RNA-sequencing Reveals Global Transcriptomic Changes in Nicotiana tabacum Responding to Topping and Treatment of Axillary-shoot Control Chemicals

Abstract

Removal of terminal buds (topping) and control of the formation of axillary shoots (suckers) are common agronomic practices that significantly impact the yield and quality of various crop plants. Application of chemicals (suckercides) to plants following topping is an effective method for sucker control. However, our current knowledge of the influence of topping, and subsequent suckercide applications, to gene expression is limited. We analyzed the differential gene expression using RNA-sequencing in tobacco (Nicotiana tabacum) that are topped, or treated after topping by two different suckercides, the contact-localized-systemic, Flupro® (FP), and contact, Off-Shoot-T®. Among the differentially expressed genes (DEGs), 179 were identified as common to all three conditions. DEGs, largely related to wounding, phytohormone metabolism and secondary metabolite biosynthesis, exhibited significant upregulation following topping, and downregulation after suckercide treatments. DEGs related to photosynthetic processes were repressed following topping and suckercide treatments. Moreover, topping and FP-treatment affect the expression of auxin and cytokinin signaling pathway genes that are possibly involved in axillary shoot formation. Our results provide insights into the global change of plant gene expression in response to topping and suckercide treatments. The regulatory elements of topping-inducible genes are potentially useful for the development of a chemical-free sucker control system.

The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis

“…Low quality and contaminated reads were removed as described previously 74 . Sequences smaller than 18 nucleotide (nt) and larger than 24 nt were also removed.…”

“…To analyze the effect of MeJA on C. roseus transcriptome, publically available RNAseq data were obtained from the sequence read archive database (accession number PRJNA185483). Raw reads were cleaned and filtered as described previously 74 . Finally, cleaned reads were mapped to the C. roseus reference sequence 41 with Bowtie2 75 , and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were calculated by eXpress 83 .…”

Comparative Transcriptomic Analysis of Two Brassica napus Near-Isogenic Lines Reveals a Network of Genes That Influences Seed Oil Accumulation

“…Raw Illumina sequence reads were processed using the prinseq-lite-0.20.4 ( Schmieder and Edwards, 2011 ) for removal of low-quality reads ( Singh et al, 2015 ). Subsequently, pre-processed reads were assessed for quality control with FastQC (version 0.11.3; Babraham Bioinformatics, Cambridge, UK).…”

A differentially regulated AP2/ERF transcription factor gene cluster acts downstream of a MAP kinase cascade to modulate terpenoid indole alkaloid biosynthesis in Catharanthus roseus

“…In order to analyze the expression patterns of C. roseus PKs and TIA pathway genes, transcriptome data for five different tissues (flower, mature leaf, immature leaf, stem and root) were obtained from the Sequence Read Archive (SRA) database at the National Center for Biotechnology Information (accession number SRA030483). Raw reads were processed and reads per kilobase of transcript per million mapped reads (RPKM) value was calculated as described before (Singh et al, 2015). Pairwise Pearson correlation coefficients for each transcript was calculated using RPKM.…”