1
|
Park K, Kwak IS. Growth retardation and suppression of ubiquitin-dependent catabolic processes in the brackish water clam Corbicula japonica in response to salinity changes and bioaccumulation of toxic heavy metals. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122554. [PMID: 37717895 DOI: 10.1016/j.envpol.2023.122554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
The brackish water clam (Corbicula japonica) is constantly exposed to stressful salinity gradients and high levels of heavy metals in the freshwater-saltwater interface of estuary environments, which are introduced from upstream regions and land. To identify the key molecular pathways involved in the response to salinity changes and heavy metal bioaccumulation, we obtained the transcriptomes of C. japonica inhabiting different salinities and heavy metal distributions in Gwangyang Bay (Korea) using RNA sequencing. Among a total of 404,486 assembled unigenes, 5534 differentially expressed genes were identified in C. japonica inhabiting different conditions, 1549 of which were significantly upregulated and 1355 were significantly downregulated. Correlation analyses revealed distinct gene expression patterns between the low and high conditions of salinity and heavy metal bioaccumulation. Functional annotation revealed significant downregulation of genes involved in "ubiquitin-dependent protein catabolic process," "tricarboxylic acid cycle," and "intracellular protein transport" in C. japonica from the high condition compared to the low condition. Transcription and translation pathways were significantly enriched in the high condition. Additionally, upon comparison of the low and high conditions by qRT-PCR and proteasome enzyme activity analyses, our findings demonstrated that environmental stress could suppress the ubiquitin-proteasome complex (UPC). Additionally, transcriptomic changes under high salinity stress conditions may be related to an increase in cellular protection by defense enzymes, which leads to more energy being required and a disruption of energy homeostasis. Ultimately, this could cause growth retardation in the clam C. japonica. In summary, this study provides the first evidence of UPC suppression induced by a combination of high salinity and heavy metal bioaccumulation stress in C. japonica, which could compromise the survival and growth of estuarine bivalves.
Collapse
Affiliation(s)
- Kiyun Park
- Fisheries Science Institute, Chonnam National University, Yeosu, 59626, South Korea
| | - Ihn-Sil Kwak
- Fisheries Science Institute, Chonnam National University, Yeosu, 59626, South Korea; Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, South Korea.
| |
Collapse
|
2
|
Zhao H, Wang Q, Zhao H, Chen C. Transcriptome profiles revealed high- and low-salinity water altered gill homeostasis in half-smooth tongue sole (Cynoglossus semilaevis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100989. [PMID: 35421665 DOI: 10.1016/j.cbd.2022.100989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Salinity is an important environmental factor that affects fish growth, development, and reproduction. As euryhaline fish, half-smooth tongue sole (Cynoglossus semilaevis) are a suitable species for deciphering the salinity adaptation mechanism of fish; however, the molecular mechanisms underlying low- and high-salinity responses remain unclear. In this study, RNA-seq was applied to characterize the genes and regulatory pathways involved in C. semilaevis gill responses to high- (32 ppt), low- (8 ppt), and control-salinity (24 ppt) water. Gills were rich in mitochondria-rich cells (MRCs) in high salinity. Compared with control, 2137 and 218 differentially expressed genes (DEGs) were identified in low and high salinity, respectively. The enriched functions of most DEGs were metabolism, ion transport, regulation of cell cycle, and immune response. The DEGs involved in oxidative phosphorylation, citrate cycle, and fatty acid metabolism were down-regulated in low salinity. For ion transport, high and low salinity significantly altered the expressions of prlr, ca12, and cftr. In cell cycle arrest and cellular repair, gadd45b, igfbp5, and igfbp2 were significantly upregulated in high and low salinity. For immune response, il10, il34, il12b, and crp increased in high and low salinity. Our findings suggested that alterations in material and energy metabolism, ions transport, cell cycle arrest, cellular repair, and immune response, are required to maintain C. semilaevis gill homeostasis under high and low salinity. This study provides insight into the divergence of C. semilaevis osmoregulation mechanisms acclimating to high and low salinity, which will serve as reference for the healthy culture of C. semilaevis.
Collapse
Affiliation(s)
- Huiyan Zhao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| | - Qingkui Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China.
| | - Honghao Zhao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| | - Chengxun Chen
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| |
Collapse
|
3
|
Association study between relative expression levels of eight genes and growth rate in Hungarian common carp ( Cyprinus carpio). Saudi J Biol Sci 2022; 29:630-639. [PMID: 35002460 PMCID: PMC8716967 DOI: 10.1016/j.sjbs.2021.09.036] [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: 05/19/2021] [Revised: 09/11/2021] [Accepted: 09/12/2021] [Indexed: 11/20/2022] Open
Abstract
One of the most important issues in improving the competitiveness of the fish production sector is to improve the growth rate of fish. The genetic background to this trait is at present poorly understood. In this study, we compared the relative gene expression levels of the Akt1s1, FGF, GH, IGF1, MSTN, TLR2, TLR4 and TLR5 genes in blood in groups of common carps (Cyprinus carpio), which belonged to different growth types and phenotypes. Fish were divided into groups based on growth rate (normal group: n = 6; slow group: n = 6) and phenotype (scaled group: n = 6; mirror group: n = 6). In the first 18 weeks, we measured significant differences (p < 0.05) between groups in terms of body weight and body length. Over the next 18 weeks, the fish in the slow group showed more intense development. In the same period, the slow group was characterized by lower expression levels for most genes, whereas GH and IGF1 mRNA levels were higher compared to the normal group. We found that phenotype was not a determining factor in differences of relative expression levels of the genes studied.
Collapse
|
4
|
Borges VD, Zebral YD, Costa PG, da Silva Fonseca J, Klein RD, Bianchini A. Metal Accumulation and Ion Regulation in the Fish Hyphessobrycon luetkenii Living in a Site Chronically Contaminated by Copper: Insights from Translocation Experiments. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 82:62-71. [PMID: 34664084 DOI: 10.1007/s00244-021-00895-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Fish living in the João Dias creek (southern Brazil) have to deal with trace-metal contamination in the long-term basis, as this aquatic environment has been historically impacted by copper mining activities. In order to survive in this harsh environment, the local biota had to develop adaptations related to pollution tolerance. The aim of this study was to test if biochemical mechanisms related to osmoregulation were among these adaptations, using translocation experiments. Water ionic and trace-metal compositions were measured in a nonmetal impacted site (NMIS) and in a metal impacted site (MIS) of this creek. Also, whole-body metal accumulation, ion concentration and branchial enzyme activity (Na,K-ATPase and carbonic anhydrase) were evaluated in Hyphessobrycon luetkenii. In both NMIS and MIS, fish were collected and immediately stored, kept caged or translocated from sites. The result shows that waterborne Cu was 3.4-fold higher at the MIS. Accordingly, animals that had contact with this site showed elevated whole-body Cu levels. Moreover, both translocated groups showed elevated Na,K-ATPase activity. Additionally, fish translocated from the NMIS to the MIS showed lower carbonic anhydrase activity. These findings indicate that H. luetkenii chronically or acutely exposed to naturally elevated waterborne Cu showed a rapid Cu bioaccumulation but was unable to readily excrete it. Moreover, classic Cu osmoregulatory toxicity related to Na,K-ATPase inhibition was not observed. Conversely, impacts in ammonia excretion related to carbonic anhydrase inhibition may have occurred.
Collapse
Affiliation(s)
- Vinícius Dias Borges
- Programa de Pós-Graduação em Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900, Rio Grande, RS, Brazil
| | - Yuri Dornelles Zebral
- Programa de Pós-Graduação em Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900, Rio Grande, RS, Brazil
| | - Patrícia Gomes Costa
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900, Rio Grande, RS, Brazil
| | - Juliana da Silva Fonseca
- Programa de Pós-Graduação em Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900, Rio Grande, RS, Brazil
| | - Roberta Daniele Klein
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900, Rio Grande, RS, Brazil
| | - Adalto Bianchini
- Programa de Pós-Graduação em Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Avenida Itália km 8, Campus Carreiros, 96.203-900, Rio Grande, RS, Brazil.
| |
Collapse
|
5
|
Transcriptome Profiling Reveals a Divergent Adaptive Response to Hyper- and Hypo-Salinity in the Yellow Drum, Nibea albiflora. Animals (Basel) 2021; 11:ani11082201. [PMID: 34438658 PMCID: PMC8388402 DOI: 10.3390/ani11082201] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Global warming and certain climate disasters (typhoon, tsunami, etc.) can lead to fluctuation in seawater salinity that causes salinity stress in fish. The aim of this study was to investigate the functional genes and relevant pathways in response to salinity stress in the yellow drum. Genes and pathways related to signal transduction, osmoregulation, and metabolism may be involved in the adaptive regulation to salinity in the yellow drum. Additionally, the genes under salinity stress were mainly divided into three expression trends. Our results provided novel insights into further study of the salinity adaptability of euryhaline fishes. Abstract The yellow drum (Nibea albiflora) is an important marine economic fish that is widely distributed in the coastal waters of the Northwest Pacific. In order to understand the molecular regulatory mechanism of the yellow drum under salinity stress, in the present study, transcriptome analysis was performed under gradients with six salinities (10, 15, 20, 25, 30, and 35 psu). Compared to 25 psu, 907, 1109, 1309, 18, and 243 differentially expressed genes (DEGs) were obtained under 10, 15, 20, 30, and 35 psu salinities, respectively. The differential gene expression was further validated by quantitative real-time PCR (qPCR). The results of the tendency analysis showed that all DEGs of the yellow drum under salinity fluctuation were mainly divided into three expression trends. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the PI3K-Akt signaling pathway, Jak-STAT signaling pathway as well as the glutathione metabolism and steroid biosynthesis pathways may be the key pathways for the salinity adaptive regulation mechanism of the yellow drum. G protein-coupled receptors (GPCRs), the solute carrier family (SLC), the transient receptor potential cation channel subfamily V member 6 (TRPV6), isocitrate dehydrogenase (IDH1), and fructose-bisphosphate aldolase C-B (ALDOCB) may be the key genes in the response of the yellow drum to salinity stress. This study explored the transcriptional patterns of the yellow drum under salinity stress and provided fundamental information for the study of salinity adaptability in this species.
Collapse
|
6
|
Goehlich H, Sartoris L, Wagner KS, Wendling CC, Roth O. Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope With Ancestral Salinity Levels. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.626442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibriobacteria) stressor using six different populations of the broad-nosed pipefishSyngnathus typhlethat originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected withVibrio alginolyticusbacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation,trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.
Collapse
|
7
|
Berdan EL, Fuller RC, Kozak GM. Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity. J Evol Biol 2020; 34:157-174. [PMID: 33118222 PMCID: PMC7894299 DOI: 10.1111/jeb.13725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 01/24/2023]
Abstract
Adaptation to different environments can directly and indirectly generate reproductive isolation between species. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are sister species that have diverged across a salinity gradient and are reproductively isolated by habitat, behavioural, extrinsic and intrinsic post-zygotic isolation. We asked if salinity adaptation contributes indirectly to other forms of reproductive isolation via linked selection and hypothesized that low recombination regions, such as sex chromosomes or chromosomal rearrangements, might facilitate this process. We conducted QTL mapping in backcrosses between L. parva and L. goodei to explore the genetic architecture of salinity tolerance, behavioural isolation and intrinsic isolation. We mapped traits relative to a chromosome that has undergone a centric fusion in L. parva (relative to L. goodei). We found that the sex locus appears to be male determining (XX-XY), was located on the fused chromosome and was implicated in intrinsic isolation. QTL associated with salinity tolerance were spread across the genome and did not overly co-localize with regions associated with behavioural or intrinsic isolation. This preliminary analysis of the genetic architecture of reproductive isolation between Lucania species does not support the hypothesis that divergent natural selection for salinity tolerance led to behavioural and intrinsic isolation as a by-product. Combined with previous studies in this system, our work suggests that adaptation as a function of salinity contributes to habitat isolation and that reinforcement may have contributed to the evolution of behavioural isolation instead, possibly facilitated by linkage between behavioural isolation and intrinsic isolation loci on the fused chromosome.
Collapse
Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Rebecca C Fuller
- Department of Animal Biology, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts-Dartmouth, Dartmouth, MA, USA
| |
Collapse
|
8
|
Song J, Brill RW, McDowell JR. Plasticity in Standard and Maximum Aerobic Metabolic Rates in Two Populations of an Estuarine Dependent Teleost, Spotted Seatrout ( Cynoscion nebulosus). BIOLOGY 2019; 8:biology8020046. [PMID: 31197073 PMCID: PMC6627818 DOI: 10.3390/biology8020046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/16/2019] [Accepted: 06/11/2019] [Indexed: 01/28/2023]
Abstract
We studied the effects of metabolic cold adaptation (MCA) in two populations of a eurythermal species, spotted seatrout (Cynoscion nebulosus) along the U.S. East Coast. Fish were captured from their natural environment and acclimated at control temperatures 15 °C or 20 °C. Their oxygen consumption rates, a proxy for metabolic rates, were measured using intermittent flow respirometry during acute temperature decrease or increase (2.5 °C per hour). Mass-specific standard metabolic rates (SMR) were higher in fish from the northern population across an ecologically relevant temperature gradient (5 °C to 30 °C). SMR were up to 37% higher in the northern population at 25 °C and maximum metabolic rates (MMR) were up to 20% higher at 20 °C. We found evidence of active metabolic compensation in the southern population from 5 °C to 15 °C (Q10 < 2), but not in the northern population. Taken together, our results indicate differences in metabolic plasticity between the northern and southern populations of spotted seatrout and provide a mechanistic basis for predicting population-specific responses to climate change.
Collapse
Affiliation(s)
- Jingwei Song
- Virginia Institute of Marine Science, William & Mary, P.O. Box 1346, Gloucester Point, VA 23062, USA.
| | - Richard W Brill
- Virginia Institute of Marine Science, William & Mary, P.O. Box 1346, Gloucester Point, VA 23062, USA.
| | - Jan R McDowell
- Virginia Institute of Marine Science, William & Mary, P.O. Box 1346, Gloucester Point, VA 23062, USA.
| |
Collapse
|
9
|
She Z, Li L, Meng J, Jia Z, Que H, Zhang G. Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas. Sci Rep 2018; 8:8683. [PMID: 29875442 PMCID: PMC5989259 DOI: 10.1038/s41598-018-26953-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/17/2018] [Indexed: 02/07/2023] Open
Abstract
The Pacific oyster Crassostrea gigas is an important cultivated shellfish. As a euryhaline species, it has evolved adaptive mechanisms responding to the complex and changeable intertidal environment that it inhabits. To investigate the genetic basis of this salinity adaptation mechanism, we conducted a genome-wide association study using phenotypically differentiated populations (hyposalinity and hypersalinity adaptation populations, and control population), and confirmed our results using an independent population, high-resolution melting, and mRNA expression analysis. For the hyposalinity adaptation, we determined 24 genes, including Cg_CLCN7 (chloride channel protein 7) and Cg_AP1 (apoptosis 1 inhibitor), involved in the ion/water channel and transporter mechanisms, free amino acid and reactive oxygen species metabolism, immune responses, and chemical defence. Three SNPs located on these two genes were significantly differentiated between groups, as was Cg_CLCN7. For the hypersalinity adaptation, the biological process for positive regulating the developmental process was enriched. Enriched gene functions were focused on transcriptional regulation, signal transduction, and cell growth and differentiation, including calmodulin (Cg_CaM) and ficolin-2 (Cg_FCN2). These genes and polymorphisms possibly play an important role in oyster hyposalinity and hypersalinity adaptation. They not only further our understanding of salinity adaptation mechanisms but also provide markers for highly adaptable oyster strains suitable for breeding.
Collapse
Affiliation(s)
- Zhicai She
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou University, Qinzhou, 535011, Guangxi, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China. .,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China. .,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.
| | - Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China
| | - Zhen Jia
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou University, Qinzhou, 535011, Guangxi, China
| | - Huayong Que
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China. .,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.
| |
Collapse
|
10
|
Czypionka T, Goedbloed DJ, Steinfartz S, Nolte AW. Plasticity and evolutionary divergence in gene expression associated with alternative habitat use in larvae of the European Fire Salamander. Mol Ecol 2018; 27:2698-2713. [PMID: 29742304 DOI: 10.1111/mec.14713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 03/27/2018] [Accepted: 04/11/2018] [Indexed: 12/21/2022]
Abstract
Transcriptomes of organisms reveal differentiation associated with the use of different habitats. However, this leaves open how much of the observed differentiation can be attributed to genetic differences or to transcriptional plasticity. In this study, we disentangle causes of differential gene expression in larvae of the European fire salamander from the Kottenforst forest in Germany. Larvae inhabit permanent streams and ephemeral ponds and represent an example of a young evolutionary split associated with contrasting ecological conditions. We hypothesized that adaptation towards differences in water temperature plays a role because the thermal regime between stream and pond habitats differs notably. Tissue samples from tail fins of larvae were collected to study gene expression using microarrays. We found ample evidence for differentiation among larvae occupying different habitats in nature with 2,800 of 11,797 genes being differentially expressed. We then quantified transcriptional plasticity towards temperature and genetic differentiation based on controlled temperature laboratory experiments. Gene-by-environment interactions modelling revealed that 28% of the gene expression divergence observed among samples in nature could be attributed to plasticity related to water temperature. Expression patterns of only a small number of 101 genes were affected by the genotype. Our analysis demonstrates that effects of environmental factors must be taken into account to explain variation of gene expression in salamanders in nature. Notwithstanding, it provides first evidence that genetic factors determined gene expression divergence between pond and stream ecotypes and could be involved in adaptive evolution.
Collapse
Affiliation(s)
- Till Czypionka
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Daniel J Goedbloed
- Department of Evolutionary Biology, Unit Molecular Ecology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sebastian Steinfartz
- Department of Evolutionary Biology, Unit Molecular Ecology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Arne W Nolte
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Ecological Genomics, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| |
Collapse
|
11
|
Tine M. Evidence of the Complexity of Gene Expression Analysis in Fish Wild Populations. Int J Genomics 2017; 2017:1258396. [PMID: 29201893 PMCID: PMC5672613 DOI: 10.1155/2017/1258396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/24/2017] [Accepted: 09/18/2017] [Indexed: 11/17/2022] Open
Abstract
The present work examines the induction of the band 3 anion transport protein, mitogen-activated protein kinase, and lactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations. The differential expression was also not associated with the population genetic structure inferred from neutral markers. The results suggest that the differential expression observed is not the result of evolutionary forces such as genetic drift or adaptation by natural selection. Instead, it can be speculated that genes responded to various abiotic and biotic stressors, including factors intrinsic to animals. This study provides clear evidence of the complexity of gene expression analysis in wild populations and shows that more attention needs to be paid when selecting candidates as potential biomarkers for monitoring adaptive responses to a specific environmental perturbation.
Collapse
Affiliation(s)
- Mbaye Tine
- UFR des Sciences Agronomiques, de l'Aquaculture et des Technologies Alimentaires (UFR S2ATA), Universite Gaston Berger (UGB), Route de Ngallele BP 234, Saint-Louis, Senegal
| |
Collapse
|
12
|
Li A, Li L, Song K, Wang W, Zhang G. Temperature, energy metabolism, and adaptive divergence in two oyster subspecies. Ecol Evol 2017; 7:6151-6162. [PMID: 28861221 PMCID: PMC5574764 DOI: 10.1002/ece3.3085] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/11/2017] [Accepted: 04/25/2017] [Indexed: 01/04/2023] Open
Abstract
Comparisons of related species that have diverse spatial distributions provide an efficient way to investigate adaptive evolution in face of increasing global warming. The oyster subjected to high environmental selections is a model species as sessile marine invertebrate. This study aimed to detect the adaptive divergence of energy metabolism in two oyster subspecies from the genus Crassostrea—C. gigas gigas and C. gigas angulata—which are broadly distributed along the northern and southern coasts of China, respectively. We examined the effects of acute thermal stress on energy metabolism in two oyster subspecies after being common gardened for one generation in identical conditions. Thermal responses were assessed by incorporating physiological, molecular, and genomic approaches. Southern oysters exhibited higher fluctuations in metabolic rate, activities of key energetic enzymes, and levels of thermally induced gene expression than northern oysters. For genes involved in energy metabolism, the former displayed higher basal levels of gene expression and a more pronounced downregulation of thermally induced expression, while the later exhibited lower basal levels and a less pronounced downregulation of gene expression. Contrary expression pattern was observed in oxidative stress gene. Besides, energy metabolic tradeoffs were detected in both subspecies. Furthermore, the genetic divergence of a nonsynonymous SNP (SOD‐132) and five synonymous SNPs in other genes was identified and validated in these two subspecies, which possibly affects downstream functions and explains the aforementioned phenotypic variations. Our study demonstrates that differentiations in energy metabolism underlie the plasticity of adaptive divergence in two oyster subspecies and suggest C. gigas angulata with moderate phenotypic plasticity has higher adaptive potential to cope with exacerbated global warming.
Collapse
Affiliation(s)
- Ao Li
- Key Laboratory of Experimental Marine BiologyInstitute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,University of Chinese Academy of Sciences Beijing China
| | - Li Li
- Key Laboratory of Experimental Marine BiologyInstitute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,Laboratory for Marine Fisheries and Aquaculture Qingdao National Laboratory for Marine Science and Technology Qingdao Shandong China.,National & Local Joint Engineering Key Laboratory of Ecological Mariculture Institute of Oceanology Chinese Academy of Sciences Qingdao Shandong China
| | - Kai Song
- Key Laboratory of Experimental Marine BiologyInstitute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,National & Local Joint Engineering Key Laboratory of Ecological Mariculture Institute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao Shandong China
| | - Wei Wang
- Key Laboratory of Experimental Marine BiologyInstitute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,National & Local Joint Engineering Key Laboratory of Ecological Mariculture Institute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao Shandong China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine BiologyInstitute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,National & Local Joint Engineering Key Laboratory of Ecological Mariculture Institute of Oceanology Chinese Academy of Sciences Qingdao Shandong China.,Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao Shandong China
| |
Collapse
|
13
|
O'Connor CM, Marsh-Rollo SE, Ghio SC, Balshine S, Aubin-Horth N. Is there convergence in the molecular pathways underlying the repeated evolution of sociality in African cichlids? Horm Behav 2015. [PMID: 26204804 DOI: 10.1016/j.yhbeh.2015.07.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite wide variation in the complexity of social interactions across taxa, the basic behavioral components of sociality appear to be modulated by conserved hormone pathways. Specifically, the nonapeptide hormones oxytocin and vasopressin and their receptors have been implicated in regulating diverse social behaviors across vertebrates. Here, we took advantage of the repeated evolution of cooperative breeding in African cichlids to investigate whether there are consistent brain gene expression patterns of isotocin and arginine vasotocin (teleost homologues of oxytocin and vasopressin), as well as their receptors, between four closely related pairs of social (cooperative) and non-social (non-cooperative) species. We first found that the coding sequences for the five genes studied were highly conserved across the eight species. This is the first study to examine the expression of both isotocin receptors, and so we performed a phylogenetic analysis that suggests that these two isotocin receptors are paralogues that arose during the teleost genome duplication. When we then examined brain gene expression patterns relative to social system, we found that there were whole-brain gene expression differences between the social and non-social species in many of the species pairs. However, these relationships varied in both the direction and magnitude among the four species pairs. In conclusion, our results suggest high sequence conservation and species-specific gene expression patterns relative to social behavior for these candidate hormone pathways in the cichlid fishes.
Collapse
Affiliation(s)
- Constance M O'Connor
- Aquatic Behavioural Ecology Lab, Department of Psychology, Neuroscience, and Behaviour, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
| | - Susan E Marsh-Rollo
- Aquatic Behavioural Ecology Lab, Department of Psychology, Neuroscience, and Behaviour, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Sergio Cortez Ghio
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Sigal Balshine
- Aquatic Behavioural Ecology Lab, Department of Psychology, Neuroscience, and Behaviour, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Nadia Aubin-Horth
- Département de Biologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| |
Collapse
|
14
|
Czypionka T, Krugman T, Altmüller J, Blaustein L, Steinfartz S, Templeton AR, Nolte AW. Ecological transcriptomics – a non‐lethal sampling approach for endangered fire salamanders. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Till Czypionka
- Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| | - Tamar Krugman
- Institute of Evolution and Department of Evolutionary and Environmental Biology University of Haifa Haifa 3498838 Israel
| | - Janine Altmüller
- Cologne Centre for Genomics University of Cologne Weyertal 115b 50931 Köln Germany
| | - Leon Blaustein
- Institute of Evolution and Department of Evolutionary and Environmental Biology University of Haifa Haifa 3498838 Israel
| | - Sebastian Steinfartz
- Department of Evolutionary Biology Unit Molecular Ecology Technische Universität Braunschweig 38106 Braunschweig Germany
| | - Alan R. Templeton
- Institute of Evolution and Department of Evolutionary and Environmental Biology University of Haifa Haifa 3498838 Israel
| | - Arne W. Nolte
- Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| |
Collapse
|
15
|
She Z, Li L, Qi H, Song K, Que H, Zhang G. Candidate Gene Polymorphisms and their Association with Glycogen Content in the Pacific Oyster Crassostrea gigas. PLoS One 2015; 10:e0124401. [PMID: 25951187 PMCID: PMC4423957 DOI: 10.1371/journal.pone.0124401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/13/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Pacific oyster Crassostrea gigas is an important cultivated shellfish that is rich in nutrients. It contains high levels of glycogen, which is of high nutritional value. To investigate the genetic basis of this high glycogen content and its variation, we conducted a candidate gene association analysis using a wild population, and confirmed our results using an independent population, via targeted gene resequencing and mRNA expression analysis. RESULTS We validated 295 SNPs in the 90 candidate genes surveyed for association with glycogen content, 86 of were ultimately genotyped in all 144 experimental individuals from Jiaonan (JN). In addition, 732 SNPs were genotyped via targeted gene resequencing. Two SNPs (Cg_SNP_TY202 and Cg_SNP_3021) in Cg_GD1 (glycogen debranching enzyme) and one SNP (Cg_SNP_4) in Cg_GP1 (glycogen phosphorylase) were identified as being associated with glycogen content. The glycogen content of individuals with genotypes TT and TC in Cg_SNP_TY202 was higher than that of individuals with genotype CC. The transcript abundance of both glycogen-associated genes was differentially expressed in high glycogen content and low glycogen content individuals. CONCLUSIONS This study identified three polymorphisms in two genes associated with oyster glycogen content, via candidate gene association analysis. The transcript abundance differences in Cg_GD1 and Cg_GP1 between low- and the high-glycogen content individuals suggests that it is possible that transcript regulation is mediated by variations of Cg_SNP_TY202, Cg_SNP_3021, and Cg_SNP_4. These findings will not only provide insights into the genetic basis of oyster quality, but also promote research into the molecular breeding of oysters.
Collapse
Affiliation(s)
- Zhicai She
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Li
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Haigang Qi
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Kai Song
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Huayong Que
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Guofan Zhang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| |
Collapse
|
16
|
Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq. G3-GENES GENOMES GENETICS 2015; 5:1335-49. [PMID: 25911227 PMCID: PMC4502368 DOI: 10.1534/g3.115.017699] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon.
Collapse
|
17
|
Ronkin D, Seroussi E, Nitzan T, Doron-Faigenboim A, Cnaani A. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 13:35-43. [DOI: 10.1016/j.cbd.2015.01.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 11/27/2022]
|
18
|
Hemmer-Hansen J, Therkildsen NO, Pujolar JM. Population genomics of marine fishes: next-generation prospects and challenges. THE BIOLOGICAL BULLETIN 2014; 227:117-132. [PMID: 25411371 DOI: 10.1086/bblv227n2p117] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past few years, technological advances have facilitated giant leaps forward in our ability to generate genome-wide molecular data, offering exciting opportunities for gaining new insights into the ecology and evolution of species where genomic information is still limited. Marine fishes are valuable organisms for advancing our understanding of evolution on historical and contemporary time scales, and here we highlight areas in which research on these species is likely to be particularly important in the near future. These include possibilities for gaining insights into processes on ecological time scales, identifying genomic signatures associated with population divergence under gene flow, and determining the genetic basis of phenotypic traits. We also consider future challenges pertaining to the implementation of genome-wide coverage through next-generation sequencing and genotyping methods in marine fishes. Complications associated with fast decay of linkage disequilibrium, as expected for species with large effective population sizes, and the possibility that adaptation is associated with both soft selective sweeps and polygenic selection, leaving complex genomic signatures in natural populations, are likely to challenge future studies. However, the combination of high genome coverage and new statistical developments offers promising solutions. Thus, the next generation of studies is likely to truly facilitate the transition from population genetics to population genomics in marine fishes. This transition will advance our understanding of basic evolutionary processes and will offer new possibilities for conservation and management of valuable marine resources.
Collapse
Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark;
| | | | - José Martin Pujolar
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
| |
Collapse
|
19
|
Meier K, Hansen MM, Normandeau E, Mensberg KLD, Frydenberg J, Larsen PF, Bekkevold D, Bernatchez L. Local adaptation at the transcriptome level in brown trout: evidence from early life history temperature genomic reaction norms. PLoS One 2014; 9:e85171. [PMID: 24454810 PMCID: PMC3891768 DOI: 10.1371/journal.pone.0085171] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/23/2013] [Indexed: 01/19/2023] Open
Abstract
Local adaptation and its underlying molecular basis has long been a key focus in evolutionary biology. There has recently been increased interest in the evolutionary role of plasticity and the molecular mechanisms underlying local adaptation. Using transcriptome analysis, we assessed differences in gene expression profiles for three brown trout (Salmo trutta) populations, one resident and two anadromous, experiencing different temperature regimes in the wild. The study was based on an F2 generation raised in a common garden setting. A previous study of the F1 generation revealed different reaction norms and significantly higher QST than FST among populations for two early life-history traits. In the present study we investigated if genomic reaction norm patterns were also present at the transcriptome level. Eggs from the three populations were incubated at two temperatures (5 and 8 degrees C) representing conditions encountered in the local environments. Global gene expression for fry at the stage of first feeding was analysed using a 32k cDNA microarray. The results revealed differences in gene expression between populations and temperatures and population × temperature interactions, the latter indicating locally adapted reaction norms. Moreover, the reaction norms paralleled those observed previously at early life-history traits. We identified 90 cDNA clones among the genes with an interaction effect that were differently expressed between the ecologically divergent populations. These included genes involved in immune- and stress response. We observed less plasticity in the resident as compared to the anadromous populations, possibly reflecting that the degree of environmental heterogeneity encountered by individuals throughout their life cycle will select for variable level of phenotypic plasticity at the transcriptome level. Our study demonstrates the usefulness of transcriptome approaches to identify genes with different temperature reaction norms. The responses observed suggest that populations may vary in their susceptibility to climate change.
Collapse
Affiliation(s)
- Kristian Meier
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Québec, Canada
| | - Karen-Lise D. Mensberg
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jane Frydenberg
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | | | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Québec, Canada
| |
Collapse
|
20
|
Larsen PF, Nielsen EE, Hansen MM, Wang T, Meier K, Pertoldi C, Loeschcke V. Tissue specific haemoglobin gene expression suggests adaptation to local marine conditions in North Sea flounder (Platichthys flesus L.). Genes Genomics 2013. [DOI: 10.1007/s13258-013-0101-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
21
|
Salmenkova EA. Molecular genetic bases of adaptation processes and approaches to their analysis. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413010110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
22
|
Abstract
It is becoming increasingly clear that local adaptation can occur even in the face of high gene flow and limited overall genomic differentiation among populations (reviewed by Nosil et al. 2009). Thus, one important task for molecular ecologists is to sift through genomic data to identify the genes that matter for local adaptation (Hoffmann & Willi 2008; Stapley et al. 2010). Recent advances in high-throughput molecular technologies have facilitated this search, and a variety of approaches can be applied, including those grounded in population genetics [e.g. outlier analysis (Pavlidis et al. 2008)], classical and quantitative genetics [e.g. quantitative trait locus analysis (MacKay et al. 2009)], and cellular and molecular biology [e.g. transcriptomics (Larsen et al. 2011)]. However, applying these approaches in nonmodel organisms that lack extensive genetic and genomic resources has been a formidable challenge. In this issue, Papakostas et al. (2012). demonstrate how one such approach – high-throughput label-free proteomics (reviewed by Gstaiger & Aebersold 2009; Domon & Aebersold 2010) – can be applied to detect genes that may be involved in local adaptation in a species with limited genomic resources. Using this approach, they identified genes that may be implicated in local adaptation to salinity in European whitefish (Coregonus lavaretus L.) and provide insight into the mechanisms by which fish cope with changes in this critically important environmental parameter.
Collapse
Affiliation(s)
- Anne C Dalziel
- Department of Zoology, University of British Columbia,Vancouver, BC, Canada.
| | | |
Collapse
|
23
|
CZYPIONKA TILL, CHENG JIE, POZHITKOV ALEXANDER, NOLTE ARNEW. Transcriptome changes after genome-wide admixture in invasive sculpins (Cottus). Mol Ecol 2012; 21:4797-810. [DOI: 10.1111/j.1365-294x.2012.05645.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
24
|
PAPAKOSTAS SPIROS, VASEMÄGI ANTI, VÄHÄ JUHAPEKKA, HIMBERG MIKAEL, PEIL LAURI, PRIMMER CRAIGR. A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus). Mol Ecol 2012; 21:3516-30. [DOI: 10.1111/j.1365-294x.2012.05553.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
25
|
Tine M, Guinand B, Durand JD. Variation in gene expression along a salinity gradient in wild populations of the euryhaline black-chinned tilapia Sarotherodon melanotheron. JOURNAL OF FISH BIOLOGY 2012; 80:785-801. [PMID: 22471799 DOI: 10.1111/j.1095-8649.2012.03220.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This study evaluated variation in expression of 11 genes within and among six wild populations of the black-chinned tilapia Sarotherodon melanotheron distributed along a salinity gradient from 0 to 100. Previous laboratory studies had shown that expression of these genes was sensitive to water salinity; the current study confirmed that a number of them also varied in expression in wild populations along the salinity gradient. Principal component analysis (PCA) first distinguished two, not mutually exclusive, sets of genes: trade-off genes that were highly expressed at one or other extreme of the salinity gradient and stress genes that were up-regulated at the two salinity extremes (i.e. a U-shaped expression pattern). The PCA clearly partitioned the populations into three groups based on their gene expression patterns and their position along the salinity gradient: a freshwater (GL; 0) population, four brackish and seawater (GB, HB, SM, SF; ranging from 20 to 50) populations and a hypersaline (SK, 100) population. Individual variation in gene expression was significantly greater within the populations at the extreme compared to intermediate salinities. These results reveal phenotypically plastic regulation of gene expression in S. melanotheron, and greater osmoregulatory and plasticity costs at extreme salinities, where fitness-related traits are known to be altered.
Collapse
Affiliation(s)
- M Tine
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany.
| | | | | |
Collapse
|
26
|
Sellin Jeffries MK, Mehinto AC, Carter BJ, Denslow ND, Kolok AS. Taking microarrays to the field: differential hepatic gene expression of caged fathead minnows from Nebraska watersheds. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:1877-1885. [PMID: 22165990 DOI: 10.1021/es2039097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This study aimed to evaluate the utility of microarrays as a biomonitoring tool in field studies. A 15,000-oligonucleotide microarray was used to measure the hepatic gene expression of fathead minnows (Pimephales promelas) caged in four Nebraska, USA watersheds - the Niobrara and Dismal Rivers (low-impact agricultural sites) and the Platte and Elkhorn Rivers (high-impact agricultural sites). Gene expression profiles were site specific and fish from the low- and high-impact sites aggregated into distinct groups. Over 1500 genes were differentially regulated between fish from the low- and high-impact sites. Many gene expression differences (1218) were also noted when the Platte and Elkhorn minnows were compared to one another and Platte fish experienced a higher degree of transcript alterations than Elkhorn fish. These findings indicate that there are differences between the low-impact and high-impact sites, as well as between the two high-impact sites. Historical water quality data support these results as only trace levels of agrichemicals have been detected at the low-impact sites, while substantial levels of agrichemicals have been reported at the high-impact sites with agrichemical loads at the Platte generally exceeding those at the Elkhorn. Overall, this study demonstrates that microarrays can be utilized to discriminate sites with different contaminant loads from one another.
Collapse
Affiliation(s)
- Marlo K Sellin Jeffries
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska - Medical Center, Omaha, Nebraska 68198, United States.
| | | | | | | | | |
Collapse
|
27
|
Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
Collapse
Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| |
Collapse
|
28
|
Larsen PF, Nielsen EE, Meier K, Olsvik PA, Hansen MM, Loeschcke V. Differences in salinity tolerance and gene expression between two populations of Atlantic cod (Gadus morhua) in response to salinity stress. Biochem Genet 2011; 50:454-66. [PMID: 22205502 DOI: 10.1007/s10528-011-9490-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 05/31/2011] [Indexed: 10/14/2022]
Abstract
Populations of marine fish, even from contrasting habitats, generally show low genetic differentiation at neutral genetic markers. Nevertheless, there is increasing evidence for differences in gene expression among populations that may be ascribed to adaptive divergence. Studying variation in salinity tolerance and gene expression among Atlantic cod (Gadus morhua) from two populations distributed across a steep salinity gradient, we observed high mortality (45% North Sea cod and 80% Baltic Sea cod) in a reciprocal common garden setup. Quantitative RT-PCR assays for expression of hsp70 and Na/K-ATPase α genes demonstrated significant differences in gene regulation within and between populations and treatment groups despite low sample sizes. Most interesting are the significant differences observed in expression of the Na/K-ATPase α gene in gill tissue between North Sea and Baltic cod. The findings strongly suggest that Atlantic cod are adapted to local saline conditions, despite relatively low levels of neutral genetic divergence between populations.
Collapse
Affiliation(s)
- P F Larsen
- Department of Biological Sciences, Aarhus University, Ny Munkegade, 8000, Aarhus C, Denmark.
| | | | | | | | | | | |
Collapse
|
29
|
|
30
|
Giordano D, Russo R, di Prisco G, Verde C. Molecular adaptations in Antarctic fish and marine microorganisms. Mar Genomics 2011; 6:1-6. [PMID: 22578653 DOI: 10.1016/j.margen.2011.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/01/2011] [Accepted: 09/07/2011] [Indexed: 01/10/2023]
Abstract
The Antarctic marine environment is one of the most extreme on Earth due to its stably low temperature and high oxygen content. Here we discuss various aspects of the molecular adaptations evolved by Antarctic fish and marine microorganisms living in this environment. This review will in particular focus on: (i) the genetic/genomic bases of adaptation in Antarctic notothenioid fish; (ii) the role of neuroglobin recently identified in the brain of Antarctic icefish; (iii) the structural and functional features of globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125.
Collapse
Affiliation(s)
- Daniela Giordano
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy
| | | | | | | |
Collapse
|