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Transcriptomic response of bermudagrass to 7 days of drought, salt, heat and submergence

ABSTRACT: Purpose: We aimed to dissect response of bermudagrass to drought, salt, submergence and heat stresses and identify stress responsive genes inbermudagrass. Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.Paired-end clean reads were aligned to the reference genome of TAIR10 and rice protein sequence from MSU (version_7.0) using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated . Differential expression analysis of abiotic stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, 12 samples with two biological replicates per treatment were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified genes modulated by different abiotic stress treatments.

ORGANISM(S): Cynodon dactylon

PROVIDER: GSE140362 | GEO | 2022/11/01

REPOSITORIES: GEO

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