scholarly journals Transcriptome-wide identification of MAPKKK genes in bermudagrass (Cynodon dactylon L.) and their potential roles in low temperature stress responses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10159
Author(s):  
Wei Wang ◽  
An Shao ◽  
Erick Amombo ◽  
Shugao Fan ◽  
Xiao Xu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Stress Responses ◽  
Cynodon Dactylon ◽  
Diploid Species ◽  
Low Temperature Stress ◽  
Biological Processes ◽  
Mapk Cascades

As upstream components of MAPK cascades, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascades. MAPK cascades are universal modules of signal transduction in eukaryotic organisms and play crucial roles in plant development processes and in responses to biotic and abiotic stress and signal transduction. Members of the MAPKKK gene family have been identified in several plants,however, MAPKKKs have not been systematically studied in bermudagrass (Cynodon dactylon L.). In this study, 55 potential CdMAPKKKs were produced from bermudagrass transcriptome data, of which 13 belonged to the MEKK, 38 to the Raf, and 4 to the ZIK subfamily. Multiple alignment and conserved motif analysis of CdMAPKKKs supported the evolutionary relationships inferred from phylogenetic analyses. Moreover, the distribution pattern in Poaceae species indicated that members of the MAPKKK family were conserved among almost all diploid species, and species-specific polyploidy or higher duplication ratios resulted in an expansion of the MAPKKK family. In addition, 714 co-functional links which were significantly enriched in signal transduction, responses to temperature stimuli, and other important biological processes of 55 CdMAPKKKs were identified using co-functional gene networks analysis; 30 and 19 co-functional genes involved in response to cold or heat stress, respectively, were also identified. Results of promoter analyses, and interaction network investigation of all CdMAPKKKs based on the rice homologs suggested that CdMAPKKKs are commonly associated with regulation of numerous biological processes. Furthermore, 12 and 13 CdMAPKKKs were significantly up- and downregulated, respectively, in response to low temperature stress; among them, six CdMAPKKKs were significantly induced by low temperature stress, at least at one point in time. This is the first study to conduct identification and functional analysis of the MAPKKK gene family in bermudagrass, and our results provide a foundation for further research on the functions of CdMAPKKKs in response to low temperature stress.

scholarly journals Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

2020 ◽  
Author(s):  
Changbing Huang ◽  
Chun Jiang ◽  
limin Jin ◽  
Huanchao Zhang
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Stress Responses ◽  
Target Genes ◽  
Low Temperature Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Cold Tolerant

Abstract Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

scholarly journals Roles of C-Repeat Binding Factors-Dependent Signaling Pathway in Jasmonates-Mediated Improvement of Chilling Tolerance of Postharvest Horticultural Commodities

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Libin Wang ◽  
Xiuxiu Sun ◽  
Weiqi Luo ◽  
Chunlu Qian
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Signaling Pathway ◽  
Temperature Stress ◽  
Chilling Injury ◽  
Chilling Tolerance ◽  
Low Temperature Stress ◽  
Signal Molecules ◽  
Biotic Stresses ◽  
Dependent Signaling Pathway

C-repeat binding factor- (CBF-) dependent signaling pathway is proposed to be a key responder to low temperature stress in plant. Jasmonates (JAs), the endogenous signal molecules in plant, participate in plant defense against (a)biotic stresses; however, the mechanism has not been fully clarified so far. With the progress made in JAs biopathway, signal transduction, and their relationship with CBF-dependent signaling pathway, our knowledge of the roles of the CBF-dependent signaling pathway in JAs-mediated improvement of chilling tolerance accumulates. In this review, we firstly briefly review the chilling injury (CI) characteristics of postharvest horticultural commodities, then introduce the biopathway and signal transduction of JAs, subsequently summarize the roles of the CBF-dependent signaling pathway under low temperature stress, and finally describe the linkage between JAs signal transduction and the CBF-dependent signaling pathway.

scholarly journals Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

2021 ◽  
Author(s):  
Li Ma ◽  
Jing Bai ◽  
Jia Xu ◽  
Weiliang Qi ◽  
Haiyun Li ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Brassica Rapa ◽  
Cold Resistance ◽  
Resistance Mechanism ◽  
Northern China ◽  
Low Temperature Stress ◽  
Oilseed Crop ◽  
Cold Response

Abstract Winter Brassica rapa is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. APX plays important roles in response of this plant to abiotic stress and in scavenging free radicals. In this study, 59 DEPs were isolated and identified from winter B. rapa and B. napus using bidirectional electrophoresis, and APX was found to be differentially expressed in these two species. Therefore, the roles of APX proteins in the cold response and superoxide metabolism pathways in both rapeseed species were further investigated. And comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profile in APX gene family. Most of the BrAPX genes were specifically expressed under low temperature stress and behaved significantly differently in cold-tolerant and cold-sensitive varieties. qPCR was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress, and these candidate genes and proteins may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

scholarly journals Genome-Wide Analysis of NAC Gene Family in Betula pendula

Forests ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 741 ◽  
Author(s):  
Song Chen ◽  
Xin Lin ◽  
Dawei Zhang ◽  
Qi Li ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Betula Pendula ◽  
Low Temperature Stress ◽  
Specific Expression ◽  
Genome Wide ◽  
Nac Gene Family ◽  
Cold Responses ◽  
Insight Into

NACs (NAM, ATAF1/2, and CUC2) are plant-specific transcription factors that play diverse roles in various plant developmental processes. In this study, we identified the NAC gene family in birch (Betula pendula) and further analyzed the function of BpNACs. Phylogenetic analysis reveals that the 114 BpNACs can be divided into seven subfamilies. We investigated the expression levels of these BpNACs in different tissues of birch including roots, xylem, leaves, and flowers, and the results showed that the BpNACs seem to be expressed higher in xylem and roots than leaves and flowers. In addition to tissue-specific expression analysis, we investigated the expression of BpNACs under low-temperature stress. A total of 21 BpNACs were differentially expressed under low-temperature stress, of which 17 were up-regulated, and four were down-regulated. Using the gene expression data, we reconstructed the gene co-expression network for the 21 low-temperature-responsive BpNACs. In conclusion, our results provide insight into the evolution of NAC genes in the B. pendula genome, and provide a basis for understanding the molecular mechanism for BpNAC-mediated cold responses in birch.

scholarly journals Transcriptome Analysis Combined With Glutathione S-transferase 1 Gene Family Whole-genome Identification Reveals the Mechanism Underlying the Exogenous Application of 5-aminolevulinic Acid to Alleviate Low Temperature Stress in Solanum Lycopersicum Seedling

2020 ◽  
Author(s):  
Zhengda Zhang ◽  
Tao Liu ◽  
Zhen Kang ◽  
Jiwen Xu ◽  
Shichun Yang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Stress Resistance ◽  
Aminolevulinic Acid ◽  
Low Temperature Stress ◽  
Tomato Genome ◽  
Glutathione S Transferase ◽  
Cis Acting ◽  
Gst Activity

Abstract Background: Transcriptome sequencing was conducted to screen out genes that actively respond to exogenous 5-aminolevulinic acid (ALA) induction under low temperature stress. The study used two versions of the tomato genome database to strictly screen and identify tomato glutathione S-transferase (GST) gene families and carried out the related bioinformatics analysis of tomato GST gene family. The expression pattern of SlGST genes induced by exogenous application ALA under low temperature stress was also analysed. Related physiological indicators were determined, and related chemical stains were performed.Results: RNA sequencing (RNA-seq) results showed that the expression of SlGST gene was different under various treatments, and a large number of SlGST genes widely responded to ALA induction under low temperature stress. Sixty-nine full-length GST genes were identified by screening the two versions of tomato genome databases combined with protein domain analysis. Analysis of gene family phylogenetic tree divided the tomato GST gene family into eight subfamilies. Tandem replication of genes is one of the driving forces for the evolution of tomato GST gene family, and a large number of cis-acting elements are related to stress resistance on the promoter of the GST gene family. Exogenous ALA application under low temperature stress induces a broad response of tomato leaf SlGST gene (qRT-PCR verification), increases GST activity and decreases reactive oxygen species (ROS) accumulation.Conclusions: RNA sequencing results revealed that a large number of tomato GST genes are differentially expressed, and Sixty-nine GSTs are identified in the tomato genome. Tandem replication of genes is the driving force for 68 the evolution of tomato GST family, and the promoter contains a large number of cis-acting elements related to stress resistance. Test results show that exogenous ALA induces the expression of SlGST genes under low temperature stress, thereby increasing GST activity to eliminate the ROS produced under low temperature stress and increase the tomato tolerance.

Comparative Transcriptome Analysis Between Cold-Tolerant and Sensitive Brassica Oleracea L. in Response to Low Temperature Stress

2021 ◽  
Author(s):  
Shuhan Jiang ◽  
Dongjian Xia ◽  
Qian Dai ◽  
Yuxia Luo ◽  
Yao Chen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Low Temperature ◽  
Brassica Oleracea ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Transcriptome Analysis ◽  
Low Temperature Stress ◽  
Biological Processes ◽  
The Common ◽  
Go Terms

Abstract Background: Brassica oleracea L. occupies an important position in the annual production of vegetables. But during winter Brassica oleracea L. often suffers from low temperatures and even sub-zero temperatures. Through transcriptome analysis and identification, the pathways involved in cold tolerance of Brassica oleracea L. were analyzed and candidate genes related to cold tolerance of Brassica oleracea L. were identified.Results: Under low temperature stress, a large number of significantly different genes were found in Zhonggan1229 (ZG, low temperature tolerance) and Yingchun (YN, low temperature sensitive). There were 3902 significantly up-regulated genes and 5309 significantly down-regulated genes in ZG, and 4253 significantly up-regulated genes and 5938 significantly down-regulated genes in YN. Among them, 1844 different genes are the specific different genes in ZG and 6089 genes are the common different genes to response the low temperature stress. By annotating the specific different genes in ZG, 26 of the top 30 enriched GO terms belonged to biological processes, 4 terms belonged to molecular functions. By annotating the common different genes, 23 GO terms belonged to biological processes, 1 GO term belonged to molecular functions, and 6 GO terms belonged to cellular components. Circadian rhythms of plants and Plant hormone signal transduction were not only significantly enriched in the two analyzed genes, but also the effects of low temperature stress were most significant. Among the unique different genes in ZG, 154 genes were annotated into transcription factor families, and 79 genes were up-regulated and 75 genes were down-regulated, the encoding of MYB-related proteins was the largest group. Among the different genes shared by the two varieties, 516 genes were annotated into corresponding transcription factor families, 211 genes were up-regulated and 296 genes were down-regulated, however, there were 4 genes that were up-regulated in ZG but down-regulated in YN, and 5 genes that were down-regulated in ZG but up-regulated in YN, the largest group was the protein encoding ERF.Conclusions: The results identified important genes, pathways, and transcription factors that respond to low temperature stress, provided cold tolerance gene resources for the subsequent cold tolerance breeding research of Brassica oleracea L..

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