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Kaganer AW, Ossiboff RJ, Keith NI, Schuler KL, Comizzoli P, Hare MP, Fleischer RC, Gratwicke B, Bunting EM. Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220810. [PMID: 36756057 PMCID: PMC9890126 DOI: 10.1098/rsos.220810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited understanding of amphibian host, Bd and microbiome interactions. We conducted a vaccination and infection experiment using Eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) challenged with Bd to observe infection, skin microbial communities and gene expression of host skin, pathogen and microbiome throughout the experiment. Most animals survived high Bd loads regardless of their vaccination status and vaccination did not affect pathogen load, but host gene expression differed based on vaccination. Oral vaccination (exposure to killed Bd) stimulated immune gene upregulation while topically and sham-vaccinated animals did not significantly upregulate immune genes. In early infection, topically vaccinated animals upregulated immune genes but orally and sham-vaccinated animals downregulated immune genes. Bd increased pathogenicity-associated gene expression in late infection when Bd loads were highest. The microbiome was altered by Bd, but there was no correlation between anti-Bd microbe abundance or richness and pathogen burden. Our observations suggest that hellbenders initially generate a vigorous immune response to Bd, which is ineffective at controlling disease and is subsequently modulated. Interactions with antifungal skin microbiota did not influence disease progression.
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Affiliation(s)
- Alyssa W. Kaganer
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
| | - Robert J. Ossiboff
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Nicole I. Keith
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Biology Department, Hamilton College, Clinton, NY, 13323, USA
| | - Krysten L. Schuler
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierre Comizzoli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Matthew P. Hare
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Robert C. Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
| | - Elizabeth M. Bunting
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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2
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Sex differences in immune gene expression in the brain of a small shorebird. Immunogenetics 2022; 74:487-496. [PMID: 35084547 PMCID: PMC8792134 DOI: 10.1007/s00251-022-01253-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/17/2022] [Indexed: 11/30/2022]
Abstract
Males and females often exhibit differences in behaviour, life histories, and ecology, many of which are typically reflected in their brains. Neuronal protection and maintenance include complex processes led by the microglia, which also interacts with metabolites such as hormones or immune components. Despite increasing interest in sex-specific brain function in laboratory animals, the significance of sex-specific immune activation in the brain of wild animals along with the variables that could affect it is widely lacking. Here, we use the Kentish plover (Charadrius alexandrinus) to study sex differences in expression of immune genes in the brain of adult males and females, in two wild populations breeding in contrasting habitats: a coastal sea-level population and a high-altitude inland population in China. Our analysis yielded 379 genes associated with immune function. We show a significant male-biased immune gene upregulation. Immune gene expression in the brain did not differ in upregulation between the coastal and inland populations. We discuss the role of dosage compensation in our findings and their evolutionary significance mediated by sex-specific survival and neuronal deterioration. Similar expression profiles in the coastal and inland populations suggest comparable genetic control by the microglia and possible similarities in pathogen pressures between habitats. We call for further studies on gene expression of males and females in wild population to understand the implications of immune function for life-histories and demography in natural systems.
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3
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Savage AE, Gratwicke B, Hope K, Bronikowski E, Fleischer RC. Sustained immune activation is associated with susceptibility to the amphibian chytrid fungus. Mol Ecol 2020; 29:2889-2903. [PMID: 32700351 DOI: 10.1111/mec.15533] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/06/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
The disease chytridiomycosis caused by the fungus Bd has devastated amphibian populations worldwide. Functional genomic contributions to host susceptibility remain enigmatic and vary between species and populations. We conducted experimental Bd infections in Rana yavapaiensis, a species with intraspecific variation in chytridiomycosis susceptibility, to assess the skin and spleen transcriptomic response to infection over time. We predicted that increased immune gene expression would be associated with a positive disease outcome, but we instead found that surviving frogs had significantly reduced immune gene expression compared to susceptible frogs and to uninfected controls. MHC class IIβ gene expression was also significantly higher in susceptible frogs compared to surviving frogs. Furthermore, susceptible frogs expressed a significantly larger number of distinct class IIβ alleles, demonstrating a negative correlation between class IIβ expression, functional diversity, and survival. Expression of the MHC class IIβ locus previously associated with Bd disease outcomes was a significant predictor of Bd infection intensity at early infection stages but not at late infection stages, suggesting initial MHC-linked immune processes are important for ultimate disease outcomes. We infer through disease association and phylogenetic analysis that certain MHC variants are linked to the immune expression that was negatively associated with survival, and we hypothesize that frogs that did not express these alleles could better survive infections. Our study finds that MHC expression at early and late infection stages predicts Bd infection intensity, and suggests that generating a sustained immune response against Bd may be counterproductive for surviving chytridiomycosis in this partially susceptible species.
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Affiliation(s)
- Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Brian Gratwicke
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Katharine Hope
- Center for Animal Care Sciences, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Edward Bronikowski
- Center for Animal Care Sciences, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
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4
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Ellison A, Zamudio K, Lips K, Muletz‐Wolz C. Temperature‐mediated shifts in salamander transcriptomic responses to the amphibian‐killing fungus. Mol Ecol 2020; 29:325-343. [DOI: 10.1111/mec.15327] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/04/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Amy Ellison
- School of Natural Sciences Bangor University Bangor UK
| | - Kelly Zamudio
- Department of Ecology & Evolutionary Biology Cornell University Ithaca NY USA
| | - Karen Lips
- Department of Biology University of Maryland College Park MD USA
| | - Carly Muletz‐Wolz
- Department of Biology University of Maryland College Park MD USA
- Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park Washington DC USA
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5
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Bast J, Parker DJ, Dumas Z, Jalvingh KM, Tran Van P, Jaron KS, Figuet E, Brandt A, Galtier N, Schwander T. Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Mol Biol Evol 2019; 35:1668-1677. [PMID: 29659991 PMCID: PMC5995167 DOI: 10.1093/molbev/msy058] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recombination is a fundamental process with significant impacts on genome evolution. Predicted consequences of the loss of recombination include a reduced effectiveness of selection, changes in the amount of neutral polymorphisms segregating in populations, and an arrest of GC-biased gene conversion. Although these consequences are empirically well documented for nonrecombining genome portions, it remains largely unknown if they extend to the whole genome scale in asexual organisms. We identify the consequences of asexuality using de novo transcriptomes of five independently derived, obligately asexual lineages of stick insects, and their sexual sister-species. We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
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Affiliation(s)
- Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kirsten M Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emeric Figuet
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Nicolas Galtier
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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6
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Survival, gene and metabolite responses of Litoria verreauxii alpina frogs to fungal disease chytridiomycosis. Sci Data 2018; 5:180033. [PMID: 29509187 PMCID: PMC5839156 DOI: 10.1038/sdata.2018.33] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
The fungal skin disease chytridiomycosis has caused the devastating decline and extinction of hundreds of amphibian species globally, yet the potential for evolving resistance, and the underlying pathophysiological mechanisms remain poorly understood. We exposed 406 naïve, captive-raised alpine tree frogs (Litoria verreauxii alpina) from multiple populations (one evolutionarily naïve to chytridiomycosis) to the aetiological agent Batrachochytrium dendrobatidis in two concurrent and controlled infection experiments. We investigated (A) survival outcomes and clinical pathogen burdens between populations and clutches, and (B) individual host tissue responses to chytridiomycosis. Here we present multiple interrelated datasets associated with these exposure experiments, including animal signalment, survival and pathogen burden of 355 animals from Experiment A, and the following datasets related to 61 animals from Experiment B: animal signalment and pathogen burden; raw RNA-Seq reads from skin, liver and spleen tissues; de novo assembled transcriptomes for each tissue type; raw gene expression data; annotation data for each gene; and raw metabolite expression data from skin and liver tissues. These data provide an extensive baseline for future analyses.
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7
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Grogan LF, Cashins SD, Skerratt LF, Berger L, McFadden MS, Harlow P, Hunter DA, Scheele BC, Mulvenna J. Evolution of resistance to chytridiomycosis is associated with a robust early immune response. Mol Ecol 2018; 27:919-934. [DOI: 10.1111/mec.14493] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/30/2017] [Accepted: 09/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Laura F. Grogan
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
- Griffith Wildlife Disease Ecology Group Environmental Futures Research Institute School of Environment Griffith University Nathan QLD Australia
- Genetics and Computational Biology QIMR Berghofer Medical Research Institute Brisbane QLD Australia
| | - Scott D. Cashins
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
| | - Lee F. Skerratt
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
| | - Lee Berger
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
| | | | - Peter Harlow
- Taronga Conservation Society Australia Mosman NSW Australia
| | - David A. Hunter
- Ecosystems and Threatened Species South West Region Office of Environment and Heritage NSW Department of Premier and Cabinet Queanbeyan NSW Australia
| | - Ben C. Scheele
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
- Fenner School of Environment and Society Australian National University Canberra ACT Australia
| | - Jason Mulvenna
- Genetics and Computational Biology QIMR Berghofer Medical Research Institute Brisbane QLD Australia
- School of Biomedical Sciences The University of Queensland Brisbane QLD Australia
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8
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Seasonal differences in the testicular transcriptome profile of free-living European beavers (Castor fiber L.) determined by the RNA-Seq method. PLoS One 2017; 12:e0180323. [PMID: 28678806 PMCID: PMC5498055 DOI: 10.1371/journal.pone.0180323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/14/2017] [Indexed: 11/20/2022] Open
Abstract
The European beaver (Castor fiber L.) is an important free-living rodent that inhabits Eurasian temperate forests. Beavers are often referred to as ecosystem engineers because they create or change existing habitats, enhance biodiversity and prepare the environment for diverse plant and animal species. Beavers are protected in most European Union countries, but their genomic background remains unknown. In this study, gene expression patterns in beaver testes and the variations in genetic expression in breeding and non-breeding seasons were determined by high-throughput transcriptome sequencing. Paired-end sequencing in the Illumina HiSeq 2000 sequencer produced a total of 373.06 million of high-quality reads. De novo assembly of contigs yielded 130,741 unigenes with an average length of 1,369.3 nt, N50 value of 1,734, and average GC content of 46.51%. A comprehensive analysis of the testicular transcriptome revealed more than 26,000 highly expressed unigenes which exhibited the highest homology with Rattus norvegicus and Ictidomys tridecemlineatus genomes. More than 8,000 highly expressed genes were found to be involved in fundamental biological processes, cellular components or molecular pathways. The study also revealed 42 genes whose regulation differed between breeding and non-breeding seasons. During the non-breeding period, the expression of 37 genes was up-regulated, and the expression of 5 genes was down-regulated relative to the breeding season. The identified genes encode molecules which are involved in signaling transduction, DNA repair, stress responses, inflammatory processes, metabolism and steroidogenesis. Our results pave the way for further research into season-dependent variations in beaver testes.
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9
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Dean R, Wright AE, Marsh‐Rollo SE, Nugent BM, Alonzo SH, Mank JE. Sperm competition shapes gene expression and sequence evolution in the ocellated wrasse. Mol Ecol 2016; 26:505-518. [DOI: 10.1111/mec.13919] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/31/2016] [Accepted: 11/03/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Rebecca Dean
- Department of Genetics, Evolution and Environment University College London London UK
- School of Biological Sciences Monash University Clayton VIC Australia
| | - Alison E. Wright
- Department of Genetics, Evolution and Environment University College London London UK
| | - Susan E. Marsh‐Rollo
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
- Department of Psychology Neuroscience & Behaviour McMaster University Hamilton Ontario Canada
| | - Bridget M. Nugent
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Department of Biomedical Sciences University of Pennsylvania Philadelphia PA USA
| | - Suzanne H. Alonzo
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Judith E. Mank
- Department of Genetics, Evolution and Environment University College London London UK
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10
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Vizán-Rico HI, Gómez-Zurita J. Testis-specific RNA-Seq of Calligrapha (Chrysomelidae) as a transcriptomic resource for male-biased gene inquiry in Coleoptera. Mol Ecol Resour 2016; 17:533-545. [PMID: 27288908 DOI: 10.1111/1755-0998.12554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
Abstract
We report the architecture of testis transcriptomes of four closely related species of Calligrapha (Chrysomelidae) beetles, which diverged during the last 3 million years. Five cDNA libraries were sequenced using Illumina HiSeq technology, retrieving 102 884-176 514 assembled contigs, of which ~33-45% of these longer than 499 nt were functionally annotated. Annotation and sequence similarity comparisons of these libraries revealed high homogeneity in gene composition and the presence of several functional candidates related to reproduction or reproductive processes (0.72-1.08% of annotated sequences). Stringent sequence similarity analyses of these transcriptomes against empirically demonstrated male-biased genes in Drosophila melanogaster and Tribolium castaneum allowed the identification of 77 homologues in Calligrapha, possible candidates of male-biased expression. Some of these genes - including CG9313, Tektin-A or tomboy40 - were confirmed as orthologs of these male-biased genes using phylogenetic inference and available model insect data, increasing our confidence that they represent functional homologues too. Our transcriptomes are a valuable transcriptomic resource for the analysis of male-biased genes in Calligrapha, which has the added interest of including several female-only species. But it simultaneously represents a landmark for similar studies in Coleoptera, broadening the taxonomic diversity currently represented by the model species T. castaneum, and incipient genomic data in other herbivorous lineages, including weevils, longhorn beetles and leaf beetles.
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Affiliation(s)
- Helena I Vizán-Rico
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Univ. Pompeu Fabra), Barcelona, 08003, Spain
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Univ. Pompeu Fabra), Barcelona, 08003, Spain
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11
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Rispe C, Legeai F, Papura D, Bretaudeau A, Hudaverdian S, Le Trionnaire G, Tagu D, Jaquiéry J, Delmotte F. De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms. BMC Genomics 2016; 17:219. [PMID: 26968158 PMCID: PMC4787006 DOI: 10.1186/s12864-016-2530-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/24/2016] [Indexed: 11/28/2022] Open
Abstract
Background Grapevine phylloxera, an insect related to true aphids, is a major historic pest of viticulture only controlled through the selection of resistant rootstocks or through quarantine regulations where grapevine is cultivated own-rooted. Transcriptomic data could help understand the bases of its original life-traits, including a striking case of polyphenism, with forms feeding on roots and forms feeding in leaf-galls. Comparisons with true aphids (for which complete genomes have been sequenced) should also allow to link differences in life-traits of the two groups with changes in gene repertoires or shifts in patterns of expression. Results We sequenced transcriptomes of the grapevine phylloxera (Illumina technology), choosing three life-stages (adults on roots or on leaf galls, and eggs) to cover a large catalogue of transcripts, and performed a de novo assembly. This resulted in 105,697 contigs, which were annotated: most contigs had a best blastx hit to the pea aphid (phylogenetically closest complete genome), while very few bacterial hits were recorded (except for Probionibacterium acnes). Coding sequences were predicted from this data set (17,372 sequences), revealing an extremely high AT-bias (at the third codon position). Differential expression (DE) analysis among root-feeding and gall-feeding showed that i) the root-feeding form displayed a much larger number of differentially expressed transcripts ii) root-feeding biased genes were enriched in some categories, for example cuticular proteins and genes associated with cell-cell signaling iii) leaf-galling-biased genes were enriched in genes associated with the nucleus and DNA-replication, suggesting a metabolism more oriented towards fast and active multiplication. We also identified a gene family with a very high expression level (copies totaling nearly 10 % of the reads) in the grapevine phylloxera (both in root and leaf galling forms), but usually expressed at very low levels in true aphids (except in sexual oviparous females). These transcripts thus appear to be associated with oviparity. Conclusions Our study illustrated major intraspecific changes in transcriptome profiles, related with different life-styles (and the feeding on roots versus in leaf-galls). At a different scale, we could also illustrate one major shift in expression levels associated with changes in life-traits that occurred along evolution and that respectively characterize (strictly oviparous) grapevine phylloxera and (mostly viviparous) true aphids. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2530-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claude Rispe
- Present Address: BIOEPAR, INRA, Oniris, La Chantrerie, F-44307, Nantes, France. .,IGEPP, INRA, F-35653, Le Rheu cedex, France.
| | - Fabrice Legeai
- IGEPP, BIPAA, INRA, Campus Beaulieu, Rennes, France.,Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes, France
| | | | - Anthony Bretaudeau
- IGEPP, BIPAA, INRA, Campus Beaulieu, Rennes, France.,Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genouest, Campus Beaulieu, Rennes, France
| | | | | | - Denis Tagu
- IGEPP, INRA, F-35653, Le Rheu cedex, France
| | - Julie Jaquiéry
- IGEPP, INRA, F-35653, Le Rheu cedex, France.,Present address: University of Rennes 1, UMR CNRS 6553 EcoBio, 35042, Rennes, France
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12
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Ockendon NF, O'Connell LA, Bush SJ, Monzón-Sandoval J, Barnes H, Székely T, Hofmann HA, Dorus S, Urrutia AO. Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes. Mol Ecol Resour 2015; 16:446-58. [PMID: 26358618 PMCID: PMC4982090 DOI: 10.1111/1755-0998.12465] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 08/01/2015] [Accepted: 08/14/2015] [Indexed: 01/10/2023]
Abstract
Next‐generation sequencing methods, such as RNA‐seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA‐seq annotation methods using reference genomes from related species have yet to be robustly characterized. Here we conduct a comprehensive power analysis employing RNA‐seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping (DGM), where transcript short reads are aligned directly to the reference genome, significantly outperforms the widely used de novo and guided assembly‐based methods in both the quantity and accuracy of gene detection. Our analysis also reveals that DGM recovers a more representative profile of Gene Ontology functional categories, which are often used to interpret emergent patterns in genomewide expression analyses. Lastly, analysis of available primate RNA‐seq data demonstrates the applicability of our observations across diverse taxa. Our quantification of annotation accuracy and reduced gene detection associated with sequence divergence thus provides empirically derived guidelines for the design of future gene expression studies in species without sequenced genomes.
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Affiliation(s)
- Nina F Ockendon
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.,Milner Centre, University of Bath, Bath, BA2 7AY, UK
| | - Lauren A O'Connell
- FAS Centre for Systems Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Stephen J Bush
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.,Milner Centre, University of Bath, Bath, BA2 7AY, UK
| | - Jimena Monzón-Sandoval
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.,Milner Centre, University of Bath, Bath, BA2 7AY, UK
| | - Holly Barnes
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.,Milner Centre, University of Bath, Bath, BA2 7AY, UK
| | - Tamás Székely
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.,Milner Centre, University of Bath, Bath, BA2 7AY, UK
| | - Hans A Hofmann
- Center for Computational Biology and Bioinformatics, Department of Integrative Biology, The University of Texas, Austin, TX, 78712, USA
| | - Steve Dorus
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
| | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.,Milner Centre, University of Bath, Bath, BA2 7AY, UK
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13
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Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation. Genetics 2015; 201:587-98. [PMID: 26245831 DOI: 10.1534/genetics.115.179234] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/27/2015] [Indexed: 11/18/2022] Open
Abstract
Regional variation in sex-specific gene regulation has been observed across sex chromosomes in a range of animals and is often a function of sex chromosome age. The avian Z chromosome exhibits substantial regional variation in sex-specific regulation, where older regions show elevated levels of male-biased expression. Distinct sex-specific regulation also has been observed across the male hypermethylated (MHM) region, which has been suggested to be a region of nascent dosage compensation. Intriguingly, MHM region regulatory features have not been observed in distantly related avian species despite the hypothesis that it is situated within the oldest region of the avian Z chromosome and is therefore orthologous across most birds. This situation contrasts with the conservation of other aspects of regional variation in gene expression observed on the avian sex chromosomes but could be the result of sampling bias. We sampled taxa across the Galloanserae, an avian clade spanning 90 million years, to test whether regional variation in sex-specific gene regulation across the Z chromosome is conserved. We show that the MHM region is conserved across a large portion of the avian phylogeny, together with other sex-specific regulatory features of the avian Z chromosome. Our results from multiple lines of evidence suggest that the sex-specific expression pattern of the MHM region is not consistent with nascent dosage compensation.
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14
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Chen YC, Harrison PW, Kotrschal A, Kolm N, Mank JE, Panula P. Expression change in Angiopoietin-1 underlies change in relative brain size in fish. Proc Biol Sci 2015; 282:20150872. [PMID: 26108626 PMCID: PMC4590489 DOI: 10.1098/rspb.2015.0872] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/26/2015] [Indexed: 12/29/2022] Open
Abstract
Brain size varies substantially across the animal kingdom and is often associated with cognitive ability; however, the genetic architecture underpinning natural variation in these key traits is virtually unknown. In order to identify the genetic architecture and loci underlying variation in brain size, we analysed both coding sequence and expression for all the loci expressed in the telencephalon in replicate populations of guppies (Poecilia reticulata) artificially selected for large and small relative brain size. A single gene, Angiopoietin-1 (Ang-1), a regulator of angiogenesis and suspected driver of neural development, was differentially expressed between large- and small-brain populations. Zebra fish (Danio rerio) morphants showed that mild knock down of Ang-1 produces a small-brained phenotype that could be rescued with Ang-1 mRNA. Translation inhibition of Ang-1 resulted in smaller brains in larvae and increased expression of Notch-1, which regulates differentiation of neural stem cells. In situ analysis of newborn large- and small-brained guppies revealed matching expression patterns of Ang-1 and Notch-1 to those observed in zebrafish larvae. Taken together, our results suggest that the genetic architecture affecting brain size in our population may be surprisingly simple, and Ang-1 may be a potentially important locus in the evolution of vertebrate brain size and cognitive ability.
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Affiliation(s)
- Yu-Chia Chen
- Neuroscience Center and Institute of Biomedicine, Anatomy, University of Helsinki, Haartmaninkatu 8, Helsinki 00290, Finland
| | - Peter W Harrison
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Alexander Kotrschal
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden Department of Zoology/Ethology, Stockholm University, Svante Arrhenius väg 18B, Stockholm 10691, Sweden
| | - Niclas Kolm
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden Department of Zoology/Ethology, Stockholm University, Svante Arrhenius väg 18B, Stockholm 10691, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Pertti Panula
- Neuroscience Center and Institute of Biomedicine, Anatomy, University of Helsinki, Haartmaninkatu 8, Helsinki 00290, Finland
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15
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Ellison AR, Tunstall T, DiRenzo GV, Hughey MC, Rebollar EA, Belden LK, Harris RN, Ibáñez R, Lips KR, Zamudio KR. More than skin deep: functional genomic basis for resistance to amphibian chytridiomycosis. Genome Biol Evol 2014; 7:286-98. [PMID: 25539724 PMCID: PMC4316636 DOI: 10.1093/gbe/evu285] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The amphibian-killing chytrid fungus Batrachochytrium dendrobatidis (Bd) is one of the most generalist pathogens known, capable of infecting hundreds of species globally and causing widespread population declines and extinctions. However, some host species are seemingly unaffected by Bd, tolerating or clearing infections without clinical signs of disease. Variation in host immune responses is commonly evoked for these resistant or tolerant species, yet to date, we have no direct comparison of amphibian species responses to infection at the level of gene expression. In this study, we challenged four Central American frog species that vary in Bd susceptibility, with a sympatric virulent strain of the pathogen. We compared skin and spleen orthologous gene expression using differential expression tests and coexpression gene network analyses. We found that resistant species have reduced skin inflammatory responses and increased expression of genes involved in skin integrity. In contrast, only highly susceptible species exhibited suppression of splenic T-cell genes. We conclude that resistance to chytridiomycosis may be related to a species’ ability to escape the immunosuppressive activity of the fungus. Moreover, our results indicate that within-species differences in splenic proteolytic enzyme gene expression may contribute to intraspecific variation in survival. This first comparison of amphibian functional immunogenomic architecture in response to Bd provides insights into key genetic mechanisms underlying variation in disease outcomes among amphibian species.
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Affiliation(s)
- Amy R Ellison
- Department of Ecology and Evolutionary Biology, Cornell University
| | - Tate Tunstall
- Department of Biology, University of Maryland, College Park
| | | | | | | | | | | | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panamá
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University
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16
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Finseth FR, Harrison RG. A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird. PLoS One 2014; 9:e108550. [PMID: 25279728 PMCID: PMC4184788 DOI: 10.1371/journal.pone.0108550] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 08/30/2014] [Indexed: 12/21/2022] Open
Abstract
De novo assembled transcriptomes, in combination with RNA-Seq, are powerful tools to explore gene sequence and expression level in organisms without reference genomes. Investigators must first choose which high throughput sequencing platforms will provide data most suitable for their experimental goals. In this study, we explore the utility of 454 and Illumina sequences for de novo transcriptome assembly and downstream RNA-Seq applications in a reproductive gland from a non-model bird species, the Japanese quail (Coturnix japonica). Four transcriptomes composed of either pure 454 or Illumina reads or mixtures of read types were assembled and evaluated for the same cost. Illumina assemblies performed best for de novo transcriptome characterization in terms of contig length, transcriptome coverage, and complete assembly of gene transcripts. Improvements over the Hybrid assembly were marginal, with the exception that the addition of 454 data significantly increased the number of genes annotated. The Illumina assembly provided the best reference to align an independent set of RNA-Seq data as ∼84% of reads mapped to single genes in the transcriptome. Contigs constructed solely from 454 data may impose problems for RNA-Seq as our 454 transcriptome revealed a high number of indels and many ambiguously mapped reads. Correcting the 454 transcriptome with Illumina reads was an effective strategy to deal with indel and frameshift errors inherent to the 454 transcriptome, but at the cost of transcriptome coverage. In the absence of a reference genome, we find that Illumina reads alone produced a high quality transcriptome appropriate for RNA-Seq gene expression analyses.
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Affiliation(s)
- Findley R. Finseth
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Richard G. Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
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17
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Balakrishnan CN, Mukai M, Gonser RA, Wingfield JC, London SE, Tuttle EM, Clayton DF. Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior. PeerJ 2014; 2:e396. [PMID: 24883256 PMCID: PMC4034602 DOI: 10.7717/peerj.396] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/06/2014] [Indexed: 02/04/2023] Open
Abstract
Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel's white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as an important determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.
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Affiliation(s)
| | - Motoko Mukai
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University , Ithaca, NY , USA ; Department of Neurobiology, Physiology and Behavior, University of California , Davis, CA , USA
| | - Rusty A Gonser
- Department of Biology and The Center for Genomic Advocacy (TCGA), Indiana State University , Terre Haute, IN , USA
| | - John C Wingfield
- Department of Neurobiology, Physiology and Behavior, University of California , Davis, CA , USA
| | - Sarah E London
- Department of Psychology, University of Chicago , Chicago, IL , USA
| | - Elaina M Tuttle
- Department of Biology and The Center for Genomic Advocacy (TCGA), Indiana State University , Terre Haute, IN , USA
| | - David F Clayton
- Division of Biological & Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London , London , UK
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18
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Ellison AR, Savage AE, DiRenzo GV, Langhammer P, Lips KR, Zamudio KR. Fighting a losing battle: vigorous immune response countered by pathogen suppression of host defenses in the chytridiomycosis-susceptible frog Atelopus zeteki. G3 (BETHESDA, MD.) 2014; 4:1275-89. [PMID: 24841130 PMCID: PMC4455776 DOI: 10.1534/g3.114.010744] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/15/2014] [Indexed: 01/13/2023]
Abstract
The emergence of the disease chytridiomycosis caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) has been implicated in dramatic global amphibian declines. Although many species have undergone catastrophic declines and/or extinctions, others appear to be unaffected or persist at reduced frequencies after Bd outbreaks. The reasons behind this variance in disease outcomes are poorly understood: differences in host immune responses have been proposed, yet previous studies suggest a lack of robust immune responses to Bd in susceptible species. Here, we sequenced transcriptomes from clutch-mates of a highly susceptible amphibian, Atelopus zeteki, with different infection histories. We found significant changes in expression of numerous genes involved in innate and inflammatory responses in infected frogs despite high susceptibility to chytridiomycosis. We show evidence of acquired immune responses generated against Bd, including increased expression of immunoglobulins and major histocompatibility complex genes. In addition, fungal-killing genes had significantly greater expression in frogs previously exposed to Bd compared with Bd-naïve frogs, including chitinase and serine-type proteases. However, our results appear to confirm recent in vitro evidence of immune suppression by Bd, demonstrated by decreased expression of lymphocyte genes in the spleen of infected compared with control frogs. We propose susceptibility to chytridiomycosis is not due to lack of Bd-specific immune responses but instead is caused by failure of those responses to be effective. Ineffective immune pathway activation and timing of antibody production are discussed as potential mechanisms. However, in light of our findings, suppression of key immune responses by Bd is likely an important factor in the lethality of this fungus.
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Affiliation(s)
- Amy R Ellison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
| | - Anna E Savage
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853 Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013
| | - Grace V DiRenzo
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | - Penny Langhammer
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
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19
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Perry JC, Harrison PW, Mank JE. The ontogeny and evolution of sex-biased gene expression in Drosophila melanogaster. Mol Biol Evol 2014; 31:1206-19. [PMID: 24526011 PMCID: PMC3995337 DOI: 10.1093/molbev/msu072] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Sexually dimorphic phenotypes are thought to largely result from sex differences in gene expression, and genes with sex-biased expression have been well characterized in adults of many species. Although most sexual dimorphisms manifest in adults, many result from sex-specific developmental trajectories, implying that juveniles may exhibit significant levels of sex-biased expression. However, it is unclear how much sex-biased expression occurs before reproductive maturity and whether preadult sex-biased genes should exhibit the same evolutionary dynamics observed for adult sex-biased genes. In order to understand the continuity, or lack thereof, and evolutionary dynamics of sex-biased expression throughout the life cycle, we examined sex-biased genes in pre-gonad tissue of two preadult stages and compared them with the adult gonad of Drosophila melanogaster. We found that the majority of the genome is sex-biased at some point in the life cycle, with some genes exhibiting conserved sex-biased expression and others displaying stage-specific sex bias. Our results also reveal a far more complex pattern of evolution for sex-biased genes throughout development. The most rapid evolutionary divergence occurred in genes expressed only in larvae within each sex, compared with continuously expressed genes. In females—but not males—this pattern appeared to be due to relaxed purifying selection in larva-limited genes. Furthermore, genes that retained male bias throughout life evolved more rapidly than stage-specific male-biased genes, due to stronger purifying selection in stage-specific genes. However, female-biased genes that were specific to larvae evolved most rapidly, a pattern that could not be definitively attributed to differences in adaptive evolution or purifying selection, suggesting that pleiotropic constraints on protein-coding sequences can arise when genes are broadly expressed across developmental stages. These results indicate that the signature of sex-specific selection can be detected well before reproductive maturity and is strongest during development.
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20
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Clayton DF, London SE. Advancing avian behavioral neuroendocrinology through genomics. Front Neuroendocrinol 2014; 35:58-71. [PMID: 24113222 DOI: 10.1016/j.yfrne.2013.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 12/14/2022]
Abstract
Genome technologies are transforming all areas of biology, including the study of hormones, brain and behavior. Annotated reference genome assemblies are rapidly being produced for many avian species. Here we briefly review the basic concepts and tools used in genomics. We then consider how these are informing the study of avian behavioral neuroendocrinology, focusing in particular on lessons from the study of songbirds. We discuss the impact of having a complete "parts list" for an organism; the transformational potential of studying large sets of genes at once instead one gene at a time; the growing recognition that environmental and behavioral signals trigger massive shifts in gene expression in the brain; and the prospects for using comparative genomics to uncover the genetic roots of behavioral variation. Throughout, we identify promising new directions for bolstering the application of genomic information to further advance the study of avian brain and behavior.
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Affiliation(s)
- David F Clayton
- Biological & Experimental Psychology Division, School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, Committee on Neurobiology, University of Chicago, 940 E 57th Street, Chicago, IL, USA.
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21
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Mank JE. Sex chromosome dosage compensation: definitely not for everyone. Trends Genet 2013; 29:677-83. [DOI: 10.1016/j.tig.2013.07.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/03/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
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22
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Masculinization of gene expression is associated with exaggeration of male sexual dimorphism. PLoS Genet 2013; 9:e1003697. [PMID: 23966876 PMCID: PMC3744414 DOI: 10.1371/journal.pgen.1003697] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 06/19/2013] [Indexed: 01/24/2023] Open
Abstract
Gene expression differences between the sexes account for the majority of sexually dimorphic phenotypes, and the study of sex-biased gene expression is important for understanding the genetic basis of complex sexual dimorphisms. However, it has been difficult to test the nature of this relationship due to the fact that sexual dimorphism has traditionally been conceptualized as a dichotomy between males and females, rather than an axis with individuals distributed at intermediate points. The wild turkey (Meleagris gallopavo) exhibits just this sort of continuum, with dominant and subordinate males forming a gradient in male secondary sexual characteristics. This makes it possible for the first time to test the correlation between sex-biased gene expression and sexually dimorphic phenotypes, a relationship crucial to molecular studies of sexual selection and sexual conflict. Here, we show that subordinate male transcriptomes show striking multiple concordances with their relative phenotypic sexual dimorphism. Subordinate males were clearly male rather than intersex, and when compared to dominant males, their transcriptomes were simultaneously demasculinized for male-biased genes and feminized for female-biased genes across the majority of the transcriptome. These results provide the first evidence linking sexually dimorphic transcription and sexually dimorphic phenotypes. More importantly, they indicate that evolutionary changes in sexual dimorphism can be achieved by varying the magnitude of sex-bias in expression across a large proportion of the coding content of a genome. Males and females exhibit many differences in morphology, behavior and physiology, yet they share the vast majority of their genomes. Most differences between the sexes are therefore thought to be the product of gene expression differences between females and males. Studies of sex differences in expression assume that genes expressed more in males encode male traits, and genes expressed more in females encode female traits, and this assumption is a key foundation to genetic studies of sexual dimorphism and sexual conflict. Despite this key assumption, this relationship has yet to be empirically tested, as the main model organisms for studies of sex-biased gene expression lack multiple male and female morphs. Here, we use the two male morphs in the wild turkey to show that the magnitude of male-biased gene expression correlates with the manifestation of sexually dimorphic traits. Males with less manifestation of sexual dimorphism in phenotype were both demasculinized for male-biased genes, as well as feminized for female-biased genes. This pattern encompassed the majority of expressed loci, suggesting that evolutionary changes in the magnitude of sexual dimorphism may be achieved by small changes in the magnitude of sex-biased transcription across thousands of genes.
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