Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites

Abstract Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab seeds from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.Results: We present the first ever transcriptome assembly of S. serrata obtained from a massive data set containing ~66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Based on sequence comparison to the fruitfly and shrimp proteomes, our assembly contains several thousands of almost full-length transcripts. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis of difference in heat response showed that between Cagayan and Bataan, there were 389 differently differentially expressed (DDE) genes associated with 48 signalling and stress-response pathways; and between Cagayan and Bicol, there were 101 DDE genes affecting 8 pathways.Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

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Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles

BMC Genomics ◽

10.1186/s12864-021-07891-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Anish M.S. Shrestha ◽

Crissa Ann I. Lilagan ◽

Joyce Emlyn B. Guiao ◽

Maria Rowena R. Romana-Eguia ◽

Ma. Carmen Ablan Lagman

Keyword(s):

Heat Stress ◽

Stress Response ◽

Transcriptome Assembly ◽

The Philippines ◽

Scylla Serrata ◽

Rna Seq ◽

Data Set ◽

Heat Stress Response ◽

Site Analysis ◽

Mangrove Crab

Abstract Background The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response. Results We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts – 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways. Conclusion In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

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Genome-wide characterization of differentially expressed genes provides insights into regulatory network of heat stress response in radish (Raphanus sativus L.)

Functional & Integrative Genomics ◽

10.1007/s10142-017-0587-3 ◽

2018 ◽

Vol 18 (2) ◽

pp. 225-239 ◽

Cited By ~ 12

Author(s):

Ronghua Wang ◽

Yi Mei ◽

Liang Xu ◽

Xianwen Zhu ◽

Yan Wang ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Differentially Expressed Genes ◽

Regulatory Network ◽

Raphanus Sativus ◽

Differentially Expressed ◽

Heat Stress Response ◽

Genome Wide ◽

Raphanus Sativus L

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RNA-Seq-mediated transcriptomic analysis of heat stress response in a polar Chlorella sp. (Trebouxiophyceae, Chlorophyta)

Journal of Applied Phycology ◽

10.1007/s10811-018-1455-9 ◽

2018 ◽

Vol 30 (6) ◽

pp. 3103-3119 ◽

Cited By ~ 2

Author(s):

Sze-Wan Poong ◽

Kok-Keong Lee ◽

Phaik-Eem Lim ◽

Tun-Wen Pai ◽

Chiew-Yen Wong ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Transcriptomic Analysis ◽

Rna Seq ◽

Heat Stress Response ◽

Chlorella Sp

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Comparative transcriptomic analysis of the heat stress response in the filamentous fungus Metarhizium anisopliae using RNA-Seq

Applied Microbiology and Biotechnology ◽

10.1007/s00253-014-5763-y ◽

2014 ◽

Vol 98 (12) ◽

pp. 5589-5597 ◽

Cited By ~ 35

Author(s):

Zhang-Xun Wang ◽

Xia-Zhi Zhou ◽

Hui-Min Meng ◽

Yu-Jun Liu ◽

Quan Zhou ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Filamentous Fungus ◽

Metarhizium Anisopliae ◽

Transcriptomic Analysis ◽

Rna Seq ◽

Heat Stress Response ◽

Comparative Transcriptomic Analysis

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Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague–Dawley Rats as Response to Heat Stress Challenges

Frontiers in Genetics ◽

10.3389/fgene.2021.651979 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jinhuan Dou ◽

Angela Cánovas ◽

Luiz F. Brito ◽

Ying Yu ◽

Flavio S. Schenkel ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Metabolic Pathways ◽

Adrenal Glands ◽

Functional Enrichment ◽

Rna Seq ◽

Sprague Dawley ◽

Mammal Species ◽

Heat Stress Response ◽

Sprague Dawley Rats

Understanding heat stress physiology and identifying reliable biomarkers are paramount for developing effective management and mitigation strategies. However, little is known about the molecular mechanisms underlying thermal tolerance in animals. In an experimental model of Sprague–Dawley rats subjected to temperatures of 22 ± 1°C (control group; CT) and 42°C for 30 min (H30), 60 min (H60), and 120 min (H120), RNA-sequencing (RNA-Seq) assays were performed for blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120). A total of 53, 1,310, and 1,501 differentially expressed genes (DEGs) were significantly identified in the blood (P < 0.05 and |fold change (FC)| >2), liver (P < 0.01, false discovery rate (FDR)–adjusted P = 0.05 and |FC| >2) and adrenal glands (P < 0.01, FDR-adjusted P = 0.05 and |FC| >2), respectively. Of these, four DEGs, namely Junb, P4ha1, Chordc1, and RT1-Bb, were shared among the three tissues in CT vs. H120 comparison. Functional enrichment analyses of the DEGs identified in the blood (CT vs. H120) revealed 12 biological processes (BPs) and 25 metabolic pathways significantly enriched (FDR = 0.05). In the liver, 133 BPs and three metabolic pathways were significantly detected by comparing CT vs. H30, H60, and H120. Furthermore, 237 BPs were significantly (FDR = 0.05) enriched in the adrenal glands, and no shared metabolic pathways were detected among the different heat-stressed groups of rats. Five and four expression patterns (P < 0.05) were uncovered by 73 and 91 shared DEGs in the liver and adrenal glands, respectively, over the different comparisons. Among these, 69 and 73 genes, respectively, were proposed as candidates for regulating heat stress response in rats. Finally, together with genome-wide association study (GWAS) results in cattle and phenome-wide association studies (PheWAS) analysis in humans, five genes (Slco1b2, Clu, Arntl, Fads1, and Npas2) were considered as being associated with heat stress response across mammal species. The datasets and findings of this study will contribute to a better understanding of heat stress response in mammals and to the development of effective approaches to mitigate heat stress response in livestock through breeding.

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Heat Stress-Responsive Transcriptome Analysis in the Liver Tissue of Hu Sheep

Genes ◽

10.3390/genes10050395 ◽

2019 ◽

Vol 10 (5) ◽

pp. 395 ◽

Cited By ~ 5

Author(s):

Yaokun Li ◽

Lingxuan Kong ◽

Ming Deng ◽

Zhiquan Lian ◽

Yinru Han ◽

...

Keyword(s):

Heat Stress ◽

Molecular Mechanism ◽

Stress Responses ◽

Animal Health ◽

Transcriptome Profiling ◽

Differentially Expressed ◽

Rna Seq ◽

Heat Stress Response ◽

Ppar Signaling ◽

Hu Sheep

Heat stress has a severe effect on animal health and can reduce the productivity and reproductive efficiency; it is therefore necessary to explore the molecular mechanism involved in heat stress response, which is helpful for the cultivation of an animal breed with resistance to heat stress. However, little research about heat stress-responsive molecular analysis has been reported in sheep. Therefore, in this study, RNA sequencing (RNA-Seq) was used to investigate the transcriptome profiling in the liver of Hu sheep with and without heat stress. In total, we detected 520 and 22 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with metabolic processes, the regulation of biosynthetic processes, and the regulation of glucocorticoid; additionally, they were significantly enriched in the heat stress related pathways, including the carbon metabolism, the PPAR signaling pathway, and vitamin digestion and absorption. The co-located differentially expressed lncRNA Lnc_001782 might positively influence the expression of the corresponding genes APOA4 and APOA5, exerting co-regulative effects on the liver function. Thus, we made the hypothesis that Lnc_001782, APOA4 and APOA5 might function synergistically to regulate the anti-heat stress ability in Hu sheep. This study provides a catalog of Hu sheep liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying heat stress responses.

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RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans

International Journal of Molecular Sciences ◽

10.3390/ijms20225603 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5603 ◽

Cited By ~ 1

Author(s):

Dong Xue ◽

Wenzheng Liu ◽

Yun Chen ◽

Yingying Liu ◽

Jiahui Han ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Deinococcus Radiodurans ◽

Regulatory System ◽

Hypothetical Protein ◽

Stress Factors ◽

Heat Stress Response ◽

Heat Response ◽

Shock Proteins ◽

In Cells

Deinococcus radiodurans is best known for its extraordinary resistance to diverse environmental stress factors, such as ionizing radiation, ultraviolet (UV) irradiation, desiccation, oxidation, and high temperatures. The heat response of this bacterium is considered to be due to a classical, stress-induced regulatory system that is characterized by extensive transcriptional reprogramming. In this study, we investigated the key functional genes involved in heat stress that were expressed and accumulated in cells (R48) following heat treatment at 48 °C for 2 h. Considering that protein degradation is a time-consuming bioprocess, we predicted that to maintain cellular homeostasis, the expression of the key functional proteins would be significantly decreased in cells (RH) that had partly recovered from heat stress relative to their expression in cells (R30) grown under control conditions. Comparative transcriptomics identified 15 genes that were significantly downregulated in RH relative to R30, seven of which had previously been characterized to be heat shock proteins. Among these genes, three hypothetical genes (dr_0127, dr_1083, and dr_1325) are highly likely to be involved in response to heat stress. Survival analysis of mutant strains lacking DR_0127 (a DNA-binding protein), DR_1325 (an endopeptidase-like protein), and DR_1083 (a hypothetical protein) showed a reduction in heat tolerance compared to the wild-type strain. These results suggest that DR_0127, DR_1083, and DR_1325 might play roles in the heat stress response. Overall, the results of this study provide deeper insights into the transcriptional regulation of the heat response in D. radiodurans.

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A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans

Biomolecules ◽

10.3390/biom10010022 ◽

2019 ◽

Vol 10 (1) ◽

pp. 22 ◽

Cited By ~ 1

Author(s):

Dong Xue ◽

Yun Chen ◽

Jiang Li ◽

Jiahui Han ◽

Zhengfu Zhou ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Environmental Stress ◽

Noncoding Rna ◽

Deinococcus Radiodurans ◽

Pcr Analysis ◽

Resistant Bacteria ◽

Rna Seq ◽

Environmental Stress Response ◽

Heat Stress Response

Deinococcus radiodurans is an extremely resistant bacteria that has evolved masterful strategies to enable survival under various environmental stress conditions. Heat stress is a major environmental stress factor that can cause denaturation of proteins, membrane disruption, and oxidative stress. Previous studies have examined the mechanisms of the heat stress response by analyzing changes in protein levels; however, little is known about the role of small noncoding RNAs (ncRNAs), which are known to play important regulatory functions in bacteria during various environmental stress response. The ncRNA dsr11 of D. radiodurans was previously identified by RNA-seq and Northern blot. In this study, we showed that the transcription level of dsr11 was up-regulated 4.2-fold under heat stress by qRT-PCR analysis. Heat tolerance assay showed that deleting dsr11 significantly inhibited the viability under high temperature conditions. To assess the influence of dsr11 on the D. radiodurans transcriptome, 157 genes were found differentially expressed in the knock-out mutant by RNA-seq experiment. Combining RNA-seq and in silico analysis, we found that trmE (tRNA modification GTPase) and dr_0651 (arginase) were likely to be the direct targets of dsr11. Further microscale thermophoresis results demonstrated that dsr11 can directly bind to the mRNA of trmE and dr_0651. Our results indicated that dsr11 can enhance the tolerance to heat stress of D. radiodurans by binding to trmE and dr_0651 mRNA. Overall, these results extend our understanding of ncRNA regulation and provide new insights into the heat stress response in D. radiodurans.

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