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Natural variation analysis of perennial ryegrass in response to abiotic stress highlights LpHSFC1b as a positive regulator of heat stress

ABSTRACT: Purpose: We aimed to dissect response of Perennial_ryegrass to drought, heat and cold stresses and identify stress responsive genes in Perennial_ryegrass. Methods: The sequencing libraries was constructed using NEBNext® UltraTM RNA Library Prep Kit for Illumina®, sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean data (clean reads) were obtained after removing reads containing poly-N or adapter, and low quality reads from raw data. Transcriptome assembly was accomplished based on the left.fq.gz and right.fq.gz using Trinity. Gene function was annotated based on the following databases: NR (NCBI non-redundant protein sequences), Pfam (Protein family), KOG/COG/eggNOG (Clusters of Orthologous Groups of proteins), Swiss-Prot (A manually annotated and reviewed protein sequence database), KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology). Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). Genes with an adjusted P-value<0.05 and fold change>2 found by DESeq were assigned as differentially expressed. Results:In total, four samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 5 G clean bases were generated for each sample.After sequencing quality control, a total 137822219 clean reads and 41.05 G clean bases were generated. The Q30 base percentage of each sample was higher than 91.0% (Table S1). A total of 32840 unigenes were obtained after transcriptome assembly. Comparative analysis identified genes modulated by drought, heat and cold stresses

ORGANISM(S): Lolium perenne

PROVIDER: GSE141654 | GEO | 2020/11/08

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study are studies the response of annual Zea mays ssp. mexicana L. under cold and drought stress Methods: The seedlings of zea may ssp. mexicana L. were generated by Illumina HiSeq2500 deep-sequencing. In order to generate a global overview of Zea mexicana transcriptome data, 3 of complement DNA (cDNA) libraries were prepared from RNA isolated from root, stem, and leave mixed tissues of Zea Mexicana from Control (24℃), Cold (4℃) and Drought (PEG2000, 20%) treatments and each teatment has two repetitions. The sequence reads that passed quality filters were merged and de novo to generate all transcripts set by Trinity with default parameter, which will be treated as reference genome. The number of paired-reads of each sample were mapped to reference genome by Bowtie software v1.1.1 and the number of mapped reads were calculated by RSEM. qRT-PCR validation was performed using BIO-RAD CFX96 sequence detection system and SYBR Green assays. Results: Using RNA-Seq technology with the Trinity assembled method, we generated a seedling plant transcriptome at a sequencing size of 51.78Gb of Zea mays ssp. mexicana L. from pooled RNA samples which included control (CK), cold (4℃) and drought (PEG2000, 20%) stressed plant samples. A total of 414,232,462 high quality clean reads were used to conduct de novo assembly and annotation of genes without reference genome information. All of these reads were assembled into 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp). A total of 3,504 up-regulated and 1,220 down-regulated genes were detected under cold stress and 532 up-regulated and 82 down-regulated genes were detected under drought stress. A Venn diagram indicated that 208 genes were affected by both cold and drought stresses. 3 cold stress pathways and 5 drought related pathways showed significant KEGG pathways. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The ABA dependent pathway, trehalose synthetic pathway and CBF6 gene of ICE1-CBF pathway may play important roles in the DEGs co-up-regulated by both stresses of Zea mays ssp. mexicana L. Conclusions: We analyzed transcriptome data and gene expression profile information from seedlings of Zea mays ssp. mexicana L. under cold and drought stresses. Together these data provides the most comprehensive sequence study available for Zea mays ssp. mexicana L. and provides some important functional genes and molecular mechanism information for improving the quality characteristic of maize in the future.

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Natural variation analysis of perennial ryegrass in response to abiotic stress highlights LpHSFC1b as a positive regulator of heat stress

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