Medicago ruthenica is a perennial forage legume with the remarkable ability to survive under unfavorable environmental conditions. It has been identified as an excellent species of Medicago that can ...adapt to various environmental stresses including low temperature, drought, and salinity. To investigate its potential as a genetic resource, we performed transcriptome sequencing and analysis in M. ruthenica under abiotic stresses. We generated >120 million reads from six cDNA libraries, resulting in 79,249 unique transcripts, most of which were highly similar to transcripts from M. truncatula (44,608, 56.3%) and alfalfa (M. sativa, 48,023, 60.6%). Based on gene expression profiles, 2,721 transcripts were identified as abiotic stress responsive genes which were predicted to be mainly involved in phytohormone signaling pathways, transcriptional regulation, and ROS-scavenging. These results suggest that they play critical roles in the response to abiotic stress. In summary, we identified genes in our transcriptome dataset involved in the regulation of the abiotic stress response in M. ruthenica which will provide a valuable resource for the future identification and functional analysis of candidate genes for adaption to unfavorable conditions. The genes identified here could be also useful for improving stress tolerance traits in alfalfa through molecular breeding in the future.
Calcium-dependent protein kinases (CDPKs) are an important class of calcium-sensitive response proteins that play an important regulatory role in response to abiotic stresses. To date, little is ...known about the CDPK genes in white clover. White clover is a high-quality forage grass with high protein content, but it is susceptible to cold stress. Therefore, we performed a genome-wide analysis of the CDPK gene family in white clover and identified 50 members of the CDPK genes. Phylogenetic analysis using CDPKs from the model plant Arabidopsis divided the TrCDPK genes into four groups based on their sequence similarities. Motif analysis showed that TrCDPKs within the same group had similar motif compositions. Gene duplication analysis revealed the evolution and expansion of TrCDPK genes in white clover. Meanwhile, a genetic regulatory network (GRN) containing TrCDPK genes was reconstructed, and gene ontology (GO) annotation analysis of these functional genes showed that they contribute to signal transduction, cellular response to stimuli, and biological regulation, all of which are important processes in response to abiotic stresses. To determine the function of TrCDPK genes, we analyzed the RNA-seq dataset and found that most TrCDPK genes were highly up-regulated under cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiments, implying that TrCDPK genes are involved in various gene regulatory pathways in response to cold stress. Our study may help to further investigate the function of TrCDPK genes and their role in response to cold stress, which is important for understanding the molecular mechanisms of cold tolerance in white clover and improving its cold tolerance.
In recent years, green environment protection has received widespread research interest. In this study, a green, bio-based compound, adenosine triphosphate (ATP), was introduced into the intumescent ...flame retardant system to improve the flame retardant properties of waterborne fireproof coatings. The flame retardant properties of the sample with 2 wt% ATP were characterized by fire resistance tests, thermogravimetric analysis, cone calorimetric analysis, and other tests. The results revealed that the 2 wt% ATP coating sample exhibited a reduced fire resistance temperature of approximately 73°C at 60 min compared with that of the blank sample (i.e., the unmodified sample), and the residual carbon increased from 28% to 36% at 800°C. Furthermore, the peak of the heat release rate and the total heat release for the sample with 2 wt% ATP were 7.87% and 14.10% lower than those for the blank sample, respectively. Additionally, the total smoke production and peak smoke release rate for the modified sample were 33.60% and 22.54% lower than those for the blank sample, respectively. Therefore, this work provides a good prospect for the application of bio-based ATP, which can be applied in the fabrication of fire-resistant and smoke-suppressive coatings for structural steel and also provides a simple and efficient strategy for green, bio-based flame retardants, which is expected to expand their application scope in fireproof coatings.
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AbstractThe GRAS transcription factor (TF) is a plant-specific regulator that plays a critical role in plant growth, development and response to various abiotic stresses. While the functions of many ...GRAS TFs have been extensively studied in numerous model plants with fully sequenced genomes, the GRAS TFs in white clover (Trifolium repens L.) remain elusive despite the sequencing of its genome. To bridge this knowledge gap, homologs of GRAS TFs from Arabidopsis were employed and subjected to a genome-wide blast against white clover proteins. This analysis identified and characterized 102 putative GRAS genes, designated as TrGRAS, based on the presence of GRAS domains in positive blast hits. Concurrently, an exploration of their gene structures, classification, evolutionary relationships and conservative motifs provided insights into the distinctive features of TrGRAS in white clover. Furthermore, gene duplication analysis revealed an expansion of TrGRAS genes in the PAT1 and LISCL subfamilies, indicating functional diversity within the white clover genome. Lastly, RNA-seq and quantitative reverse transcription-PCR (qRT-PCR) experiments confirmed their higher expression during the early or intermittent responses to cold stress, suggesting their potential and crucial roles in determining the cold tolerances of white clover. The analysis of TrGRAS genes, coupled with expression studies, contributes to the functional characterization of TrGRAS genes in white clover. This knowledge is pivotal for informing genetic improvement strategies in future breeding efforts aimed at enhancing cold tolerance in white clover.
Winter damage, especially in northern climates, is a major limitation of the utilization of perennial forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic ...breeding. However, freezing tolerance is a complex trait that is determined by many genes. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed small RNA sequencing analysis under cold (4°) and freezing (-8°) stress. The sequencing results revealed that 173 known, and 24 novel miRNAs were expressed, and that the expression of 35 miRNAs was affected by cold and/or freezing stress. Meanwhile, 105 target genes cleaved by these miRNAs were characterized by degradome sequencing. These targets were associated with biological regulation, cellular processes, metabolic processes, and response to stress. Interestingly, most of them were characterized as transcription factors (TFs), including auxin response factors, SBP, NAC, AP2/ERF, and GRF, which play important roles in plant abiotic responses. In addition, important miRNAs and mRNAs involved in nodulation were also identified, for example, the relationship between miR169 and the TF CCAAT (also named as NF-YA/HAP2), which suggested that nodulation has an important function in freezing tolerance in alfalfa. Our results provide valuable information to help determine the molecular mechanisms of freezing tolerance in alfalfa, which will aid the application of these miRNAs and their targets in the improvement of freezing tolerance in alfalfa and related plants.
Heat shock protein 70 (Hsp70) is a crucial member of the Hsp family, which is present in many animals, and acts as a chaperone to protect the organism from damage caused by various environmental ...stresses, particularly unfavorable temperatures. In this study, we used homologous gene search and domain analysis to identify sixteen Hsp70 genes (named as CiHSP genes) from the genome of grass carp (Ctenopharyngodon idella). These genes were classified into ten subfamilies based on their conserved structures and phylogenetic analysis. To investigate the biological functions of CiHSP genes in grass carp, we analyzed public RNA-Seq data, and found that most members of the CiHSP gene family were highly expressed in the brain and kidney, suggesting potential roles in protecting brain cells and participating in fish immunological processes. Additionally, these CiHSP genes were characterized as responding to high density and high temperature stress, with most members significantly upregulated under high temperature conditions. These findings demonstrate the critical roles of CiHSP genes in grass carp development and their response to environmental stress, which will provide valuable insights for determining their function and potential application in fish production in the future.
White clover (
L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is ...a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover.
In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress.
The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand the molecular mechanism of cold tolerance in white clover and improve its cold tolerance.
White clover (Trifolium repens L.) is an important legume forage, which is widely distributed in cool-season regions. Therefore, cold stress is a major environmental factor limiting its growth and ...production, while little is known about the its cold tolerance at molecular level. In the present study, we performed time-course RNA-seq analysis under cold stress. RNA-seq results suggested that genes associated with "oxidoreductase activity" and "transcription regulator activity" are more likely related to the response of white clover to cold stress. To identify the specific gene modules and the hub genes of white clover in response to cold stress, we applied weighted gene co-expression network analyses (WGCNA) to transcriptome data. We also found that gene modules that focus on protein kinase activity, DNA-binding transcription factor activity and oxidoreductase activity, are more likely to be involved in the response of white clover to cold stress. Especially, we identified several AP2/ERF TF genes and CDPK genes as pivotal genes in white clover in response to cold stress, which would provide helpful insights into the molecular mechanisms underlying the response of white clover to cold stress.
Alfalfa (Medicago sativa L.) is an important perennial forage, with high nutritional value, which is widely grown in the world. Because of low freezing tolerance, its distribution and production are ...threatened and limited by winter weather. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed transcriptome sequencing analysis under cold (4 °C) and freezing (-8 °C) stresses. More than 66 million reads were generated, and we identified 5767 transcripts differentially expressed in response to cold and/or freezing stresses. These results showed that these genes were mainly classified as response to stress, transcription regulation, hormone signaling pathway, antioxidant, nodule morphogenesis, etc., implying their important roles in response to cold and freezing stresses. Furthermore, nine CBF transcripts differentially expressed were homologous to CBF genes of Mt-FTQTL6 site, conferring freezing tolerance in M. truncatula, which indicated that a genetic mechanism controlling freezing tolerance was conservative between M. truncatula and M. sativa. In summary, this transcriptome dataset highlighted the gene regulation response to cold and/or freezing stresses in alfalfa, which provides a valuable resource for future identification and functional analysis of candidate genes in determining freezing tolerance.
The brown frog (Rana dybowskii) exhibits a wide distribution and is extensively cultured in northeast China. This species undergoes a prolonged period of hibernation lasting from several months to ...half a year. The frog’s fallopian tubes are considered a valuable tonic medicine known as “Oviducts Ranae” in traditional Chinese medicine. To enhance comprehension of the molecular mechanism underlying the process of emergence from hibernation, a transcriptome-based comparative analysis was performed on differentially expressed genes (DEGs) across various organs of female frogs during hibernation and upon emergence. The organs examined encompassed the brain, liver, spleen, fallopian tube, and ovary. Subsequently, GO and KEGG enrichment analyses were performed to gain further insights into these DEGs. A total of 51,634 transcripts were identified in all five tissues. The spleen exhibited the highest number of DEGs, with 3651 members, while the liver, brain, and fallopian tube had 3182, 3115, and 3186 DEGs, respectively. The ovary had the lowest number of DEGs, with only 1661. Interestingly, only 45 genes were found to be differentially expressed in all five tissues, and GO enrichment analysis revealed distinct functional differences among the DEGs in the various tissues. Only two meaningful DEG-enriched KEGG pathways, “00310 Lysine degradation” and “05202 Transcriptional misregulation in cancer”, were present in all five tissues, and the pathway “B 09182 Protein families: genetic information processing” was significantly enriched in four tissues except the ovary, and it had the most enriched DEGs. Our findings offer insights to grasp the factors that need to be controlled in the design of overwintering sites and offer a novel perspective for the conservation and management of the overwintering population of female R. dybowskii.
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