Integrated Full-Length Transcriptome and MicroRNA Sequencing Approaches Provide Insights Into Salt Tolerance in Mangrove (Sonneratia apetala Buch.-Ham.)

Abstract

MicroRNAs (miRNAs) are small RNA molecules that serve as key players in plant stress responses. Although stress-regulated miRNAs have been explored in various plants, they are not well studied in mangroves. Herein, we combined PacBio isoform sequencing (Iso-Seq) with BGISEQ short-read RNA-seq to probe the role of miRNAs in the salt stress response of the mangrove plant, Sonneratia apetala Buch.-Ham. A total of 1,702,463 circular consensus sequencing reads were generated that produced 295,501 nonredundant full-length transcripts from the leaves of a 1-year-old S. apetala. After sequencing nine small RNA libraries constructed from control and 1- and 28-day 300 mM NaCl treatments, we identified 143 miRNAs (114 known and 29 novel) from a total of >261 million short reads. With the criteria of |log2FC| ≥ 1 and q-value < 0.05, 42 and 70 miRNAs were differentially accumulated after 1- and 28-day salt treatments, respectively. These differential accumulated miRNAs potentially targeted salt-responsive genes encoding transcription factors, ion homeostasis, osmotic protection, and detoxificant-related proteins, reminiscent of their responsibility for salinity adaptation in S. apetala. Particularly, 62 miRNAs were Sonneratia specific under salt stress, of which 34 were co-expressed with their 131 predicted targets, thus producing 140 miRNA–target interactions. Of these, 82 miRNA-target pairs exhibited negative correlations. Eighteen miRNA targets were categorized for the ‘environmental information processing’ during KEGG analysis and were related to plant hormone signal transduction (ko04075), MAPK signaling pathway–plant (ko04016), and ABC transporters (ko02010). These results underscored miRNAs as possible contributors to mangrove success in severe environments and offer insights into an miRNA-mediated regulatory mechanism of salt response in S. apetala.

PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in Sonneratia apetala

“…In this scenario, Iso-seq (isoform sequencing) offers crucial technical support and several advantages, including high throughput and an ability to generate lengthy fragments. Despite being a halophyte, with a high salt tolerance capacity, only a limited number of mechanistic studies have been conducted on S. apetala [23]. Our study provides a first draft of the leaf transcriptome of this mangrove plant (S. apetala) by analyzing the salt stress response at two time points with the help of a combination of PacBio long-read RNA sequencing and RNA-seq sequencing methods.…”

“…The amplified double-stranded DNA was repaired for damage, end-repaired and ligated with SMRT adapters before constructing the full-length transcriptome sequencing library. Then, the SMRT library was sequenced to a data size of 30 GB through the PacBio platform following the methods described by Chen et al [23].…”

Integration of mRNA and miRNA analysis reveals the molecular mechanisms of sugar beet (Beta vulgaris L.) response to salt stress

“…The miRNAs confer important roles in plant development and growth, including cell differentiation 18 , organ development such as the roots 19 , 20 , flowering 21 , 22 , and fruit development 23 , 24 . In addition to their physiological and metabolic roles, miRNAs are also actively involved in plants’ abiotic stress responses, including drought 25 , high temperature 26 , low temperature 27 , and saline-alkali stress 28 , 29 .…”