Transcriptomic and proteomic feature of salt stress-regulated network in Jerusalem artichoke (Helianthus tuberosus L.) root based on de novo assembly sequencing analysis

Planta ◽  
2017 ◽  
Vol 247 (3) ◽  
pp. 715-732 ◽  
Author(s):  
Aiqin Zhang ◽  
Dongming Han ◽  
Yu Wang ◽  
Huifang Mu ◽  
Tong Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
De Novo Assembly ◽  
De Novo ◽  
Jerusalem Artichoke ◽  
Sequencing Analysis ◽  
Helianthus Tuberosus

scholarly journals Salt stress induced differential metabolic responses in the sprouting tubers of Jerusalem artichoke (Helianthus tuberosus L.)

PLoS ONE ◽  
2020 ◽  
Vol 15 (6) ◽  
pp. e0235415
Author(s):  
Hui-Xi Zou ◽  
Dongsheng Zhao ◽  
Haihong Wen ◽  
Nan Li ◽  
Weiguo Qian ◽  
...  
Keyword(s):  
Salt Stress ◽  
Jerusalem Artichoke ◽  
Metabolic Responses ◽  
Helianthus Tuberosus

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

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuping Xiong ◽  
Haifeng Yan ◽  
Hanzhi Liang ◽  
Yueya Zhang ◽  
Beiyi Guo ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Rna Sequencing ◽  
Plant Hormone ◽  
De Novo ◽  
Sequencing Analysis ◽  
Salt Tolerant ◽  
Mangrove Plant ◽  
Next Generation Sequencing Technology ◽  
Go Terms

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.

scholarly journals RNA-Seq Analysis and De Novo Transcriptome Assembly of Jerusalem Artichoke (Helianthus tuberosus Linne)

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e111982 ◽  
Author(s):  
Won Yong Jung ◽  
Sang Sook Lee ◽  
Chul Wook Kim ◽  
Hyun-Soon Kim ◽  
Sung Ran Min ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
De Novo Transcriptome Assembly ◽  
Rna Seq ◽  
De Novo Transcriptome

scholarly journals Expression of Genes Related to Plant Hormone Signal Transduction in Jerusalem artichoke (Helianthus tuberosus L.) Seedlings Under Salt Stress

2021 ◽  
Author(s):  
Yue Yang ◽  
Wang Jueyun ◽  
Ren Wencai ◽  
Zhaosheng Zhou ◽  
Long Xiaohua ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Abscisic Acid ◽  
Salt Stress ◽  
Plant Hormone ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Expression Of Genes ◽  
Gene Functions

Background: Jerusalem artichoke (Helianthus tuberosus L.) is tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, the plant physiology, biochemistry and gene transcription are likely to undergo large changes. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h, 6 h, 12 h, 24 h and 48 h, with 150,129 unigenes and 9023 DEGs (Differentially Expressed Genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among the groups convergence. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belongs to PYL (abscisic acid receptor PYR / PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (Genes such as jasmonate ZIM-domain gene) and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qPCR of 12 randomly selected genes confirmed the accuracy of RNA-seq. Conclusions: Under the impact of high salinity (300mM) environment, Jerusalem artichoke in the seedling stage was difficult to survive for a long time, and the phenotype was severe in the short term. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern.

RNA-Seq De Novo Assembly of Red Pitaya (Hylocereus polyrhizus) Roots and Differential Transcriptome Analysis in Response to Salt Stress

2019 ◽  
Vol 12 (2) ◽  
pp. 55-66 ◽  
Author(s):  
Quandong Nong ◽  
Mingyong Zhang ◽  
Jiantong Chen ◽  
Mei Zhang ◽  
Huaping Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
De Novo Assembly ◽  
De Novo ◽  
Rna Seq ◽  
Hylocereus Polyrhizus

De novo assembly of mulberry (Morus alba L.) transcriptome and identification of candidate unigenes related to salt stress responses

2017 ◽  
Vol 64 (5) ◽  
pp. 738-748 ◽  
Author(s):  
C. Y. Liu ◽  
X. Q. Liu ◽  
D. P. Long ◽  
B. N. Cao ◽  
Z. H. Xiang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
De Novo Assembly ◽  
De Novo ◽  
Morus Alba

scholarly journals Expression of Genes Related to Plant Hormone Signal Transduction in Jerusalem Artichoke (Helianthus tuberosus L.) Seedlings under Salt Stress

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 163
Author(s):  
Yang Yue ◽  
Jueyun Wang ◽  
Wencai Ren ◽  
Zhaosheng Zhou ◽  
Xiaohua Long ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Plant Hormone ◽  
Jerusalem Artichoke ◽  
Helianthus Tuberosus ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Expression Of Genes ◽  
Gene Functions

Background: Jerusalem artichoke (Helianthus tuberosus L.) is moderately tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artichoke exposure to salt stress, gene transcription is likely to undergo large changes. Previous studies have hinted at the importance of temporal expression analysis in plant transcriptome research. Elucidating these changes may be of great significance to understanding the salt tolerance mechanisms of it. Results: We obtained high-quality transcriptome from leaves and roots of Jerusalem artichoke exposed to salinity (300 mM NaCl) for 0 h (hour), 6 h, 12 h, 24 h, and 48 h, with 150 and 129 unigenes and 9023 DEGs (differentially expressed genes). The RNA-seq data were clustered into time-dependent groups (nine clusters each in leaves and roots); gene functions were distributed evenly among them. KEGG enrichment analysis showed the genes related to plant hormone signal transduction were enriched in almost all treatment comparisons. Under salt stress, genes belonging to PYL (abscisic acid receptor PYR/PYL family), PP2C (Type 2C protein phosphatases), GH3 (Gretchen Hagen3), ETR (ethylene receptor), EIN2/3 (ethylene-insensitive protein 2/3), JAZ (genes such as jasmonate ZIM-domain gene), and MYC2 (Transcription factor MYC2) had extremely similar expression patterns. The results of qRT-PCR of 12 randomly selected and function known genes confirmed the accuracy of RNA-seq. Conclusions: Under the influence of high salinity (300 mM) environment, Jerusalem artichoke suffer serious damage in a short period of time. Based on the expression of genes on the time scale, we found that the distribution of gene functions in time is relatively even. Upregulation of the phytohormone signal transduction had a crucial role in the response of Jerusalem artichoke seedlings to salt stress, and the genes of abscisic acid, auxin, ethylene, and jasmonic acid had the most obvious change pattern. Research emphasized the regulatory role of hormones under high salt shocks and provided an explorable direction for the study of plant salt tolerance mechanisms.

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