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

Poong, Sze-Wan; Lee, Kok Keong; Lim, Phaik Eem; Pai, Tun-Wen; Wong, Chiew Yen; Phang, Siew Moi; Chen, Chien‐Ming; Yang, Cing Han; Liu, Chun Cheng

doi:10.1007/s10811-018-1455-9

Cited by 18 publications

(6 citation statements)

References 76 publications

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“…It has been hypothesized that response to acute stress may be dependent on the magnitude of stress organisms experience throughout their lifetime, with organisms that have existed in an environment with high temperature variations having broad thermal tolerance and high Uu more up-regulated on the first site than second, uU less up-regulated in the first site than second, dD less down-regulated in the first, Dd more down-regulated in the first, UD up-regulated in the first while down-regulated in the second, and DU down-regulated in the first while up-regulated in the second capacity for acclimation [40,41]. In addition to this, the fewer number of DE genes coupled with higher percentage of down-regulated genes observed in Cagayan population is analogous to the observations in a study done by Poong et al [42], wherein it is considered a strategy for 'energy and resources saving' of heat-acclimated cells. Owing to the broad heat tolerance of the Cagayan population due to natural exposure to highly variable temperature, transcription and translation of non-essential proteins has become unnecessary which consequently saves cell energy and resources.…”

Section: Within-site Main-effect Of Heat Stress Suggests Differences ...supporting

confidence: 88%

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

et al. 2021

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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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Section: Within-site Main-effect Of Heat Stress Suggests Differences ...supporting

confidence: 88%

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

et al. 2021

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“…Our work adds to a growing body of research on how heat stress affects psychrophilic algae (Barati, Lim, Gan, Poong, & Phang, 2018;Boo et al, 2013;Chong, Chu, Othman, & Phang, 2011;Hwang, Jung, & Jin, 2008;Poong et al, 2018;Possmayer et al, 2011;Su et al, 2016), a topic that is particularly relevant given recent trends in climate change. The Antarctic continent is one of the most rapidly warming locations on Earth (Chapman & Walsh, 2007).…”

Section: A Constitutive Stress Response Is a Key Psychrophilic Adapta...mentioning

confidence: 92%

A constitutive stress response is a result of low temperature growth in the Antarctic green algaChlamydomonassp.UWO241

Cvetkovska

Zhang

Vakulenko

et al. 2021

Plant Cell & Environment

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The Antarctic green alga Chlamydomonas sp. UWO241 is an obligate psychrophile that thrives in the cold (4–6°C) but is unable to survive at temperatures ≥18°C. Little is known how exposure to heat affects its physiology or whether it mounts a heat stress response in a manner comparable to mesophiles. Here, we dissect the responses of UWO241 to temperature stress by examining its growth, primary metabolome and transcriptome under steady‐state low temperature and heat stress conditions. In comparison with Chlamydomonas reinhardtii, UWO241 constitutively accumulates metabolites and proteins commonly considered as stress markers, including soluble sugars, antioxidants, polyamines, and heat shock proteins to ensure efficient protein folding at low temperatures. We propose that this results from life at extreme conditions. A shift from 4°C to a non‐permissive temperature of 24°C alters the UWO241 primary metabolome and transcriptome, but growth of UWO241 at higher permissive temperatures (10 and 15°C) does not provide enhanced heat protection. UWO241 also fails to induce the accumulation of HSPs when exposed to heat, suggesting that it has lost the ability to fine‐tune its heat stress response. Our work adds to the growing body of research on temperature stress in psychrophiles, many of which are threatened by climate change.

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“…It is possible that the constant exposure to highly variable temperature prompted an increase in heat tolerance in this group which resulted in a lesser number of DE genes observed. It has been hypothesized that response to acute stress may be dependent on the magnitude of stress organisms experience throughout their lifetime, with organisms that have existed in an environment with high temperature variations having broad thermal tolerance and high capacity for acclimation [33,34] In addition to this, the fewer number of DE genes coupled with higher percentage of downregulated genes observed in Cagayan population is analogous to the observations in a study done by Poong et al [35], wherein it is considered a strategy for 'energy and resources saving' of heatacclimated cells. Owing to the broad heat tolerance of the Cagayan population due to natural exposure to highly variable temperature, transcription and translation of non-essential proteins has become unnecessary which consequently saves cell energy and resources.…”

Section: Discussionmentioning

confidence: 57%

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

Shrestha¹,

Lilagan²,

Guiao³

et al. 2020

Preprint

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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.

show abstract

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

Cited by 18 publications

References 76 publications

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

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

A constitutive stress response is a result of low temperature growth in the Antarctic green algaChlamydomonassp.UWO241

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

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

Cited by 18 publications

References 76 publications

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

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

A constitutive stress response is a result of low temperature growth in the Antarctic green algaChlamydomonassp.UWO241

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

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