De novo transcriptome sequencing of two cultivated jute species under salinity stress

Abstract

Soil salinity, a major environmental stress, reduces agricultural productivity by restricting plant development and growth. Jute (Corchorus spp.), a commercially important bast fiber crop, includes two commercially cultivated species, Corchorus capsularis and Corchorus olitorius. We conducted high-throughput transcriptome sequencing of 24 C. capsularis and C. olitorius samples under salt stress and found 127 common differentially expressed genes (DEGs); additionally, 4489 and 492 common DEGs were identified in the root and leaf tissues, respectively, of both Corchorus species. Further, 32, 196, and 11 common differentially expressed transcription factors (DTFs) were detected in the leaf, root, or both tissues, respectively. Several Gene Ontology (GO) terms were enriched in NY and YY. A Kyoto Encyclopedia of Genes and Genomes analysis revealed numerous DEGs in both species. Abscisic acid and cytokinin signal pathways enriched respectively about 20 DEGs in leaves and roots of both NY and YY. The Ca2+, mitogen-activated protein kinase signaling and oxidative phosphorylation pathways were also found to be related to the plant response to salt stress, as evidenced by the DEGs in the roots of both species. These results provide insight into salt stress response mechanisms in plants as well as a basis for future breeding of salt-tolerant cultivars.

Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

“…In this study, the expression of PYL4 was downregulated, while PP2Cs and SAPK3 were both upregulated; PP2Cs and SAPK3 displayed the same expression trends in both drought-stressed and ABA-treated hemp plants. Similar findings were also reported in drought- or salinity-stressed tomato and jute plants [ 23 , 61 ] and ABA-treated tomato plants [ 62 ]. Additionally, a gene encoding PYL4 was also downregulated in drought-stressed potato plants [ 30 ]; CsPYL3 was downregulated, although CsPYL1 , CsPYL2 , CsPP2C2 , and CsSnKR2.2 were upregulated in roots and stems of cucumber seedlings under drought conditions [ 63 ].…”

“…High-throughput sequencing has become a powerful tool in many research fields due to its cost-efficiency and rapidness [ 17 – 23 ]. The data yielded facilitates the development of genetic analyses and functional genomics studies among species, especially for many nonmodel plants.…”

Construction of a high-resolution genetic map and identification of quantitative trait loci for salt tolerance in jute (Corchous spp.)

“…However, most previous studies of salt tolerance in jute have focused only on the morphological, physiological, and proteomic components [26]. To our knowledge, only two studies [9, 27] related to the salt tolerance of jute have been carried out through transcriptome sequencing, revealing a large number of differentially expressed genes underlying salt tolerance. However, the large number of differentially expressed genes made it difficult to identify the best candidate genes related to salt tolerance for practical application.…”

Jute Responses and Tolerance to Abiotic Stress: Mechanisms and Approaches

“…To explore the possible salt-stress-responsible gene, Yang et al [ 71 ] reported that, along with different transcription factors, a smaller amount of differentially expressed unigenes (DEGs) were implicated in different metabolic traits that enhanced stress tolerance in jute, such as the ABA signaling pathway, plant hormone signal transduction, and metabolism of cystine/methionine, and these were mainly noticeable in the root tissue of salt-tolerant genotypes. Similarly, another three relevant pathways enriched in root, namely, Ca 2+ - and mitogen-activated protein kinase signaling pathways and oxidative phosphorylation pathways, were identified by Yang et al [ 72 ], which were involved in the mechanism of salt stress tolerance in two jute species ( C. capsularis and C. olitorius ).…”