Dataset Information

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress.

ABSTRACT: Gossypium hirsutum, a cotton species widely cultivated around the world, is a typical cold-sensitive crop. Low-temperature (LT) stress is one of the main environmental stressors that can affect growth and the quality of cotton fibers. LT is also a major challenge for cotton survival, growth maturity and geographical distribution. However, few genome-wide transcriptional response and profiling datasets are available to explore the LT-tolerant mechanism of cotton. This study treated G. hirsutum with four LT gradients (control at 25?°C and cold temperatures at 4?°C, 10?°C and 15?°C) for 24?hour to generate 12 RNA-Seq datasets (three biological replicates per treatment) with approximately 280 million clean reads per dataset. The quality of the datasets obtained in the current study was validated through a series of quality checks including verification of RNA sample quality and RNA-Seq read quality. Data analyses included novel gene discovery, global gene expression profiling and quantitative real-time PCR. This is the first study to report genome-wide transcriptomic datasets for cotton in response to LT exposure.

SUBMITTER: Li ZB

PROVIDER: S-EPMC6785557 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress.

Li Zhi-Bo ZB Zeng Xiao-Yan XY Xu Jian-Wei JW Zhao Rui-Hai RH Wei Yi-Nong YN

Scientific data 20191009 1

Gossypium hirsutum, a cotton species widely cultivated around the world, is a typical cold-sensitive crop. Low-temperature (LT) stress is one of the main environmental stressors that can affect growth and the quality of cotton fibers. LT is also a major challenge for cotton survival, growth maturity and geographical distribution. However, few genome-wide transcriptional response and profiling datasets are available to explore the LT-tolerant mechanism of cotton. This study treated G. hirsutum wi ...[more]

PMID: 31597918

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Project description:Cotton is a commercial and economically important crop that generates billions of dollars in annual revenue worldwide. However, cotton yield is affected by a sap-sucking insect Bemisia tabaci (whitefly), and whitefly-borne cotton leaf curl disease (CLCuD). The causative agent of devastating CLCuD is led by the viruses belonging to the genus Begomovirus (family Geminiviridae), collectively called cotton leaf curl viruses. Unfortunately, the extensively cultivated cotton (Gossypium hirsutum) species are highly susceptible and vulnerable to CLCuD. Yet, the concomitant influence of whitefly and CLCuD on the susceptible G. hirsutum transcriptome has not been interpreted. In the present study we have employed an RNA Sequencing (RNA-Seq) transcriptomics approach to explore the differential gene expression in susceptible G. hirsutum variety upon infection with viruliferous whiteflies. Comparative RNA-Seq of control and CLCuD infected plants was done using Illumina HiSeq 2500. This study yielded 468 differentially expressed genes (DEGs). Among them, we identified 220 up and 248 downregulated DEGs involved in disease responses and pathogen defense. We selected ten genes for downstream RT-qPCR analyses on two cultivars, Karishma and MNH 786 that are susceptible to CLCuD. We observed a similar expression pattern of these genes in both susceptible cultivars that was also consistent with our transcriptome data further implying a wider application of our global transcription study on host susceptibility to CLCuD. We next performed weighted gene co-expression network analysis that revealed six modules. This analysis also identified highly co-expressed genes as well as 55 hub genes that co-express with ≥ 50 genes. Intriguingly, most of these hub genes are shown to be downregulated and enriched in cellular processes. Under-expression of such highly co-expressed genes suggests their roles in favoring the virus and enhancing plant susceptibility to CLCuD. We also discuss the potential mechanisms governing the establishment of disease susceptibility. Overall, our study provides a comprehensive differential gene expression analysis of G. hirsutum under whitefly-mediated CLCuD infection. This vital study will advance the understanding of simultaneous effect of whitefly and virus on their host and aid in identifying important G. hirsutum genes which intricate in its susceptibility to CLCuD.

Dataset Information

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress.

Publications

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress.

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