De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree ( Bruguiera gymnorhiza)

Int J Mol Sci. 2021 Sep 13;22(18):9874. doi: 10.3390/ijms22189874.


Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

Keywords: RNA-Seq; abiotic stress; de novo assembly; gene expression; mangrove; salt stress; transcriptome.

MeSH terms

  • Adaptation, Physiological / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant / genetics
  • Molecular Sequence Annotation
  • Osmotic Pressure / drug effects*
  • Plant Leaves / drug effects
  • Plant Leaves / genetics
  • Plant Leaves / growth & development
  • Rhizophoraceae / genetics*
  • Rhizophoraceae / growth & development
  • Salinity
  • Salt Tolerance / genetics
  • Sodium Chloride / adverse effects
  • Stress, Physiological / genetics*
  • Transcriptome / genetics*
  • Trees


  • Sodium Chloride