium sp. P6W grown in the medium supplemented with ABA or fructose as the carbon source. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP189498) and have been assigned BioProject accession PRJNA529223.

Data description
The dataset contains cleaned sequencing data obtained through the transcriptome sequencing of Novosphingobium sp. P6W grown in the medium supplemented with ABA or fructose as the sole carbon source and under carbon starvation conditions. Samples for transcriptome profiling were collected at the exponential and stationary growth phases. Cleaned FASTQ files were deposited in NCBI Sequence Read Archive and accessible through the BioProject PRJNA529223. Information about bacterial culture samples is presented in Table 1. Reads were mapped onto the reference genome sequence and the coverage data were obtained. Statistics of sequence reads and sequence coverage data are shown in Table 2. PCA plot of RNA-seq data presented in Fig. 1 demonstrates the variance between sample groups and sample replicates according to gene expression levels. Each dot in the Fig. 1 indicates particular sample.

Experiment design
To identify the genes involved in ABA metabolism, the transcriptome profiles of exponential phase cultures growing in the minimal medium supplemented with ABA or fructose were compared. To exclude genes associated with stress adaptation, samples of cultures incubated under carbon starvation conditions for 24 and 48 hours were taken as corresponding controls. It was important to obtain Specifications Table   Subject  Biology  Specific subject area  Transcriptomics  Type of data  Transcriptome sequences, table,  Value of the Data These datasets will be valuable to the PGPR research community for characterizing changes in rhizobacterial gene expression caused by phytohormones and depending on environmental conditions. Downstream analysis will allow the identification of genes involved in bacterial ABA degradation. Cleaned sequencing reads can be further processed by researchers using their own bioinformatic algorithms and analyzed together with their own data.
information about the genes that decrease activity at the substrate depletion. For this purpose, samples of cultures grown in the ABA supplemented medium at the stationary phase were also taken.

Library construction and sequencing
Bacterial cultures were fixed with an equal volume of cold RNA-stabilizing solution (19% ethanol, 1% acidic phenol, pH 5.5) on ice for 30 minutes. Cells were harvested by centrifugation and RNA isolation was performed using RNA Extract Reagent (Evrogen, Russia) according to the manufacturer's protocol. DNA contaminants were removed using RNase-free DNase I kit (Ambion, USA). The integrity of the RNA was checked by Agilent 2100 bioanalyzer (USA). For rRNA removal the Ribo-Zero kit for Gram-negative bacteria (Illumina, USA) was used.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to prepare RNA-seq libraries. The resulting average size of the cDNA libraries was approximately 300 bp. Libraries were sequenced using the Illumina HiSeq 2500 sequencing platform.

Reads alignment to the reference genome
The high-quality reads were mapped onto the genome sequence of the Novosphingobium sp. P6W strain (assembly: GCA_000876675.2) (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/876/675/GCF_ 000876675.2_ASM87667v2/GCF_000876675.2_ASM87667v2_genomic.fna.gz). HISAT2 version 2.1. 0 [5] was used to build index of reference genome and align clean reads to reference genome with the following parameters: hisat2 -p -dta -x -U -S. SAM files of alignments created by HISAT2 were converted to BAM files using SAM-tools view [6]. Coverage estimates and reads mapping statistics are presented in Table 2. DESeq2 [7] was used to assess variance between sample groups and sample replicates using principle component analysis (PCA). PCA plot shown in the Fig. 1 demonstrates the overall quality of our sample collection, library preparation, and sequencing.