Sonneratia apetala is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of S. apetala. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (p < 0.001, Q < 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of S. apetala roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in S. apetala response to salt stress.

Chromium (Cr) is one of the most toxic heavy metals in the environment. The tolerance to metal stress involves sophisticated regulation of gene expression networks, which involve microRNAs (miRNAs). However, the role of miRNAs in Cr stress response in Avicennia marina has not been resolved, and was addressed here. The analysis of response characteristics revealed that morpho-physiological traits such as root length, Cr accumulation level and antioxidant enzyme activity all exhibit significant changes under Cr stress. Via sRNA sequencing, a total of 27 known and 149 novel miRNAs were identified, 63 of which showed differential expression after Cr stress (q-value < 0.001). Further, 571 miRNA-target interaction pairs were identified for differentially expressed miRNAs, corresponding to 355 target genes. GO and KEGG analyses indicated that these target genes could participate in stress-related biological processes such as signal transduction, transcription regulation, protein synthesis and the MAPK signaling pathway. 54 miRNA target genes, corresponding to 37 miRNAs such as Ama-miR160, Ama-nmiR25-5p and Ama-nmiR118-5p, were enriched for “plant signal hormone transduction” (ko04075), “phenylpropanoid biosynthesis” (ko00940) and “MAPK signaling pathway” (ko04016), which indicated an important role of these miRNAs in regulating Cr stress response in A. marina. Based on the findings, a Cr stress-responsive regulatory model was developed, offering new insights into the molecular regulatory mechanisms of Cr response. In conclusion, this study shows the identity and potential role of miRNAs in the heavy metal stress response of A. marina, and provides the foundation for future research.