Integrative Transcriptome and Proteome Analysis Identifies Major Molecular Regulation Pathways Involved in Ramie (Boehmeria nivea (L.) Gaudich) under Nitrogen and Water Co-Limitation

Abstract

Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP—glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.

Comprehensive Transcriptome and Metabolome Analyses Reveal Primary Molecular Regulation Pathways Involved in Peanut under Water and Nitrogen Co-Limitation

“…Under DS conditions, N fertilizer application increased the biomass, RWC, and pod yield by 12.10%, 36.84%, and 14.87%, respectively. Overall, N fertilizer application mitigated the adverse effects caused by DS, which is consistent with a previous study [17].…”

“…DS and N deficiency are essentially the key limiting factors for peanut growth [13,16], and the combination of nutrient deficiency and DS exacerbates adverse effects [17]. It has been demonstrated that appropriate N application can alleviate the adverse effects of DS The gene products/metabolites with red/green background boxes belong to the differential genes/metabolites detected in this study, where red represents upregulated genes/metabolites and green represents downregulated genes/metabolites.…”

“…Under water and N co-limitation, COG function annotation showed that transport and metabolism of carbohydrates and biosynthesis, transport and catabolism of secondary metabolites accounted for 14.2% and 9.6% of 1317 DEGs, respectively (Figure 5A). The number of DEGs rich in carbon metabolism regulatory pathways were determined via KEGG enrichment analysis (Figure 5B), including carbon metabolism (80), starch and sucrose metabolism (73), carbon fixation in photosynthetic organisms (39) and glyoxylate and dicarboxylate metabolism (34), while the number of DEGs in N-related metabolic pathways such as glutathione (28) and N metabolism (17) was lower. The number of DEGs in the biosynthesis of secondary metabolites pathways such as phenylpropanoid biosynthesis (46) and flavonoid biosynthesis ( 16) was also determined.…”

“…DS and N deficiency are essentially the key limiting factors for peanut growth [13,16], and the combination of nutrient deficiency and DS exacerbates adverse effects [17]. It has been demonstrated that appropriate N application can alleviate the adverse effects of DS on plant growth [18,19].…”

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

“…Transcriptome analysis of tissue-specific expression was conducted using four different tissue samples of “Zhongzhu No.1” sequenced by our laboratory. Transcriptome data of water deficit and nitrogen deficit were obtained from [ 73 ]. The additional “Zhongzhu No.2” ramie transcriptome changes in leaves of 3-week-old seedlings exposed to waterlogging for 12 h and to normal conditions were profiled using RNA-Seq data in our recent research.…”