RNA Sequencing Analysis Reveals Transcriptomic Variations in Tobacco (Nicotiana tabacum) Leaves Affected by Climate, Soil, and Tillage Factors

Abstract

The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq) analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs), soil factors (SFs), and tillage factors (TFs). We detected 4980, 2916, and 1605 differentially expressed genes (DEGs) that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs), respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.

A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus

“…The cuffdiff program was used to test for statistically significant differences in gene expression between two samples. DEGs were identified based on the following criteria: false discovery rate (FDR) <0.05 and absolute fold change >253. To identify and classify transcription factors (TFs) in B. napus , the putative amino acids were aligned with Arabidopsis TFs downloaded from the Plant Transcription Factor Database v3.0 (http://planttfdb.cbi.pku.edu.cn) and The Arabidopsis Information Resource (http://www.arabidopsis.org)54.…”

Comparative Transcriptome Analysis of Recessive Male Sterility (RGMS) in Sterile and Fertile Brassica napus Lines

“…Then, we used agriGO ( http://bioinfo.cau.edu.cn/agriGO/ ) and ReviGO ( http://revigo.irb.hr/ ) [ 41 , 42 ] to identify the putative biological functions and biochemical pathways for DEGs and find statistically overrepresented GO terms. To expand our functional analysis of DEGs involved in RGMS, we visualized biochemical pathway overlays using MapMan software ( http://mapman.gabipd.org ), as previously described [ 43 ].…”

Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato

“…A comprehensive transcriptome analysis in rice suggests that field type and macroclimate impose dramatic effects on gene expression involved in photosynthesis and development, and among these environmental factors solar radiation and temperature have consistent effects on gene expression [9]. When tobacco leaves were subjected to different climate, soil and tillage conditions, about seven hundred genes were commonly modulated by the three factors as revealed by RNA sequencing (RNA-seq) [10]. …”