Data from: Hypoxia disrupts sex-specific physiology and gene expression leading to decreased fitness in the estuarine sea anemone Nematostella vectensis
Data files
Apr 15, 2025 version files 9.22 MB
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Adult_combined_dry_weight_data.csv
2.82 KB
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Adult_fecundity_data.csv
11.06 KB
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Adult_respiration_data.csv
3.83 KB
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Adult_spawning_frequency_data.csv
192 B
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Development_success_data.csv
208 B
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Egg_size_data.csv
14.21 KB
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Larval_respiration_data.csv
552 B
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README.md
8.74 KB
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Settlement_data.csv
983 B
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Sperm_MMP_data.csv
472.79 KB
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Summary_count_table.txt
1.53 MB
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Term2gene_list.csv
1.76 MB
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Term2name_list.csv
3.05 MB
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Term2ont_list.csv
2.37 MB
Abstract
Coastal seawater hypoxia is increasing in temperate estuaries under global climate change, yet it is unknown how low oxygen conditions affect most estuarine species. We found that hypoxia has increased since the 1990s in an estuary hosting the sea anemone Nematostella vectensis (Jacques Cousteau National Estuarine Research Reserve, New Jersey, USA). Adult N. vectensis bred from anemones collected in this estuary exposed to three consecutive nights of hypoxia (dissolved oxygen = 0.5–1.5 mg L−1 for ~12 h night−1) during gametogenesis displayed decreased aerobic respiration rates and biomass, indicating metabolic disruption. Physiological declines were correlated with changes in the expression of genes related to oxygen-dependent metabolic processes, many of which are targets of hypoxia-inducible factor 1α (HIF1α), demonstrating the activity of this transcription factor for the first time in this early-diverging metazoan. The upregulation of genes involved in the unfolded protein response and endoplasmic reticulum and Golgi apparatus homeostasis suggested that misfolded proteins contributed to disrupted physiology. Notably, these responses were more pronounced in females, demonstrating sex-specific sensitivity that was also observed in reproductive outcomes, with declines in female but not male fecundity following hypoxia exposure. However, sperm from exposed males had higher mitochondrial membrane potential, indicating altered spermatogenesis. Further, crosses performed with gametes from hypoxia-exposed adults yielded strikingly low developmental success (~2%), yet larvae that did develop displayed similar respiration rates and accelerated settlement compared to controls. Overall, hypoxia depressed fitness in N. vectensis by over 95%, suggesting that even stress-tolerant estuarine species may be threatened by coastal deoxygenation.
Dataset includes files for all data associated with experiments.
Data and file structure
File 1: Adult_combined_dry_weight_data.csv
This file is for data pertaining to the dry weight of adult sea anemones collected at several time points during the experiment.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Day = day of experiment on which data were collected
-Anemone_dry_weight_g = the dry weight of an individual anemone measured in grams
File 2: Adult_fecundity_data.csv
This file is for data pertaining to the reproductive metrics quantified in anemones upon spawning induction. This file contains NA values as a result of combining data from female and male animals into a single data sheet. NA values indicate sex-specific metrics; for example, rows with data for male animals have NAs in the egg counts column as these animals do not produce eggs.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Group = culture tub in which anemones resided during the experiment; tubs were assigned unique letter codes (A-F) that were kept consistent throughout the experiment
-Sex = sex (female or male) of anemone
-Number_within_sex = unique identifier for individual anemones
-Pan_empty_weight_g = weight in grams of aluminum pan for dry weight measurement
-Pan_anemone_weight_g = weight in grams of aluminum pan and dried anemone tissue
-Anemone_dry_weight_g = Pan_anemone_weight_g - Pan_empty_weight_g
-Water_volume_mL = volume of seawater in mL that was in each spawning cup
-Egg_count_cells = the number of eggs produced by female anemones
-Eggs_mg_dry_weight = Egg_count_cells / (Anemone_dry_weight_g*1000)
-Average_egg_volume_um_3 = average volume (in um^3) of eggs produced by a female
-Average_egg_volume_um_3_SEM = standard error of mean (SEM) for Average_egg_volume_um_3 (used for plotting)
-Sperm_concentration_cells_mL = concentration of sperm produced by a male
-Sperm_concentration_M_cells_mL = Sperm_concentration_cells_mL/1000000
-Sperm_count_M_cells = perm_concentration_M_cells_mL * Water_volume_mL
-Average_sperm_red_green_ratio = average red to green fluorescence ratio for sperm produced by a male, as quantified with JC-1 via flow cytometry
-Average_sperm_red_green_ratio_SEM = SEM for Average_sperm_red_green_ratio
-Development_success_percent = percentage of larvae successfully developed in cross to which each anemone contributed gametes
-Expected_offspring = fecundity (egg or sperm count) * Development_success_percent
-Relative_fitness = relative fitness of each anemone calculated by dividing Expected_offspring by median Expected_offspring for normoxia group (by sex)
File 3: Adult_respiration_data.csv
This file is for data pertaining to the respiration rates of adult anemones.
These files have headers, which include:
-Day = day of experiment on which data were collected
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Group = culture tub in which anemones resided during the experiment; tubs were assigned unique letter codes (A-F) that were kept consistent throughout the experiment
-Anemone_number = unique identifier for individual anemones
-Anemone_volume_uL = anemone volume in uL determined via water displacement
-Well = well of respiration plate in which vial containing anemone was placed
-Vial_volume_mL = volume of wells used for respirometry
-Water_volume_mL = Vial_volume_mL - (Anemone_volume_uL*1000)
-Pan_empty_weight_g = weight in grams of aluminum pan for dry weight measurement
-Pan_anemone_weight_g = weight in grams of aluminum pan and dried anemone tissue
-Anemone_dry_weight_g = Pan_anemone_weight_g - Pan_empty_weight_g
-Respiration_rate_umol_L_min = oxygen consumption rate of anemone (within vials)
-Respiration_rate_umol_min_g = oxygen consumption rate of anemone (normalized to dry weight)
File 4: Adult_spawning frequency_data.csv
This file is for data pertaining to the number of anemones spawned in each experimental treatment.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Group = culture tub in which anemones resided during the experiment; tubs were assigned unique letter codes (A-F) that were kept consistent throughout the experiment
-Number_of_animals = number in tub
-Animals_spawned = number spawned
-Spawned_percent = Animals_spawned/Number_of_animals*100
File 5: Development_success_data.csv
This file is for data pertaining to the developmental success of eggs from female anemones.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Group = culture tub in which anemones resided during the experiment; tubs were assigned unique letter codes (A-F) that were kept consistent throughout the experiment
-Number_of_eggs = number of eggs placed in culture dish
-Number_of_larvae = number of larvae successfully developed at 3 days post-fertilization
-Development_success_percent = Number_of_larvae/Number_of_eggs*100
File 6: Egg_size_data.csv
This file is for data pertaining to the sizes of eggs produced by female anemones.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Group = culture tub in which anemones resided during the experiment; tubs were assigned unique letter codes (A-F) that were kept consistent throughout the experiment
-Anemone_number_in_group = unique identifier for individual anemones
-Egg_length_cm = egg length in cm
-Egg_width_cm = egg width in cm
-Egg_volume_um_3 = egg volume in um^3 calculated from length and width
File 7: Larval_respiration_data.csv
This file is for data pertaining to the respiration rates of larvae.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Respiration_rate_umol_L_min = respiration rate of larvae in umol/L/min
-Protein_mg = protein content of larvae
-Water_volume_L = volume of water for wells in which respiration rates were measured
-Respiration_rate_nmol_min_mg = respiration rate of larvae normalized to protein
File 8: Settlement_data.csv
This file is for data pertaining to larval settlement rates.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Days_post_fertilization = day after fertilization on which data were collected
-Replicate = technical replicate of group of 10 larvae (unique number 1-4)
-Number_of_larvae = number of larvae put in dishes for settlement trials
-Number_of_juveniles = number of animals settled into juveniles on each day
-Percent_juveniles = Number_of_juveniles/Number_of_larvae*100
File 9: Sperm_MMP_data.csv
This file is for data pertaining to sperm mitochondrial membrane potential (MMP) as determined via JC-1 dye and flow cytometry.
These files have headers, which include:
-Treatment = dissolved oxygen treatment to which anemones were exposed, either normoxia or hypoxia
-Group = culture tub in which anemones resided during the experiment; tubs were assigned unique letter codes (A-F) that were kept consistent throughout the experiment
-Anemone_number_in_group = unique identifier for individual anemones
-Red_to_green_ratio = ratio of red to green JC-1 fluorescence for individual sperm cells
Files 10-12: Term2name_, gene_, and ont_list.csv
These files are for useful information about genes used for RNAseq data analysis.
These files have headers, which include:
-term = gene ontology term code
-name = name of gene ontology term
-gene = gene with each ontology term
-ontology = type of gene ontology term (biological process, molecular function, or cellular component)
File 13: Summary_count_table.txt
This is the summary count table generated from the RNA sequencing data raw reads (see publication for details)
Sharing/Access information
Links to other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA
Code/Software
Files 1 and 2: Nematostella hypoxia repro code.Rmd and .pdf
These files contain code (in Rmarkdown and PDF formats) that was used to analyze and generate plots of data. This code can be run using the repository files.