De novo transcriptome analysis unveils regulatory pathways associated with stress tolerance in a promising C3 model of halophyte, Suaeda salsa

Abstract Suaeda salsa is a promising halophyte model to study the molecular mechanisms underlying salt tolerance in plants. To attain a thorough knowledge of transcriptomic profiles under salt stress during seedling establishment, we accomplished whole-transcriptome sequencing on the seedlings of Suaeda salsa at 30 days after exposure to 0 mM, 200 mM, 400 mM, and 800 mM NaCl. We observed that transcripts implicated in solute transport and nutrient uptake, protein synthesis, modification, hemostasis, transcriptional regulation, and phytohormone action prominently changed at different concentrations of salinity. Likewise, significant changes in the expression level of members of gene families such as MYB, bHLH, MADS/AGL, bZIP, NAC, C2C2, B3, ERF, WRKY, HB, NF-Y, C2H2 suggest them as key players in the salt tolerance of Suaeda salsa during seedling establishment. We additionally found the superfamilies of tyrosine-like protein kinase (TLK) linked to phosphorylation and Ca2+calmodulin-dependent protein kinas, enabling the signal sequence for protein activity and gene transcription under salinity stress. The novel identified autophagy ATG members, and autophagic cargo receptor protein (NBR1) was observed under salt stress suggesting that autophagy regulates rapid protein turnover as a prerequisite for salt stress tolerance in S. salsa.