ArticleBMC genomics2013
RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed.
- Molecular signatures and machine learning driven stress biomarkers for rainbow trout aquaculture and climate adaptation.Scientific reports · 2025Article
- Timing-specific parental effects of ocean warming in a coral reef fish.Proceedings. Biological sciences · 2024Article
- Article
- Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish.Heredity · 2023Article
- Transcriptome Analysis of Marbled RockfishAnimals : an open access journal from MDPI · 2023Article
- Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica.Marine biotechnology (New York, N.Y.) · 2022Article
- Aquaponics as a Promising Strategy to Mitigate Impacts of Climate Change on Rainbow Trout Culture.Animals : an open access journal from MDPI · 2022Review
- Assessing Anatomical Changes in Male Reproductive Organs in Response to Larval Crowding Using Micro-computed Tomography Imaging.Neotropical entomology · 2022Article
- Genomic reaction norms inform predictions of plastic and adaptive responses to climate change.The Journal of animal ecology · 2022Review
- Thermal regime during parental sexual maturation, but not during offspring rearing, modulates DNA methylation in brook charr (Proceedings. Biological sciences · 2022Article
- The alternative splicing landscape of a coral reef fish during a marine heatwave.Ecology and evolution · 2022Article
- Plasticity to ocean warming is influenced by transgenerational, reproductive, and developmental exposure in a coral reef fish.Evolutionary applications · 2022Article
- Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Evolutionary applications · 2022Article
- Evaluation of qPCR reference genes for taimen (Hucho taimen) under heat stress.Scientific reports · 2022Article
- Genomic Approaches for Conservation Management in Australia under Climate Change.Life (Basel, Switzerland) · 2021Review
- Comparative transcriptomics of spotted seatrout (Ecology and evolution · 2021Article
- The environmental context of inducible HSP70 expression in Eastern Brook Trout.Conservation physiology · 2021Article
- Adaptation of plasticity to projected maximum temperatures and across climatically defined bioregions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Quantitative Proteomic Profiling of Marine DiatomFrontiers in microbiology · 2020Article
- Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change.Frontiers in genetics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentifying genes of adaptive significance in a changing environment is a major focus of ecological genomics. Such efforts were restricted, until recently, to researchers studying a small group of model organisms or closely related taxa. With the advent of next generation sequencing (NGS), genomes and transcriptomes of virtually any species are now available for studies of adaptive evolution. We experimentally manipulated temperature conditions for two groups of crimson spotted rainbowfish (Melanotaenia duboulayi) and measured differences in RNA transcription between them. This non-migratory species is found across a latitudinal thermal gradient in eastern Australia and is predicted to be negatively impacted by ongoing environmental and climatic change.
resultsUsing next generation RNA-seq technologies on an Illumina HiSeq2000 platform, we assembled a de novo transcriptome and tested for differential expression across the treatment groups. Quality of the assembly was high with a N50 length of 1856 bases. Of the 107,749 assembled contigs, we identified 4251 that were differentially expressed according to a consensus of four different mapping and significance testing approaches. Once duplicate isoforms were removed, we were able to annotate 614 up-regulated transfrags and 349 that showed reduced expression in the higher temperature group.
conclusionsAnnotated blast matches reveal that differentially expressed genes correspond to critical metabolic pathways previously shown to be important for temperature tolerance in other fish species. Our results indicate that rainbowfish exhibit predictable plastic regulatory responses to temperature stress and the genes we identified provide excellent candidates for further investigations of population adaptation to increasing temperatures.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.