Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology

Background. The thyroid hormone metabolite 3-iodothyronamine (3-T1AM) is rapidly emerging as a promising compound in decreasing the heart rate and lowering the cardiac output. The aim of our study was to fully understand the molecular mechanism of 3-T1AM on cardiomyocytes and its potential targets in cardiovascular diseases. Materials and Methods. In our study, we utilized RNA-Seq to characterize the gene expression in H9C2 cells after 3-T1AM treatment. Comparative transcriptome analysis, including gene ontology, signaling pathways, disease connectivity analysis, and protein-protein interaction networks (PPI), was presented to find the critical gene function, hub genes, and related pathways. Results. A total of 1494 differently expressed genes (DEGs) were identified (192 upregulated and 1302 downregulated genes) in H9C2 cells for 3-T1AM treatment. Of these, 90 genes were associated with cardiovascular diseases. The PPI analysis indicated that 5 hub genes might be the targets of 3-T1AM. Subsequently, eight DEGs characterized using RNA-Seq were confirmed by RT-qPCR assays. Conclusions. Our study provides a comprehensive analysis of 3-T1AM on H9C2 cells and delineates a new insight into the therapeutic intervention of 3-T1AM for the cardiovascular diseases.

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Comparative transcriptome analysis of barley (Hordeum vulgare L.) glossy mutant using RNA-Seq

Revista Brasileira de Botânica ◽

10.1007/s40415-016-0328-1 ◽

2016 ◽

Vol 40 (1) ◽

pp. 247-256

Author(s):

Haiye Luan ◽

Huiquan Shen ◽

Yinghu Zhang ◽

Hui Zang ◽

Hailong Qiao ◽

...

Keyword(s):

Hordeum Vulgare ◽

Transcriptome Analysis ◽

Comparative Transcriptome ◽

Rna Seq ◽

Hordeum Vulgare L ◽

Comparative Transcriptome Analysis ◽

Glossy Mutant

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RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically

Molecular BioSystems ◽

10.1039/c3mb70232d ◽

2013 ◽

Vol 9 (11) ◽

pp. 2775 ◽

Cited By ~ 31

Author(s):

Yang Tan ◽

Juanjuan Liu ◽

Xiaohua Chen ◽

Huajun Zheng ◽

Fuli Li

Keyword(s):

Transcriptome Analysis ◽

Comparative Transcriptome ◽

Rna Seq ◽

Comparative Transcriptome Analysis ◽

Clostridium Ljungdahlii

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Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root

BMC Genomic Data ◽

10.1186/s12863-021-00962-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Sze-Ling Kong ◽

Siti Nor Akmar Abdullah ◽

Chai-Ling Ho ◽

Mohamed Hanafi bin Musa ◽

Wan-Chin Yeap

Keyword(s):

Transcriptome Analysis ◽

Oil Palm ◽

Crop Improvement ◽

Molecular Response ◽

Comparative Transcriptome ◽

Rna Seq ◽

Response Mechanism ◽

Transcriptional Responses ◽

Comparative Transcriptome Analysis ◽

Pi Deficiency

Abstract Background Phosphorus (P), in its orthophosphate form (Pi) is an essential macronutrient for oil palm early growth development in which Pi deficiency could later on be reflected in lower biomass production. Application of phosphate rock, a non-renewable resource has been the common practice to increase Pi accessibility and maintain crop productivity in Malaysia. However, high fixation rate of Pi in the native acidic tropical soils has led to excessive utilization of P fertilizers. This has caused serious environmental pollutions and cost increment. Even so, the Pi deficiency response mechanism in oil palm as one of the basic prerequisites for crop improvement remains largely unknown. Results Using total RNA extracted from young roots as template, we performed a comparative transcriptome analysis on oil palm responding to 14d and 28d of Pi deprivation treatment and under adequate Pi supply. By using Illumina HiSeq4000 platform, RNA-Seq analysis was successfully conducted on 12 paired-end RNA-Seq libraries and generated more than 1.2 billion of clean reads in total. Transcript abundance estimated by fragments per kilobase per million fragments (FPKM) and differential expression analysis revealed 36 and 252 genes that are differentially regulated in Pi-starved roots at 14d and 28d, respectively. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, hormonal signaling and gene transcription were found among the differentially expressed genes. Conclusions Our results showed that the molecular response mechanism underlying Pi starvation in oil palm is complexed and involved multilevel regulation of various sensing and signaling components. This contribution would generate valuable genomic resources in the effort to develop oil palm planting materials that possess Pi-use efficient trait through molecular manipulation and breeding programs.

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