RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress

Abstract

Background Clerodendrum inerme (L.) Gaertn, a halophyte, usually grows on coastal beaches as an important mangrove plant. The salt-tolerant mechanisms and related genes of this species that respond to short-term salinity stress are unknown for us. The de novo transcriptome of C. inerme roots was analyzed using next-generation sequencing technology to identify genes involved in salt tolerance and to better understand the response mechanisms of C. inerme to salt stress. Results Illumina RNA-sequencing was performed on root samples treated with 400 mM NaCl for 0 h, 6 h, 24 h, and 72 h to investigate changes in C. inerme in response to salt stress. The de novo assembly identified 98,968 unigenes. Among these unigenes, 46,085 unigenes were annotated in the NCBI non-redundant protein sequences (NR) database, 34,756 sequences in the Swiss-Prot database and 43,113 unigenes in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database. 52 Gene Ontology (GO) terms and 31 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were matched to those unigenes. Most differentially expressed genes (DEGs) related to the GO terms “single-organism process”, “membrane” and “catalytic activity” were significantly enriched while numerous DEGs related to the plant hormone signal transduction pathway were also significantly enriched. The detection of relative expression levels of 9 candidate DEGs by qRT-PCR were basically consistent with fold changes in RNA sequencing analysis, demonstrating that transcriptome data can accurately reflect the response of C. inerme roots to salt stress. Conclusions This work revealed that the response of C. inerme roots to saline condition included significant alteration in response of the genes related to plant hormone signaling. Besides, our findings provide numerous salt-tolerant genes for further research to improve the salt tolerance of functional plants and will enhance research on salt-tolerant mechanisms of halophytes.

Transcriptome and Metabolome Analyses Reveal Potential Salt Tolerance Mechanisms Contributing to Maintenance of Water Balance by the Halophytic Grass Puccinellia nuttalliana

“…SOD converts the superoxide radical into the less toxic hydrogen peroxide. H 2 O 2 is then scavenged by POD, CAT or other scavenging enzymes (Nikalje et al, 2018;Xiong et al, 2019). In our study, five Cu, Zn-SODs, five Fe-SOD, four Mn-SODs, four CATs, and six PODs were up-regulated by NaCl.…”

Regulation of Plant Responses to Salt Stress

“…Transcriptome sequencing techniques have been widely used to identify novel genes that are linked to the regulation of the plant salt stress response [ 119 , 120 ]. The development of next-generation sequencing technology has made it easier to screen for salt-tolerance genes [ 121 , 122 ]. The global survey of transcriptome profiles and microRNA levels of plants in response to salt stress using RNA-Seq has provided useful insights into the mechanisms of salt tolerance [ 123 ].…”

De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress

“…High-throughput sequencing technology, especially RNA sequencing (RNA-seq), has been widely used to study the molecular basis of plants in response to abiotic stress in recent years [ 13 – 15 ]. De novo transcriptome assembly by RNA-seq enables research on species without a reference genome [ 16 ].…”

“…De novo transcriptome assembly by RNA-seq enables research on species without a reference genome [ 16 ]. RNA-seq was recently used to reveal dynamic changes in the transcriptomic profile of many species, such as Pinus halepensis and Pinus massoniana [ 14 , 17 ], Populus [ 18 ], Rosa chinensis [ 19 ], halophyte plant Clerodendrum inerme (L.) Gaertn [ 15 ], and Suaeda fruticosa [ 13 ], under abiotic stress. Podocarpus macrophyllus ([Thunb.]…”