1
|
Gong J, Li Q. Comparative Transcriptome and WGCNA Analysis Reveal Molecular Responses to Salinity Change in Larvae of the Iwagaki Oyster Crassostrea Nippona. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1031-1042. [PMID: 37872465 DOI: 10.1007/s10126-023-10257-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
The Iwagaki oyster Crassostrea nippona is an important aquaculture species with significant potential for large-scale oyster farming. It is susceptible to the fluctuated salinity in the coastal area. In this study, we compared the transcriptome of Crassostrea nippona larvae under variant conditions with low-salinity stress (28, 20, 15, 10, and 5 practical salinity units (psu)) for 24 h. KEGG enrichment analysis of differentially expressed genes (DEGs) from pairwise comparisons identified several free amino acid metabolism pathway (taurine and hypotaurine, arginine and proline, glycine, and beta-alanine) contributing to the salinity change adaptation and activated "lysosome" and "apoptosis" pathway in response to the low-salinity stress (10 and 5 psu). Trend analysis revealed sustained upregulation of transmembrane transport-related genes (such as SLC family) and downregulation of ribosomal protein synthesis genes faced with decreasing salinities. In addition, 9 biomarkers in response to low-salinity stress were identified through weighted gene co-expression network analysis (WGCNA) and validated by qRT-PCR. Our transcriptome analysis provides a comprehensive view of the molecular mechanisms and regulatory networks underlying the adaptive responses of oyster larvae to hypo-salinity conditions. These findings contribute to our understanding of the complex biological processes involved in oyster resilience and adaptation to changing environmental conditions.
Collapse
Affiliation(s)
- Jianwen Gong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
2
|
Levell ST, Bedgood SA, Travis J. Plastic maternal effects of social density on reproduction and fitness in the least killifish, Heterandria formosa. Ecol Evol 2023; 13:e10074. [PMID: 37214609 PMCID: PMC10196423 DOI: 10.1002/ece3.10074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Environmental parental effects, also known as transgenerational plasticity, are widespread in plants and animals. Less well known is whether those effects contribute to maternal fitness in the same manner in different populations. We carried out a multigenerational laboratory experiment with females drawn from two populations of the least killifish, Heterandria formosa, to assess transgenerational plasticity in reproductive traits in response to differences in social density and its effects on maternal fitness. In the first and second generations, increased density decreased reproductive rate and increased offspring size in females from both populations. There were complicated patterns of transgenerational plasticity on maternal fitness that differed between females from different populations. Females from a population with historically low densities whose mothers experienced lower density had higher fitness than females whose mothers experienced higher density, regardless of their own density. The opposite pattern emerged in females from the population with historically high densities: Females whose mothers experienced higher density had higher fitness than females whose mothers experienced lower density. This transgenerational plasticity is not anticipatory but might be considered adaptive in both populations if providing those "silver spoons" enhances offspring fitness in all environments.
Collapse
Affiliation(s)
| | - Samuel A. Bedgood
- Department of Integrative BiologyOregon State UniversityCorvallisOregonUSA
| | - Joseph Travis
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| |
Collapse
|
3
|
Pruett JL, Pandelides AF, Keylon J, Willett KL, Showalter Otts S, Gochfeld DJ. Life‐stage‐dependent effects of multiple flood‐associated stressors on a coastal foundational species. Ecosphere 2022. [DOI: 10.1002/ecs2.4343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jessica L. Pruett
- National Center for Natural Products Research University of Mississippi, University Mississippi USA
| | - Ann Fairly Pandelides
- Department of BioMolecular Sciences University of Mississippi, University Mississippi USA
| | - Jaycie Keylon
- Department of BioMolecular Sciences University of Mississippi, University Mississippi USA
| | - Kristine L. Willett
- Department of BioMolecular Sciences University of Mississippi, University Mississippi USA
| | | | - Deborah J. Gochfeld
- National Center for Natural Products Research University of Mississippi, University Mississippi USA
- Department of BioMolecular Sciences University of Mississippi, University Mississippi USA
| |
Collapse
|
4
|
Strader ME, Wolak ME, Simon OM, Hofmann GE. Genetic variation underlies plastic responses to global change drivers in the purple sea urchin, Strongylocentrotus purpuratus. Proc Biol Sci 2022; 289:20221249. [PMID: 36043281 PMCID: PMC9428524 DOI: 10.1098/rspb.2022.1249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 11/12/2022] Open
Abstract
Phenotypic plasticity and adaptive evolution enable population persistence in response to global change. However, there are few experiments that test how these processes interact within and across generations, especially in marine species with broad distributions experiencing spatially and temporally variable temperature and pCO2. We employed a quantitative genetics experiment with the purple sea urchin, Strongylocentrotus purpuratus, to decompose family-level variation in transgenerational and developmental plastic responses to ecologically relevant temperature and pCO2. Adults were conditioned to controlled non-upwelling (high temperature, low pCO2) or upwelling (low temperature, high pCO2) conditions. Embryos were reared in either the same conditions as their parents or the crossed environment, and morphological aspects of larval body size were quantified. We find evidence of family-level phenotypic plasticity in response to different developmental environments. Among developmental environments, there was substantial additive genetic variance for one body size metric when larvae developed under upwelling conditions, although this differed based on parental environment. Furthermore, cross-environment correlations indicate significant variance for genotype-by-environment interactive effects. Therefore, genetic variation for plasticity is evident in early stages of S. purpuratus, emphasizing the importance of adaptive evolution and phenotypic plasticity in organismal responses to global change.
Collapse
Affiliation(s)
- Marie E. Strader
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Matthew E. Wolak
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Olivia M. Simon
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Gretchen E. Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| |
Collapse
|
5
|
Ragsdale A, Ortega-Recalde O, Dutoit L, Besson AA, Chia JHZ, King T, Nakagawa S, Hickey A, Gemmell NJ, Hore T, Johnson SL. Paternal hypoxia exposure primes offspring for increased hypoxia resistance. BMC Biol 2022; 20:185. [PMID: 36038899 PMCID: PMC9426223 DOI: 10.1186/s12915-022-01389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background In a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays and transcriptomic and methylome approaches, we use zebrafish as a model to investigate cross-generational acclimation to hypoxia. Results We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 6-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that other epigenetic mechanisms are responsible for alterations in gene expression. Conclusions Overall, our findings suggest that an epigenetic memory of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01389-x.
Collapse
Affiliation(s)
| | | | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Anne A Besson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Jolyn H Z Chia
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Tania King
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Shinichi Nakagawa
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Anthony Hickey
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Timothy Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Sheri L Johnson
- Department of Zoology, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
6
|
Affiliation(s)
- Katie E. Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Molly Albecker
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Geoffrey C. Trussell
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| |
Collapse
|
7
|
Johnson KM, Sirovy KA, Kelly MW. Differential DNA methylation across environments has no effect on gene expression in the eastern oyster. J Anim Ecol 2021; 91:1135-1147. [PMID: 34882793 DOI: 10.1111/1365-2656.13645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments. We compared patterns of global gene expression (Tag-seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters Crassostrea virginica from six full-sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments. An analysis of CpG observed/expected values (CpG O/E) across the C. virginica genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation and higher and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression. Taken together, the differential methylation results suggest that only a small portion of the C. virginica genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.
Collapse
Affiliation(s)
- Kevin M Johnson
- Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, USA.,California Sea Grant, University of California San Diego, La Jolla, CA, USA
| | - Kyle A Sirovy
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| |
Collapse
|
8
|
Griffiths JS, Johnson KM, Kelly MW. Evolutionary Change in the Eastern Oyster, Crassostrea Virginica, Following Low Salinity Exposure. Integr Comp Biol 2021; 61:1730-1740. [PMID: 34448845 DOI: 10.1093/icb/icab185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The presence of standing genetic variation will play a role in determining a population's capacity to adapt to environmentally relevant stressors. In the Gulf of Mexico, extreme climatic events and anthropogenic changes to local hydrology will expose productive oyster breeding grounds to stressful low salinity conditions. We identified genetic variation for performance under low salinity (due to the combined effects of low salinity and genetic load) using a single-generation selection experiment on larvae from two populations of the eastern oyster, Crassostrea virginica. We used pool-sequencing to test for allele frequency differences at 152 salinity-associated genes for larval families pre- and post-low salinity exposure. Our results have implications for how evolutionary change occurs during early life history stages at environmentally relevant salinities. Consistent with observations of high genetic load observed in oysters, we demonstrate evidence for purging of deleterious alleles at the larval stage in C. virginica. In addition, we observe increases in allele frequencies at multiple loci, suggesting that natural selection for low salinity performance at the larval stage can act as a filter for genotypes found in adult populations.
Collapse
Affiliation(s)
- Joanna S Griffiths
- Department of Environmental Toxicology and Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA 95616, USA
| | - Kevin M Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.,California Sea Grant, University of California San Diego, La Jolla, CA 92093, USA
| | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
9
|
Griffiths JS, Johnson KM, Sirovy KA, Yeats MS, Pan FTC, La Peyre JF, Kelly MW. Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica. Proc Biol Sci 2021; 288:20203118. [PMID: 34004136 PMCID: PMC8131124 DOI: 10.1098/rspb.2020.3118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Salinity conditions in oyster breeding grounds in the Gulf of Mexico are expected to drastically change due to increased precipitation from climate change and anthropogenic changes to local hydrology. We determined the capacity of the eastern oyster, Crassostrea virginica, to adapt via standing genetic variation or acclimate through transgenerational plasticity (TGP). We outplanted oysters to either a low- or medium-salinity site in Louisiana for 2 years. We then crossed adult parents using a North Carolina II breeding design, and measured body size and survival of larvae 5 dpf raised under low or ambient salinity. We found that TGP is unlikely to significantly contribute to low-salinity tolerance since we did not observe increased growth or survival in offspring reared in low salinity when their parents were also acclimated at a low-salinity site. However, we detected genetic variation for body size, with an estimated heritability of 0.68 ± 0.25 (95% CI). This suggests there is ample genetic variation for this trait to evolve, and that evolutionary adaptation is a possible mechanism through which oysters will persist with future declines in salinity. The results of this experiment provide valuable insights into successfully breeding low-salinity tolerance in this commercially important species.
Collapse
Affiliation(s)
- Joanna S. Griffiths
- Department of Environmental Toxicology and Department of Wildlife, Fish, and Conservation Biology, University of California, 4121 Meyer Hall, Davis, CA 95616, USA
| | - Kevin M. Johnson
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Kyle A. Sirovy
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Mark S. Yeats
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Francis T. C. Pan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jerome F. La Peyre
- Department of Veterinary Science, Louisiana State University, Baton Rouge, LA, USA
| | - Morgan W. Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| |
Collapse
|
10
|
Marshall DA, Casas SM, Walton WC, Rikard FS, Palmer TA, Breaux N, La Peyre MK, Beseres Pollack J, Kelly M, La Peyre JF. Divergence in salinity tolerance of northern Gulf of Mexico eastern oysters under field and laboratory exposure. CONSERVATION PHYSIOLOGY 2021; 9:coab065. [PMID: 34447578 PMCID: PMC8384081 DOI: 10.1093/conphys/coab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/30/2021] [Accepted: 08/18/2021] [Indexed: 05/04/2023]
Abstract
The eastern oyster, Crassostrea virginica, is a foundation species within US Gulf of Mexico (GoM) estuaries that has experienced substantial population declines. As changes from management and climate are expected to continue to impact estuarine salinity, understanding how local oyster populations might respond and identifying populations with adaptations to more extreme changes in salinity could inform resource management, including restoration and aquaculture programs. Wild oysters were collected from four estuarine sites from Texas [Packery Channel (PC): 35.5, annual mean salinity, Aransas Bay (AB): 23.0] and Louisiana [Calcasieu Lake (CL): 16.2, Vermilion Bay (VB): 7.4] and spawned. The progeny were compared in field and laboratory studies under different salinity regimes. For the field study, F1 oysters were deployed at low (6.4) and intermediate (16.5) salinity sites in Alabama. Growth and mortality were measured monthly. Condition index and Perkinsus marinus infection intensity were measured quarterly. For the laboratory studies, mortality was recorded in F1 oysters that were exposed to salinities of 2.0, 4.0, 20.0/22.0, 38.0 and 44.0 with and without acclimation. The results of the field study and laboratory study with acclimation indicated that PC oysters are adapted to high-salinity conditions and do not tolerate very low salinities. The AB stock had the highest plasticity as it performed as well as the PC stock at high salinities and as well as Louisiana stocks at the lowest salinity. Louisiana stocks did not perform as well as the Texas stocks at high salinities. Results from the laboratory studies without salinity acclimation showed that all F1 stocks experiencing rapid mortality at low salinities when 3-month oysters collected at a salinity of 24 were used and at both low and high salinities when 7-month oysters collected at a salinity of 14.5 were used.
Collapse
Affiliation(s)
- Danielle A Marshall
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Sandra M Casas
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - William C Walton
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, USA
| | - F Scott Rikard
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, USA
| | - Terence A Palmer
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Natasha Breaux
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Megan K La Peyre
- US Geological Survey, Louisiana Fish and Wildlife Cooperative Research Unit, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jennifer Beseres Pollack
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Morgan Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jerome F La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- Corresponding author: School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA. Tel: (225) 578-5419.
| |
Collapse
|