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Liu S, Lu Y, Geng D. Molecular Subgroup Classification in Alzheimer's Disease by Transcriptomic Profiles. J Mol Neurosci 2022; 72:866-879. [PMID: 35080766 DOI: 10.1007/s12031-021-01957-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/08/2021] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a progressive cognitive disorder that occurs worldwide, and the lack of disease-modifying targets and pathways is a pressing issue. This study aimed to provide new targets and pathways by performing molecular subgroup classification. After normalizing the collected data, the subgroup number was confirmed with consensus clustering. Comparisons of clinical features among subgroups were conducted to clarify the clinical traits of each subgroup. Subgroup-specific genes were identified to perform weighted gene coexpression analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out. Next, gene set enrichment analysis (GSEA) was performed. Protein-protein interaction networks were built to screen core genes and in each subgroup to perform Spearman correlation analysis with clinical traits. Sequencing profiles of 1068 AD samples collected from 2 datasets were classified into 3 subgroups. Clinical comparisons revealed that patients in subgroup III tended to be younger, while their pathological grades were the most severe. WGCNA detected four gene modules, and the turquoise module, where the dopaminergic synapse pathway was enriched, was related to subgroup I. The neurotrophin signaling pathway and TGF-beta signaling pathway were robustly enriched in the blue and brown modules, respectively, in subgroup III. Moreover, 3 hub genes in subgroup I were negatively correlated with the sum of neurofibrillary tangle (Nft) density. Conversely, hub genes in subgroups II and III exhibited positive correlations with the sum of Nft density. These results provide new pathways and targets for AD treatment.
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Affiliation(s)
- Sha Liu
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, West Huaihai Road 99, Xuzhou, 221002, Jiangsu, China
| | - Yan Lu
- Department of Neurology, The Municipal Hospital, Xuzhou Medical University, Xuzhou, 221116, Jiangsu, China
| | - Deqin Geng
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, West Huaihai Road 99, Xuzhou, 221002, Jiangsu, China.
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Bozinovic G, Feng Z, Shea D, Oleksiak MF. Cardiac physiology and metabolic gene expression during late organogenesis among F. heteroclitus embryo families from crosses between pollution-sensitive and -resistant parents. BMC Ecol Evol 2022; 22:3. [PMID: 34996355 PMCID: PMC8739662 DOI: 10.1186/s12862-022-01959-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 01/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The teleost fish Fundulus heteroclitus inhabit estuaries heavily polluted with persistent and bioaccumulative chemicals. While embryos of parents from polluted sites are remarkably resistant to toxic sediment and develop normally, embryos of parents from relatively clean estuaries, when treated with polluted sediment extracts, are developmentally delayed, displaying deformities characteristic of pollution-induced embryotoxicity. To gain insight into parental effects on sensitive and resistant phenotypes during late organogenesis, we established sensitive, resistant, and crossed embryo families using five female and five male parents from relatively clean and predominantly PAH-polluted estuaries each, measured heart rates, and quantified individual embryo expression of 179 metabolic genes. RESULTS Pollution-induced embryotoxicity manifested as morphological deformities, significant developmental delays, and altered cardiac physiology was evident among sensitive embryos resulting from crosses between females and males from relatively clean estuaries. Significantly different heart rates among several geographically unrelated populations of sensitive, resistant, and crossed embryo families during late organogenesis and pre-hatching suggest site-specific adaptive cardiac physiology phenotypes relative to pollution exposure. Metabolic gene expression patterns (32 genes, 17.9%, at p < 0.05; 11 genes, 6.1%, at p < 0.01) among the embryo families indicate maternal pollutant deposition in the eggs and parental effects on gene expression and metabolic alterations. CONCLUSION Heart rate differences among sensitive, resistant, and crossed embryos is a reliable phenotype for further explorations of adaptive mechanisms. While metabolic gene expression patterns among embryo families are suggestive of parental effects on several differentially expressed genes, a definitive adaptive signature and metabolic cost of resistant phenotypes is unclear and shows unexpected sensitive-resistant crossed embryo expression profiles. Our study highlights physiological and metabolic gene expression differences during a critical embryonic stage among pollution sensitive, resistant, and crossed embryo families, which may contribute to underlying resistance mechanisms observed in natural F. heteroclitus populations living in heavily contaminated estuaries.
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Affiliation(s)
- Goran Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA.
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
| | - Damian Shea
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Marjorie F Oleksiak
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA
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Everett MV, Antal CE, Crawford DL. The effect of short-term hypoxic exposure on metabolic gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL GENETICS AND PHYSIOLOGY 2012; 317:9-23. [PMID: 22021243 PMCID: PMC3237964 DOI: 10.1002/jez.717] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 08/04/2011] [Accepted: 08/24/2011] [Indexed: 11/09/2022]
Abstract
The long-term effect of hypoxia is to decrease both the production and use of ATP and thus decrease the reliance on mitochondrial oxidative energy production. Yet, recent studies include more immediate affects of hypoxia on gene expression and these data suggest the maintenance of mitochondrial function. To better understand the short-term physiological response to hypoxia, we quantified metabolic mRNA expression in the heart ventricles and livers of the teleost fish Fundulus grandis exposed to partial oxygen pressure of 2.8 kPa (-13.5% air saturation).Twenty-eight individuals from a single population were exposed to hypoxia for 0, 4, 8, 12, 24, 48, and 96 hr. Liver and cardiac tissues were sampled from the same individuals at 0-48 hr. At 96 hr, only cardiac tissue was assayed. Gene expression was significantly different (ANOVA, P < 0.05) for 17 of 226 metabolic genes (7.5%) in cardiac tissue and for 20 of 256 (7.8%) metabolic genes in hepatic tissue. For the two tissues examined in this study, the maximum response occurred at different times. For cardiac tissue, using Dunnett's post hoc test, most of these significant differences occurred at 96 hr of exposure. For liver, all but one significant difference occurred at 4 hr. Surprisingly, too many (relative to random expectations) of the genes with significant increase in mRNA are involved in the oxidative phosphorylation pathway: 44% of the significant genes at 96 hr in the heart and 33% of the significant genes at 4 hr in the liver are involved in the oxidative phosphorylation pathway. These data indicate that there are tissue-specific differences in the timing of the response to hypoxia, yet both cardiac and hepatic tissues have increases in mRNA that code for enzyme in the oxidative phosphorylation pathway. If these changes in mRNA produce a similar change in protein, then these data suggest that the initial response to hypoxia involves an increase in the oxidative pathway potentially as a mechanism to maintain ATP production.
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Affiliation(s)
- Meredith V. Everett
- Marine Biology and Fisheries□Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Causeway Miami, FL 33149-1098 USA
| | - Corina E. Antal
- Marine Biology and Fisheries□Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Causeway Miami, FL 33149-1098 USA
| | - Douglas L. Crawford
- Marine Biology and Fisheries□Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Causeway Miami, FL 33149-1098 USA
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Flight PA, Nacci D, Champlin D, Whitehead A, Rand DM. The effects of mitochondrial genotype on hypoxic survival and gene expression in a hybrid population of the killifish, Fundulus heteroclitus. Mol Ecol 2011; 20:4503-20. [PMID: 21980951 DOI: 10.1111/j.1365-294x.2011.05290.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The physiological link between oxygen availability and mitochondrial function is well established. However, whether or not fitness variation is associated with mitochondrial genotypes in the field remains a contested topic in evolutionary biology. In this study, we draw on a population of the teleost fish, Fundulus heteroclitus, where functionally distinct subspecies hybridize, likely as a result of past glacial events. We had two specific aims: (i) to determine the effect of mtDNA genotype on survivorship of male and female fish under hypoxic stress and (ii) to determine the effect of hypoxic stress, sex and mtDNA genotype on gene expression. We found an unexpected and highly significant effect of sex on survivorship under hypoxic conditions, but no significant effect of mtDNA genotype. Gene expression analyses revealed hundreds of transcripts differentially regulated by sex and hypoxia. Mitochondrial transcripts and other predicted pathways were among those influenced by hypoxic stress, and a transcript corresponding to the mtDNA control region was the most highly suppressed transcript under the conditions of hypoxia. An RT-PCR experiment on the control region was consistent with microarray results. Effects of mtDNA sequence variation on genome expression were limited; however, a potentially important epistasis between mtDNA sequence and expression of a nuclear-encoded mitochondrial translation protein was discovered. Overall, these results confirm that mitochondrial regulation is a major component of hypoxia tolerance and further suggest that purifying selection has been the predominant selective force on mitochondrial genomes in these two subspecies.
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Affiliation(s)
- Patrick A Flight
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Box G-W, Providence, RI 02912, USA.
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Bozinovic G, Sit TL, Hinton DE, Oleksiak MF. Gene expression throughout a vertebrate's embryogenesis. BMC Genomics 2011; 12:132. [PMID: 21356103 PMCID: PMC3062618 DOI: 10.1186/1471-2164-12-132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 02/28/2011] [Indexed: 12/25/2022] Open
Abstract
Background Describing the patterns of gene expression during embryonic development has broadened our understanding of the processes and patterns that define morphogenesis. Yet gene expression patterns have not been described throughout vertebrate embryogenesis. This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage. Results Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. Five adjacent stages have disproportionately more significant changes in gene expression (> 200 genes) relative to other stages: four to eight and eight to sixteen cell stages, onset of circulation, pre and post-hatch, and during complete yolk absorption. The fewest differences among adjacent stages occur during gastrulation. Yet, at stage 16, (pre-mid-gastrulation) the largest number of genes has peak expression. This stage has an over representation of genes in oxidative respiration and protein expression (ribosomes, translational genes and proteases). Unexpectedly, among all ribosomal genes, both strong positive and negative correlations occur. Similar correlated patterns of expression occur among all significant genes. Conclusions These data provide statistical support for the temporal dynamics of developmental gene expression during all stages of vertebrate development.
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Affiliation(s)
- Goran Bozinovic
- Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, 27695-7633, USA
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6
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Ecological and genetic assessment of spatial structure among replicate contact zones between two topminnow species. Evol Ecol 2011. [DOI: 10.1007/s10682-011-9461-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Williams LM, Oleksiak MF. Ecologically and evolutionarily important SNPs identified in natural populations. Mol Biol Evol 2011; 28:1817-26. [PMID: 21220761 DOI: 10.1093/molbev/msr004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Evolution by natural selection acts on natural populations amidst migration, gene-by-environmental interactions, constraints, and tradeoffs, which affect the rate and frequency of adaptive change. We asked how many and how rapidly loci change in populations subject to severe, recent environmental changes. To address these questions, we used genomic approaches to identify randomly selected single nucleotide polymorphisms (SNPs) with evolutionarily significant patterns in three natural populations of Fundulus heteroclitus that inhabit and have adapted to highly polluted Superfund sites. Three statistical tests identified 1.4-2.5% of SNPs that were significantly different from the neutral model in each polluted population. These nonneutral patterns in populations adapted to highly polluted environments suggest that these loci or closely linked loci are evolving by natural selection. One SNP identified in all polluted populations using all tests is in the gene for the xenobiotic metabolizing enzyme, cytochrome P4501A (CYP1A), which has been identified previously as being refractory to induction in the three highly polluted populations. Extrapolating across the genome, these data suggest that rapid evolutionary change in natural populations can involve hundreds of loci, a few of which will be shared in independent events.
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Affiliation(s)
- Larissa M Williams
- Department of Environmental and Molecular Toxicology, North Carolina State University, NC, USA
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Whitehead A, Triant DA, Champlin D, Nacci D. Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population. Mol Ecol 2010; 19:5186-203. [PMID: 20874759 DOI: 10.1111/j.1365-294x.2010.04829.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Wild populations of the killifish Fundulus heteroclitus resident in heavily contaminated North American Atlantic coast estuaries have recently and independently evolved dramatic, heritable, and adaptive pollution tolerance. We compared physiological and transcriptome responses to embryonic polychlorinated biphenyl (PCB) exposures between one tolerant population and a nearby sensitive population to gain insight into genomic, physiological and biochemical mechanisms of evolved tolerance in killifish, which are currently unknown. The PCB exposure concentrations at which developmental toxicity emerged, the range of developmental abnormalities exhibited, and global as well as specific gene expression patterns were profoundly different between populations. In the sensitive population, PCB exposures produced dramatic, dose-dependent toxic effects, concurrent with the alterations in the expression of many genes. For example, PCB-mediated cardiovascular system failure was associated with the altered expression of cardiomyocyte genes, consistent with sarcomere mis-assembly. In contrast, genome-wide expression was comparatively refractory to PCB induction in the tolerant population. Tolerance was associated with the global blockade of the aryl hydrocarbon receptor (AHR) signalling pathway, the key mediator of PCB toxicity, in contrast to the strong dose-dependent up-regulation of AHR pathway elements observed in the sensitive population. Altered regulation of signalling pathways that cross-talk with AHR was implicated as one candidate mechanism for the adaptive AHR signalling repression and the pollution tolerance that it affords. In addition to revealing mechanisms of PCB toxicity and tolerance, this study demonstrates the value of comparative transcriptomics to explore molecular mechanisms of stress response and evolved adaptive differences among wild populations.
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Affiliation(s)
- A Whitehead
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
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Louro B, Passos ALS, Souche EL, Tsigenopoulos C, Beck A, Lagnel J, Bonhomme F, Cancela L, Cerdà J, Clark MS, Lubzens E, Magoulas A, Planas JV, Volckaert FA, Reinhardt R, Canario AV. Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers. Mar Genomics 2010; 3:179-91. [DOI: 10.1016/j.margen.2010.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 12/22/2022]
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Whitehead A, Galvez F, Zhang S, Williams LM, Oleksiak MF. Functional genomics of physiological plasticity and local adaptation in killifish. J Hered 2010; 102:499-511. [PMID: 20581107 DOI: 10.1093/jhered/esq077] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation.
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Affiliation(s)
- Andrew Whitehead
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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11
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Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF. SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genet 2010; 11:32. [PMID: 20433726 PMCID: PMC2874759 DOI: 10.1186/1471-2156-11-32] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 04/30/2010] [Indexed: 02/06/2023] Open
Abstract
Background By targeting SNPs contained in both coding and non-coding areas of the genome, we are able to identify genetic differences and characterize genome-wide patterns of variation among individuals, populations and species. We investigated the utility of 454 sequencing and MassARRAY genotyping for population genetics in natural populations of the teleost, Fundulus heteroclitus as well as closely related Fundulus species (F. grandis, F. majalis and F. similis). Results We used 454 pyrosequencing and MassARRAY genotyping technology to identify and type 458 genome-wide SNPs and determine genetic differentiation within and between populations and species of Fundulus. Specifically, pyrosequencing identified 96 putative SNPs across coding and non-coding regions of the F. heteroclitus genome: 88.8% were verified as true SNPs with MassARRAY. Additionally, putative SNPs identified in F. heteroclitus EST sequences were verified in most (86.5%) F. heteroclitus individuals; fewer were genotyped in F. grandis (74.4%), F. majalis (72.9%), and F. similis (60.7%) individuals. SNPs were polymorphic and showed latitudinal clinal variation separating northern and southern populations and established isolation by distance in F. heteroclitus populations. In F. grandis, SNPs were less polymorphic but still established isolation by distance. Markers differentiated species and populations. Conclusions In total, these approaches were used to quickly determine differences within the Fundulus genome and provide markers for population genetic studies.
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Affiliation(s)
- Larissa M Williams
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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12
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Coetzer N, Gazendam I, Oelofse D, Berger DK. SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea. PLANT METHODS 2010; 6:10. [PMID: 20359330 PMCID: PMC2859861 DOI: 10.1186/1746-4811-6-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 04/01/2010] [Indexed: 05/25/2023]
Abstract
BACKGROUND Suppression subtractive hybridization is a popular technique for gene discovery from non-model organisms without an annotated genome sequence, such as cowpea (Vigna unguiculata (L.) Walp). We aimed to use this method to enrich for genes expressed during drought stress in a drought tolerant cowpea line. However, current methods were inefficient in screening libraries and management of the sequence data, and thus there was a need to develop software tools to facilitate the process. RESULTS Forward and reverse cDNA libraries enriched for cowpea drought response genes were screened on microarrays, and the R software package SSHscreen 2.0.1 was developed (i) to normalize the data effectively using spike-in control spot normalization, and (ii) to select clones for sequencing based on the calculation of enrichment ratios with associated statistics. Enrichment ratio 3 values for each clone showed that 62% of the forward library and 34% of the reverse library clones were significantly differentially expressed by drought stress (adjusted p value < 0.05). Enrichment ratio 2 calculations showed that > 88% of the clones in both libraries were derived from rare transcripts in the original tester samples, thus supporting the notion that suppression subtractive hybridization enriches for rare transcripts. A set of 118 clones were chosen for sequencing, and drought-induced cowpea genes were identified, the most interesting encoding a late embryogenesis abundant Lea5 protein, a glutathione S-transferase, a thaumatin, a universal stress protein, and a wound induced protein. A lipid transfer protein and several components of photosynthesis were down-regulated by the drought stress. Reverse transcriptase quantitative PCR confirmed the enrichment ratio values for the selected cowpea genes. SSHdb, a web-accessible database, was developed to manage the clone sequences and combine the SSHscreen data with sequence annotations derived from BLAST and Blast2GO. The self-BLAST function within SSHdb grouped redundant clones together and illustrated that the SSHscreen plots are a useful tool for choosing anonymous clones for sequencing, since redundant clones cluster together on the enrichment ratio plots. CONCLUSIONS We developed the SSHscreen-SSHdb software pipeline, which greatly facilitates gene discovery using suppression subtractive hybridization by improving the selection of clones for sequencing after screening the library on a small number of microarrays. Annotation of the sequence information and collaboration was further enhanced through a web-based SSHdb database, and we illustrated this through identification of drought responsive genes from cowpea, which can now be investigated in gene function studies. SSH is a popular and powerful gene discovery tool, and therefore this pipeline will have application for gene discovery in any biological system, particularly non-model organisms. SSHscreen 2.0.1 and a link to SSHdb are available from http://microarray.up.ac.za/SSHscreen.
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Affiliation(s)
- Nanette Coetzer
- ACGT Computational Biology and Bioinformatics Unit, Department of Biochemistry, University of Pretoria, 0002, South Africa
| | - Inge Gazendam
- Germplasm Development Division, Agricultural Research Council-Vegetable and Ornamental Plant Institute, Private Bag X293, Pretoria, 0001, South Africa
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, 0002, South Africa
| | - Dean Oelofse
- Germplasm Development Division, Agricultural Research Council-Vegetable and Ornamental Plant Institute, Private Bag X293, Pretoria, 0001, South Africa
| | - Dave K Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, 0002, South Africa
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Abstract
Natural populations v. inbred stocks provide a much richer resource for identifying the effects of nucleotide substitutions because natural populations have greater polymorphism. Additionally, natural populations offer an advantage over most common research organisms because they are subject to natural selection, and analyses of these adaptations can be used to identify biologically important changes. Among fishes, these analyses are enhanced by having a wide diversity of species (>28 000 species, more than any other group of vertebrates) living in a huge range of environments (from below freezing to > 46 degrees C, in fresh water to salinities >40 ppt.). Moreover, fishes exhibit many different life-history and reproductive strategies and have many different phenotypes and social structures. Although fishes provide numerous advantages over other vertebrate models, there is still a dearth of available genomic tools for fishes. Fishes make up approximately half of all known vertebrate species, yet <0.2% of fish species have significant genomic resources. Nonetheless, genomic approaches with fishes have provided some of the first measures of individual variation in gene expression and insights into environmental and ecological adaptations. Thus, genomic approaches with natural fish populations have the potential to revolutionize fundamental studies of diverse fish species that offer myriad ecological and evolutionary questions.
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Affiliation(s)
- M F Oleksiak
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL 33149, USA.
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14
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Aubin-Horth N, Renn SCP. Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity. Mol Ecol 2009; 18:3763-80. [PMID: 19732339 DOI: 10.1111/j.1365-294x.2009.04313.x] [Citation(s) in RCA: 256] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenotypic plasticity is the development of different phenotypes from a single genotype, depending on the environment. Such plasticity is a pervasive feature of life, is observed for various traits and is often argued to be the result of natural selection. A thorough study of phenotypic plasticity should thus include an ecological and an evolutionary perspective. Recent advances in large-scale gene expression technology make it possible to also study plasticity from a molecular perspective, and the addition of these data will help answer long-standing questions about this widespread phenomenon. In this review, we present examples of integrative studies that illustrate the molecular and cellular mechanisms underlying plastic traits, and show how new techniques will grow in importance in the study of these plastic molecular processes. These techniques include: (i) heterologous hybridization to DNA microarrays; (ii) next generation sequencing technologies applied to transcriptomics; (iii) techniques for studying the function of noncoding small RNAs; and (iv) proteomic tools. We also present recent studies on genetic model systems that uncover how environmental cues triggering different plastic responses are sensed and integrated by the organism. Finally, we describe recent work on changes in gene expression in response to an environmental cue that persist after the cue is removed. Such long-term responses are made possible by epigenetic molecular mechanisms, including DNA methylation. The results of these current studies help us outline future avenues for the study of plasticity.
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Affiliation(s)
- Nadia Aubin-Horth
- Département de Sciences biologiques, Université de Montréal, Québec, Canada.
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15
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Scott CP, Williams DA, Crawford DL. The effect of genetic and environmental variation on metabolic gene expression. Mol Ecol 2009; 18:2832-43. [PMID: 19500250 PMCID: PMC2705469 DOI: 10.1111/j.1365-294x.2009.04235.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
What is the relationship between genetic or environmental variation and the variation in messenger RNA (mRNA) expression? To address this, microarrays were used to examine the effect of genetic and environmental variation on cardiac mRNA expression for metabolic genes in three groups of Fundulus heteroclitus: (i) individuals sampled in the field (field), (ii) field individuals acclimated for 6 months to laboratory conditions (acclimated), or (iii) individuals bred for 10 successive generations in a laboratory environment (G10). The G10 individuals have significantly less genetic variation than individuals obtained in the field and had a significantly lower variation in mRNA expression across all genes in comparison to the other two groups (P = 0.001). When examining the gene specific variation, 22 genes had variation in expression that was significantly different among groups with lower variation in G10 individuals than in acclimated individuals. Additionally, there were fewer genes with significant differences in expression among G10 individuals vs. either acclimated or field individuals: 66 genes have statistically different levels of expression vs. 107 or 97 for acclimated or field groups. Based on the permutation of the data, these differences in the number of genes with significant differences among individuals within a group are unlikely to occur by chance (P < 0.01). Surprisingly, variation in mRNA expression in field individuals is lower than in acclimated individuals. Relative to the variation among individual within a group, few genes have significant differences in expression among groups (seven, 2.3%) and none of these are different between acclimated and field individuals. The results support the concept that genetic variation affects variation in mRNA expression and also suggests that temporal environmental variation associated with estuarine environments does not increase the variation among individuals or add to the differences among groups.
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Affiliation(s)
- Cinda P Scott
- Department of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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Scott CP, VanWye J, McDonald MD, Crawford DL. Technical analysis of cDNA microarrays. PLoS One 2009; 4:e4486. [PMID: 19221589 PMCID: PMC2637424 DOI: 10.1371/journal.pone.0004486] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 11/20/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND There is extensive variation in gene expression among individuals within and between populations. Accurate measures of the variation in mRNA expression using microarrays can be confounded by technical variation, which includes variation in RNA isolation procedures, day of hybridization and methods used to amplify and dye label RNA for hybridization. METHODOLOGY/PRINCIPAL FINDINGS In this manuscript we analyze the relationship between the amount of mRNA and the fluorescent signal from the microarray hybridizations demonstrating that for a wide-range of mRNA concentrations the fluorescent signal is a linear function of the amount of mRNA. Additionally, the separate isolation, labeling or hybridization of RNA does not add significant amounts of variation in microarray measures of gene expression. However, single or double rounds of amplification for labeling do have small but significant affects on 10% of genes, but this source of technical variation is easy to avoid. To examine both technical and stochastic biological variation, mRNA expression was measured from the same five individuals over a six-week time course. CONCLUSION There were few, if any, meaningful differences in gene expression among time points. Thus, microarray measures using standard laboratory procedures can be precise and quantitative and are not subject to significant random biological noise.
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Affiliation(s)
- Cinda P. Scott
- Department of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, United States of America
| | - Jeff VanWye
- Department of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, United States of America
| | - M. Danielle McDonald
- Department of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, United States of America
| | - Douglas L. Crawford
- Department of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, United States of America
- * E-mail:
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Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 2008; 138:433-51. [PMID: 18931921 DOI: 10.1007/s10709-008-9326-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
Abstract
Next generation sequencing technology affords new opportunities in ecological genetics. This paper addresses how an ecological genetics research program focused on a phenotype of interest can quickly move from no genetic resources to having various functional genomic tools. 454 sequencing and its error rates are discussed, followed by a review of de novo transcriptome assemblies focused on the first successful de novo assembly which happens to be in an ecological model system (the Glanville fritillary butterfly). The potential future developments in 454 sequencing are also covered. Particular attention is paid to the difficulties ecological geneticists are likely to encounter through reviewing relevant studies in both model and non-model systems. Various post-sequencing issues and applications of 454 generated data are presented (e.g. database management, microarray construction, molecular marker and candidate gene development). How to use species with genomic resources to inform study of those without is also discussed. In closing, some of the drawbacks of 454 sequencing are presented along with future prospects of this technology.
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18
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Dios S, Novoa B, Buonocore F, Scapigliati G, Figueras A. Genomic Resources for Immunology and Disease of Salmonid and Non-Salmonid Fish. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10641260802325484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Pardo BG, Fernández C, Millán A, Bouza C, Vázquez-López A, Vera M, Alvarez-Dios JA, Calaza M, Gómez-Tato A, Vázquez M, Cabaleiro S, Magariños B, Lemos ML, Leiro JM, Martínez P. Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens. BMC Vet Res 2008; 4:37. [PMID: 18817567 PMCID: PMC2569028 DOI: 10.1186/1746-6148-4-37] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 09/25/2008] [Indexed: 11/30/2022] Open
Abstract
Background The turbot (Scophthalmus maximus; Scophthalmidae; Pleuronectiformes) is a flatfish species of great relevance for marine aquaculture in Europe. In contrast to other cultured flatfish, very few genomic resources are available in this species. Aeromonas salmonicida and Philasterides dicentrarchi are two pathogens that affect turbot culture causing serious economic losses to the turbot industry. Little is known about the molecular mechanisms for disease resistance and host-pathogen interactions in this species. In this work, thousands of ESTs for functional genomic studies and potential markers linked to ESTs for mapping (microsatellites and single nucleotide polymorphisms (SNPs)) are provided. This information enabled us to obtain a preliminary view of regulated genes in response to these pathogens and it constitutes the basis for subsequent and more accurate microarray analysis. Results A total of 12584 cDNAs partially sequenced from three different cDNA libraries of turbot (Scophthalmus maximus) infected with Aeromonas salmonicida, Philasterides dicentrarchi and from healthy fish were analyzed. Three immune-relevant tissues (liver, spleen and head kidney) were sampled at several time points in the infection process for library construction. The sequences were processed into 9256 high-quality sequences, which constituted the source for the turbot EST database. Clustering and assembly of these sequences, revealed 3482 different putative transcripts, 1073 contigs and 2409 singletons. BLAST searches with public databases detected significant similarity (e-value ≤ 1e-5) in 1766 (50.7%) sequences and 816 of them (23.4%) could be functionally annotated. Two hundred three of these genes (24.9%), encoding for defence/immune-related proteins, were mostly identified for the first time in turbot. Some ESTs showed significant differences in the number of transcripts when comparing the three libraries, suggesting regulation in response to these pathogens. A total of 191 microsatellites, with 104 having sufficient flanking sequences for primer design, and 1158 putative SNPs were identified from these EST resources in turbot. Conclusion A collection of 9256 high-quality ESTs was generated representing 3482 unique turbot sequences. A large proportion of defence/immune-related genes were identified, many of them regulated in response to specific pathogens. Putative microsatellites and SNPs were identified. These genome resources constitute the basis to develop a microarray for functional genomics studies and marker validation for genetic linkage and QTL analysis in turbot.
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Affiliation(s)
- Belén G Pardo
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
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20
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Hirayama M, Ahsan MN, Mitani H, Watabe S. CYR61 is a novel gene associated with temperature-dependent changes in fish metabolism as revealed by cDNA microarray analysis on a medaka Oryzias latipes cell line. J Cell Biochem 2008; 104:1297-310. [PMID: 18286541 DOI: 10.1002/jcb.21708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A microarray comprising 3,514 cDNAs was constructed from a medaka EST library to elucidate the transcriptional responses associated with temperature shift from 25 to 15 degrees C in a medaka cell line. Microarray analysis revealed that the mRNA levels of 313 clones were significantly different in at least one combination of different incubation periods up to 7 days at a given incubation temperature or between 25 and 15 degrees C at a given incubation period (P < 0.05). These genes are known to be associated with various biological processes including morphogenesis, cell proliferation and response to stress. A number of genes encoding proteins which localize in extracellular areas were apparently up-regulated at 15 degrees C, whereas those localizing in intracellular areas were down-regulated at this temperature. In addition, while a number of genes represented long-term expression changes, only a few responded to short-term inductions. A typical example was CYR61, a multifunctional matricellular signaling modulator, the mRNA levels of which increased after temperature shift from 25 to 15 degrees C in 3 h, and then decreased rapidly to near the original level within 12 h. Another series of analyses by quantitative reverse transcription-PCR revealed that the mRNA levels of CYR61 at 5 degrees C were significantly higher even at 24 h after temperature shift compared to those of the cells successively maintained at 25 degrees C. These analyses suggest that remodeling and reorganizing of extracellular structure of cells are important to offset the low temperature effect and CYR61 is considered to be a novel gene associated with temperature response in poikilotherms.
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Affiliation(s)
- Makoto Hirayama
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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21
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Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008; 17:1636-47. [PMID: 18266620 DOI: 10.1111/j.1365-294x.2008.03666.x] [Citation(s) in RCA: 580] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present a de novo assembly of a eukaryote transcriptome using 454 pyrosequencing data. The Glanville fritillary butterfly (Melitaea cinxia; Lepidoptera: Nymphalidae) is a prominent species in population biology but had no previous genomic data. Sequencing runs using two normalized complementary DNA collections from a genetically diverse pool of larvae, pupae, and adults yielded 608,053 expressed sequence tags (mean length = 110 nucleotides), which assembled into 48,354 contigs (sets of overlapping DNA segments) and 59,943 singletons. BLAST comparisons confirmed the accuracy of the sequencing and assembly, and indicated the presence of c. 9000 unique genes, along with > 6000 additional microarray-confirmed unannotated contigs. Average depth of coverage was 6.5-fold for the longest 4800 contigs (348-2849 bp in length), sufficient for detecting large numbers of single nucleotide polymorphisms. Oligonucleotide microarray probes designed from the assembled sequences showed highly repeatable hybridization intensity and revealed biological differences among individuals. We conclude that 454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost-effective, and reliable method for development of functional genomic tools for nonmodel species. This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies.
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Affiliation(s)
- J Cristobal Vera
- Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA.
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22
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Dong W, Willett KL. Local expression of CYP19A1 and CYP19A2 in developing and adult killifish (Fundulus heteroclitus). Gen Comp Endocrinol 2008; 155:307-17. [PMID: 17582409 PMCID: PMC2254941 DOI: 10.1016/j.ygcen.2007.05.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 04/12/2007] [Accepted: 05/07/2007] [Indexed: 11/24/2022]
Abstract
P450 aromatase (CYP19) is the terminal enzyme in the steroidogenic pathway and catalyzes the conversion of androgens to estrogens. Fundulus heteroclitus like other teleosts, express two CYP19 genes, CYP19A1 and CYP19A2. The expression of CYP19s in Fundulus was measured by in situ hybridization throughout development. In 90 dpf (day post-fertilization) fish and adult fish, CYP19A1 was expressed in the ooplasm of early stage I oocytes (primary growth stage). Expression of CYP19A1 was localized in the follicle cell layer of late stage I (previtellogenic stage) and stage II (vitellogenic stage) follicles, but by stage III (early maturational follicles) CYP19A1 expression was localized in the vitelline envelope. Overall, CYP19A1 oocyte membrane expression gradually declined from highest expression at late stage I to nondetectable levels by stage IV. Highest expression of CYP19A2 was detected in the brain including the hypothalamus from 4, 6, 8, 10, 14 dpf embryos, 90 dpf fry fish and adult fish brain. In females compared to males, there was higher CYP19A2 expression in olfactory bulb. In addition to the brain, there was strong CYP19A2 signal in adrenal/kidney cells in 6-14 dpf embryos. This work establishes the localization and constitutive expression of CYP19s in Fundulus which can then be compared with potential disruption of CYP19A1 and CYP19A2 expression and physiological consequences caused by environmental contaminants.
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Affiliation(s)
- Wu Dong
- Department of Pharmacology and Environmental Toxicology Research Program, School of Pharmacy, The University of Mississippi, 315 Faser Hall, Box 1848, University, MS 38677, USA
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23
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Burnett KG, Bain LJ, Baldwin WS, Callard GV, Cohen S, Di Giulio RT, Evans DH, Gómez-Chiarri M, Hahn ME, Hoover CA, Karchner SI, Katoh F, MacLatchy DL, Marshall WS, Meyer JN, Nacci DE, Oleksiak MF, Rees BB, Singer TD, Stegeman JJ, Towle DW, Van Veld PA, Vogelbein WK, Whitehead A, Winn RN, Crawford DL. Fundulus as the premier teleost model in environmental biology: opportunities for new insights using genomics. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2007; 2:257-86. [PMID: 18071578 PMCID: PMC2128618 DOI: 10.1016/j.cbd.2007.09.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms.
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Affiliation(s)
- Karen G. Burnett
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson, Charleston, SC 29412, USA
| | - Lisa J. Bain
- Clemson Institute of Environmental Toxicology, Clemson University; Pendleton, SC 29670, USA
| | - William S. Baldwin
- Clemson Institute of Environmental Toxicology, Clemson University; Pendleton, SC 29670, USA
| | | | - Sarah Cohen
- Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, CA 94120, USA
| | - Richard T. Di Giulio
- Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC, USA
| | - David H. Evans
- Department of Zoology, University of Florida, Gainesville, FL 32611, USA
| | - Marta Gómez-Chiarri
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, Kingston, RI 02881, USA
| | - Mark E. Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Sibel I. Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Fumi Katoh
- Department of Biology, St. Francis Xavier University, Antigonish, N.S. B2G 2W5, Canada
| | - Deborah L. MacLatchy
- Faculty of Science, Wilfred Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - William S. Marshall
- Department of Biology, St. Francis Xavier University, Antigonish, N.S. B2G 2W5, Canada
| | - Joel N. Meyer
- Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC, USA
| | - Diane E. Nacci
- US Environmental Protection Agency Office of Research and Development, Narragansett, RI 02882, USA
| | - Marjorie F. Oleksiak
- Rosenstiel School of Marine & Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Bernard B. Rees
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Thomas D. Singer
- School of Optometry, University of Waterloo, Waterloo, ON, N2L 3G1, CANADA
| | - John J. Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - David W. Towle
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, Maine 04672, USA
| | - Peter A. Van Veld
- The College of William and Mary, Virginia Institute of Marine Science, Gloucester Point, VA 23062, USA
| | - Wolfgang K. Vogelbein
- The College of William and Mary, Virginia Institute of Marine Science, Gloucester Point, VA 23062, USA
| | - Andrew Whitehead
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Richard N. Winn
- Aquatic Biotechnology and Environmental Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Douglas L. Crawford
- Rosenstiel School of Marine & Atmospheric Science, University of Miami, Miami, FL 33149, USA
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24
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Gaj S, van Erk A, van Haaften RIM, Evelo CTA. Linking microarray reporters with protein functions. BMC Bioinformatics 2007; 8:360. [PMID: 17897448 PMCID: PMC2140066 DOI: 10.1186/1471-2105-8-360] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 09/26/2007] [Indexed: 11/17/2022] Open
Abstract
Background The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. Results This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Conclusion Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/.
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Affiliation(s)
- Stan Gaj
- Nutrigenomics Consortium, Top Institute Food and Nutrition, Wageningen, The Netherlands
- BiGCaT Bioinformatics, University Maastricht, Maastricht, The Netherlands
- Department of Human Biology, Nutrition and Toxicology Research Institute Maastricht (NUTRIM), University Maastricht, Maastricht, The Netherlands
| | - Arie van Erk
- BiGCaT Bioinformatics, University Maastricht, Maastricht, The Netherlands
- Laboratory of Experimental & Molecular Cardiology, The Interuniversity Cardiovascular institute of the Netherlands (ICIN), University Maastricht, Maastricht, The Netherlands
| | | | - Chris TA Evelo
- BiGCaT Bioinformatics, University Maastricht, Maastricht, The Netherlands
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25
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Dreyer C, Hoffmann M, Lanz C, Willing EM, Riester M, Warthmann N, Sprecher A, Tripathi N, Henz SR, Weigel D. ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata. BMC Genomics 2007; 8:269. [PMID: 17686157 PMCID: PMC1994688 DOI: 10.1186/1471-2164-8-269] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 08/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The guppy, Poecilia reticulata, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available. RESULTS With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes. CONCLUSION Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.
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Affiliation(s)
- Christine Dreyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Margarete Hoffmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Eva-Maria Willing
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Markus Riester
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Andrea Sprecher
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Namita Tripathi
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Stefan R Henz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D72076, Germany
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RICHARDSON DAVIDE, VANWYE JEFFREYD, EXUM AMYM, COWEN ROBERTK, CRAWFORD DOUGLASL. High-throughput species identification: from DNA isolation to bioinformatics. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01620.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Oleksiak MF, Roach JL, Crawford DL. Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat Genet 2004; 37:67-72. [PMID: 15568023 PMCID: PMC1447534 DOI: 10.1038/ng1483] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 11/01/2004] [Indexed: 11/08/2022]
Abstract
Individual variation in gene expression is important for evolutionary adaptation and susceptibility to diseases and pathologies. In this study, we address the functional importance of this variation by comparing cardiac metabolism to patterns of mRNA expression using microarrays. There is extensive variation in both cardiac metabolism and the expression of metabolic genes among individuals of the teleost fish Fundulus heteroclitus from natural outbred populations raised in a common environment: metabolism differed among individuals by a factor of more than 2, and expression levels of 94% of genes were significantly different (P < 0.01) between individuals in a population. This unexpectedly high variation in metabolic gene expression explains much of the variation in metabolism, suggesting that it is biologically relevant. The patterns of gene expression that are most important in explaining cardiac metabolism differ between groups of individuals. Apparently, the variation in metabolism seems to be related to different patterns of gene expression in the different groups of individuals. The magnitude of differences in gene expression in these groups is not important; large changes in expression have no greater predictive value than small changes. These data suggest that variation in physiological performance is related to the subtle variation in gene expression and that this relationship differs among individuals.
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Affiliation(s)
- Marjorie F Oleksiak
- Department of Environmental & Molecular Toxicology, North Carolina State University, Raleigh, North Carolina 27695-7633, USA
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