Comparative transcriptome analysis of the gills of Procambarus clarkii provide novel insights into the response mechanism of ammonia stress tolerance

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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Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

BMC Genomics ◽

10.1186/s12864-020-06841-2 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Pratiti Dasgupta ◽

Abhishek Das ◽

Sambit Datta ◽

Ishani Banerjee ◽

Sucheta Tripathy ◽

...

Keyword(s):

Transcriptome Analysis ◽

Indica Rice ◽

Rice Variety ◽

Comparative Transcriptome ◽

Response Mechanism ◽

Cold Response ◽

Comparative Transcriptome Analysis

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Comparative transcriptome analysis between resistant and susceptible tomato lines uncovers the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum

10.21203/rs.2.11613/v1 ◽

2019 ◽

Author(s):

Dongye Zhang ◽

Huanhuan Yang ◽

Xiangyang Xu

Keyword(s):

Transcriptome Analysis ◽

Early Stage ◽

Cladosporium Fulvum ◽

Comparative Transcriptome ◽

Response Mechanism ◽

Resistance Response ◽

Tomato Production ◽

Comparative Transcriptome Analysis ◽

Leaf Mold ◽

Mold Resistance

Abstract Background Leaf mold disease caused by Cladosporium fulvum is a major disease in cultivated tomato plants and affects global tomato production. Some Cf genes, of which Cf-16 is an effective gene for resisting tomato leaf mold, are associated with leaf mold resistance; however, the molecular mechanism is largely unknown. Results we used comparative transcriptome analysis of C. fulvum-resistant (cv. Ontario7816, including the Cf-16 gene) and C. fulvum-susceptible (cv. Moneymaker) tomato lines to identify differentially expressed genes (DEGs) at 4 and 8 days postinfection with C. fulvum. We found that the number of DEGs in the Cf-16 tomatoes was significantly higher than the number of DEGs in the Moneymaker tomatoes. In addition, 1,350 DEGs were shared among Cf-16 groups at 4 and 8 dpi, suggesting the existence of a common core of DEGs in response to C. fulvum infection. Upregulated DEGs were mainly associated with defense processes and phytohormone signaling, including salicylic acid (SA) and jasmonic acid (JA), in the Cf-16 tomato. Moreover, the SA and JA contents significantly increased in the Cf-16 tomato at the early stages of C. fulvum infection. Comprehensively, more upregulated DEGs were found in the Cf-16 tomato than in the Cf-10 and Cf-12 tomatoes at the early stage of C. fulvum infection. However, the significantly enriched defense-signaling pathways involved in Cf-16 had some distinctions from those in Cf-10 and Cf-12. Conclusion Our results provide new insights into the resistance response mechanism of Cf genes to C. fulvum, especially the unique characteristics of Cf-16 in response to C. fulvum infection.

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