Transcriptome Analysis of Ceriops tagal in Saline Environments Using RNA-Sequencing

Abstract

Identification of genes involved in mangrove species’ adaptation to salt stress can provide valuable information for developing salt-tolerant crops and understanding the molecular evolution of salt tolerance in halophiles. Ceriops tagal is a salt-tolerant mangrove tree growing in mudflats and marshes in tropical and subtropical areas, without any prior genome information. In this study, we assessed the biochemical and transcriptional responses of C. tagal to high salt treatment (500 mmol/L NaCl) by hydroponic experiments and RNA-seq. In C. tagal root tissues under salt stress, proline accumulated strongly from 3 to 12 h of treatment; meanwhile, malondialdehyde content progressively increased from 0 to 9 h, then dropped to lower than control levels by 24 h. These implied that C. tagal plants could survive salt stress through biochemical modification. Using the Illumina sequencing platform, approximately 27.39 million RNA-seq reads were obtained from three salt-treated and control (untreated) root samples. These reads were assembled into 47,111 transcripts with an average length of 514 bp and an N50 of 632 bp. Approximately 78% of the transcripts were annotated, and a total of 437 genes were putative transcription factors. Digital gene expression analysis was conducted by comparing transcripts from the untreated control to the three salt treated samples, and 7,330 differentially expressed transcripts were identified. Using k-means clustering, these transcripts were divided into six clusters that differed in their expression patterns across four treatment time points. The genes identified as being up- or downregulated are involved in salt stress responses, signal transduction, and DNA repair. Our study shows the main adaptive pathway of C. tagal in saline environments, under short-term and long-term treatments of salt stress. This provides vital clues as to which genes may be candidates for breeding salt-tolerant crops and clarifying molecular mechanisms of salt tolerance in C. tagal. The expression levels of 20 candidate genes measured by RNA-Seq were validated via qRT-PCR. Eighteen genes showed consistent expression patterns in RNA-Seq and qRT-PCR results, suggesting that the RNA-seq dataset was dependable for gene expression pattern analysis.

Ion homeostasis for salinity tolerance in plants: a molecular approach

“…TFs are powerful candidates to combat salt toxicities as they control a cascade of genes downstream, thus regulating the genetic process at many levels (Rasmussen et al 2013). Hence, analysis at the transcriptomic level will be pertinent in elucidating the molecular basis of various biological phenomena adopted by different salt‐tolerant plants (Xiao et al 2016). A transcriptomic approach can aid in scrutinizing and characterizing the stress‐related genes enabling plants to achieve cellular steady‐state.…”

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

“…An important gene participant of the proline synthetic pathway encoding delta-1-pyrroline-5-carboxylate synthase ( AcP5CS ) enzyme is upregulated in leaf tissues of A. corniculatum indicating its prime role in osmoprotection ( Fu et al., 2005 ). The transcriptome analysis of C. tagal root also revealed differential expression of proline biosynthetic genes where the active gene expression lasted from 3h to 12h of salt treatment ( Xiao et al., 2016 ). The discussion highlights the fact that most of the genetic studies are related to proline whereas the genes encoding other osmolytes are least studied.…”

Biological significance of RNA-seq and single-cell genomic research in woody plants

“…Microsatellite markers have been obtained in C. bungei and used to investigate its population genetics via RNA-seq and all markers showed good amplification results (Wang et al 2016). In another RNA-seq study, 47,111 transcripts have been identified and 7330 differentially expressed transcripts were related to abiotic stress tolerance, suggesting that the RNA-seq dataset was valuable to analysis of gene expression pattern (Xiao et al 2016).…”