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Cumplido N, Arratia G, Desvignes T, Muñoz-Sánchez S, Postlethwait JH, Allende ML. Hox genes control homocercal caudal fin development and evolution. Sci Adv 2024; 10:eadj5991. [PMID: 38241378 PMCID: PMC10798566 DOI: 10.1126/sciadv.adj5991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024]
Abstract
Ancient bony fishes had heterocercal tails, like modern sharks and sturgeons, with asymmetric caudal fins and a vertebral column extending into an elongated upper lobe. Teleost fishes, in contrast, developed a homocercal tail characterized by two separate equal-sized fin lobes and the body axis not extending into the caudal fin. A similar heterocercal-to-homocercal transition occurs during teleost ontogeny, although the underlying genetic and developmental mechanisms for either transition remain unresolved. Here, we investigated the role of hox13 genes in caudal fin formation as these genes control posterior identity in animals. Analysis of expression profiles of zebrafish hox13 paralogs and phenotypes of CRISPR/Cas9-induced mutants showed that double hoxb13a and hoxc13a mutants fail to form a caudal fin. Furthermore, single mutants display heterocercal-like morphologies not seen since Mesozoic fossil teleosteomorphs. Relaxation of functional constraints after the teleost genome duplication may have allowed hox13 duplicates to neo- or subfunctionalize, ultimately contributing to the evolution of a homocercal tail in teleost fishes.
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Affiliation(s)
- Nicolás Cumplido
- Millennium Institute Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Gloria Arratia
- University of Kansas, Department of Ecology and Evolutionary Biology and Biodiversity Institute, Lawrence, KS, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Salomé Muñoz-Sánchez
- Millennium Institute Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Miguel L. Allende
- Millennium Institute Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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2
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Desvignes T, Bista I, Herrera K, Landes A, Postlethwait JH. Cold-Driven Hemoglobin Evolution in Antarctic Notothenioid Fishes Prior to Hemoglobin Gene Loss in White-Blooded Icefishes. Mol Biol Evol 2023; 40:msad236. [PMID: 37879119 PMCID: PMC10651078 DOI: 10.1093/molbev/msad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023] Open
Abstract
Expression of multiple hemoglobin isoforms with differing physiochemical properties likely helps species adapt to different environmental and physiological conditions. Antarctic notothenioid fishes inhabit the icy Southern Ocean and display fewer hemoglobin isoforms, each with less affinity for oxygen than temperate relatives. Reduced hemoglobin multiplicity was proposed to result from relaxed selective pressure in the cold, thermally stable, and highly oxygenated Antarctic waters. These conditions also permitted the survival and diversification of white-blooded icefishes, the only vertebrates living without hemoglobin. To understand hemoglobin evolution during adaptation to freezing water, we analyzed hemoglobin genes from 36 notothenioid genome assemblies. Results showed that adaptation to frigid conditions shaped hemoglobin gene evolution by episodic diversifying selection concomitant with cold adaptation and by pervasive evolution in Antarctic notothenioids compared to temperate relatives, likely a continuing adaptation to Antarctic conditions. Analysis of hemoglobin gene expression in adult hematopoietic organs in various temperate and Antarctic species further revealed a switch in hemoglobin gene expression underlying hemoglobin multiplicity reduction in Antarctic fish, leading to a single hemoglobin isoform in adult plunderfishes and dragonfishes, the sister groups to icefishes. The predicted high hemoglobin multiplicity in Antarctic fish embryos based on transcriptomic data, however, raises questions about the molecular bases and physiological implications of diverse hemoglobin isoforms in embryos compared to adults. This analysis supports the hypothesis that the last common icefish ancestor was vulnerable to detrimental mutations affecting the single ancestral expressed alpha- and beta-globin gene pair, potentially predisposing their subsequent loss.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Iliana Bista
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt 60325, Germany
- Senckenberg Research Institute, Frankfurt 60325, Germany
| | - Karina Herrera
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Audrey Landes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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3
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Bista I, Wood JMD, Desvignes T, McCarthy SA, Matschiner M, Ning Z, Tracey A, Torrance J, Sims Y, Chow W, Smith M, Oliver K, Haggerty L, Salzburger W, Postlethwait JH, Howe K, Clark MS, William Detrich H, Christina Cheng CH, Miska EA, Durbin R. Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 2023; 14:3412. [PMID: 37296119 PMCID: PMC10256766 DOI: 10.1038/s41467-023-38567-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/05/2023] [Indexed: 06/12/2023] Open
Abstract
Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.
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Affiliation(s)
- Iliana Bista
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK.
- Naturalis Biodiversity Center, Leiden, 2333 CR, the Netherlands.
| | - Jonathan M D Wood
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Thomas Desvignes
- University of Oregon, Institute of Neuroscience, 1254 University of Oregon, 13th Avenue, Eugene, OR, 97403, USA
| | - Shane A McCarthy
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Michael Matschiner
- University of Oslo, Natural History Museum, University of Oslo, Sars' gate 1, 0562, Oslo, Norway
- University of Zurich, Department of Palaeontology and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006, Zurich, Switzerland
| | - Zemin Ning
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - James Torrance
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Ying Sims
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - William Chow
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Michelle Smith
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Walter Salzburger
- University of Basel, Zoological Institute, Department of Environmental Sciences, Vesalgasse 1, 4051, Basel, Switzerland
| | - John H Postlethwait
- University of Oregon, Institute of Neuroscience, 1254 University of Oregon, 13th Avenue, Eugene, OR, 97403, USA
| | - Kerstin Howe
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Melody S Clark
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - H William Detrich
- Northeastern University, Department of Marine and Environmental Sciences, Marine Science Centre, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - C-H Christina Cheng
- Department of Evolution, Ecology, and Behaviour, University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Eric A Miska
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023; 32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John S Sproul
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Luana S F Lins
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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5
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Parey E, Louis A, Montfort J, Bouchez O, Roques C, Iampietro C, Lluch J, Castinel A, Donnadieu C, Desvignes T, Floi Bucao C, Jouanno E, Wen M, Mejri S, Dirks R, Jansen H, Henkel C, Chen WJ, Zahm M, Cabau C, Klopp C, Thompson AW, Robinson-Rechavi M, Braasch I, Lecointre G, Bobe J, Postlethwait JH, Berthelot C, Roest Crollius H, Guiguen Y. Genome structures resolve the early diversification of teleost fishes. Science 2023; 379:572-575. [PMID: 36758078 DOI: 10.1126/science.abq4257] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- INRAE, LPGP, Rennes, France
| | - Alexandra Louis
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | | | | | - Céline Roques
- GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
| | | | - Jerome Lluch
- GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
| | | | | | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Christabel Floi Bucao
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Ming Wen
- INRAE, LPGP, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Sahar Mejri
- Florida Atlantic University, Harbor Branch Oceanographic Institute, Fort Pierce, FL, USA
| | - Ron Dirks
- Future Genomics Technologies, Leiden, Netherlands
| | - Hans Jansen
- Future Genomics Technologies, Leiden, Netherlands
| | - Christiaan Henkel
- Institute of Biology, University of Leiden, Leiden, Netherlands
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
| | - Margot Zahm
- Sigenae, GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Cédric Cabau
- Sigenae, GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Christophe Klopp
- Sigenae, GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France
- Sigenae, Genotoul Bioinfo, MIAT UR875, INRAE, Castanet Tolosan, France
| | - Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Guillaume Lecointre
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | | | | | - Camille Berthelot
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, INSERM UA12, Comparative Functional Genomics group, F-75015 Paris, France
| | - Hugues Roest Crollius
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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6
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Desvignes T, Robbins AE, Carey AZ, Bailon-Zambrano R, Nichols JT, Postlethwait JH, Stankunas K. Coordinated patterning of zebrafish caudal fin symmetry by a central and two peripheral organizers. Dev Dyn 2022; 251:1306-1321. [PMID: 35403297 PMCID: PMC9357109 DOI: 10.1002/dvdy.475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/17/2022] [Accepted: 04/03/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Caudal fin symmetry characterizes teleosts and likely contributes to their evolutionary success. However, the coordinated development and patterning of skeletal elements establishing external symmetry remains incompletely understood. We explore the spatiotemporal emergence of caudal skeletal elements in zebrafish to consider evolutionary and developmental origins of caudal fin symmetry. RESULTS Transgenic reporters and skeletal staining reveal that the hypural diastema-defining gap between hypurals 2 and 3 forms early and separates progenitors of two plates of connective tissue. Two sets of central principal rays (CPRs) synchronously, sequentially, and symmetrically emerge around the diastema. The two dorsal- and ventral-most rays (peripheral principal rays, PPRs) arise independently and earlier than adjacent CPRs. Muscle and tendon markers reveal that different muscles attach to CPR and PPR sets. CONCLUSIONS We propose that caudal fin symmetry originates from a central organizer that establishes the hypural diastema and bidirectionally patterns surrounding tissue into two plates of connective tissue and two mirrored sets of CPRs. Further, two peripheral organizers unidirectionally specify PPRs, forming a symmetric "composite" fin derived from three fields. Distinct CPR and PPR ontogenies may represent developmental modules conferring ray identities, muscle connections, and biomechanical properties. Our model contextualizes mechanistic studies of teleost fin morphological variation.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | - Amy E. Robbins
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
| | - Andrew Z. Carey
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | - Raisa Bailon-Zambrano
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045, USA
| | - James T. Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045, USA
| | | | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
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Desvignes T, Lauridsen H, Valdivieso A, Fontenele RS, Kraberger S, Murray KN, Le François NR, Detrich HW, Kent ML, Varsani A, Postlethwait JH. A parasite outbreak in notothenioid fish in an Antarctic fjord. iScience 2022; 25:104588. [PMID: 35800770 PMCID: PMC9253362 DOI: 10.1016/j.isci.2022.104588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/25/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Climate changes can promote disease outbreaks, but their nature and potential impacts in remote areas have received little attention. In a hot spot of biodiversity on the West Antarctic Peninsula, which faces among the fastest changing climates on Earth, we captured specimens of two notothenioid fish species affected by large skin tumors at an incidence never before observed in the Southern Ocean. Molecular and histopathological analyses revealed that X-cell parasitic alveolates, members of a genus we call Notoxcellia, are the etiological agent of these tumors. Parasite-specific molecular probes showed that xenomas remained within the skin but largely outgrew host cells in the dermis. We further observed that tumors induced neovascularization in underlying tissue and detrimentally affected host growth and condition. Although many knowledge gaps persist about X-cell disease, including its mode of transmission and life cycle, these findings reveal potentially active biotic threats to vulnerable Antarctic ecosystems.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Henrik Lauridsen
- Department of Clinical Medicine, Aarhus University; Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Alejandro Valdivieso
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona Spain
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Katrina N Murray
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Nathalie R Le François
- Laboratoire Physiologie, Aquaculture et Conservation, Biodôme de Montréal/Espace pour la vie, 4777 Avenue Pierre-De Coubertin, Montreal, QC H1V 1B3, Canada
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd, Nahant, MA 01908, USA
| | - Michael L Kent
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925 Cape Town, South Africa
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8
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Wen M, Pan Q, Jouanno E, Montfort J, Zahm M, Cabau C, Klopp C, Iampietro C, Roques C, Bouchez O, Castinel A, Donnadieu C, Parrinello H, Poncet C, Belmonte E, Gautier V, Avarre J, Dugue R, Gustiano R, Hà TTT, Campet M, Sriphairoj K, Ribolli J, de Almeida FL, Desvignes T, Postlethwait JH, Floi Bucao C, Robinson‐Rechavi M, Bobe J, Herpin A, Guiguen Y. An ancient truncated duplication of the anti‐Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family. Mol Ecol Resour 2022; 22:2411-2428. [PMID: 35429227 PMCID: PMC9555307 DOI: 10.1111/1755-0998.13620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus chromosome-scale genome assembly, we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication/insertion event at the root of the Siluroidei radiation that is dated to ~100 million years ago. Together these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent use of the transforming growth factor β pathway, which is often used for the recruitment of teleost master SD genes, and provides another empirical case towards firther understanding of dynamics of SD systems.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha China
- INRAE LPGP 35000 Rennes France
| | - Qiaowei Pan
- INRAE LPGP 35000 Rennes France
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | | | | | - Margot Zahm
- Plate‐forme bio‐informatique Genotoul Mathématiques et Informatique Appliquées de Toulouse INRAE Castanet Tolosan France
| | - Cédric Cabau
- SIGENAE, GenPhySE Université de Toulouse INRAE ENVT Castanet Tolosan France
| | - Christophe Klopp
- Plate‐forme bio‐informatique Genotoul Mathématiques et Informatique Appliquées de Toulouse INRAE Castanet Tolosan France
- SIGENAE, GenPhySE Université de Toulouse INRAE ENVT Castanet Tolosan France
| | | | - Céline Roques
- INRAE, US 1426, GeT‐PlaGe Genotoul, Castanet‐Tolosan France
| | | | | | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle 141 rue de la Cardonille 34094 Montpellier Cedex France
| | - Charles Poncet
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Elodie Belmonte
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Véronique Gautier
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | | | - Remi Dugue
- ISEM Univ Montpellier CNRS IRD Montpellier France
| | - Rudhy Gustiano
- Research Institute of Freshwater Fisheries (CRIFI‐RIFF) Instalasi Penelitian Perikanan Air Tawar Jalan Ragunan‐Pasar Minggu P.O. Box 7220/jkspm Jakarta 12540 Indonesia
| | - Trần Thị Thúy Hà
- Research Institute for Aquaculture No.1. Dinh Bang Tu Son, Bac Ninh Viet Nam
| | | | - Kednapat Sriphairoj
- Faculty of Natural Resources and Agro‐Industry Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus Sakon Nakhon Thailand
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce Universidade Federal de Santa Catarina Florianópolis SC Brasil
| | | | - Thomas Desvignes
- Institute of Neuroscience University of Oregon Eugene OR 97403 USA
| | | | - Christabel Floi Bucao
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
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9
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Desvignes T, Bardou P, Montfort J, Sydes J, Guyomar C, George S, Postlethwait JH, Bobe J. FishmiRNA: An evolutionarily supported microRNA annotation and expression database for ray-finned fishes. Mol Biol Evol 2022; 39:6502288. [PMID: 35020925 PMCID: PMC8826519 DOI: 10.1093/molbev/msac004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
microRNAs are important post-transcriptional regulators of gene expression involved in countless biological processes and are widely studied across metazoans. While miRNA research continues to grow, the large community of fish miRNA researchers lacks exhaustive resources consistent among species. To fill this gap, we developed FishmiRNA, an evolutionarily supported microRNA annotation and expression database for ray-finned fishes: www.fishmirna.org. The self-explanatory database contains detailed, manually-curated miRNA annotations with orthology relationships rigorously established by sequence similarity and conserved syntenies, and expression data provided for each detected mature miRNA. In just few clicks, users can download the annotation and expression database in several convenient formats either in its entirety or a subset. Simple filters and BLAST search options also permit the simultaneous exploration and visual comparison of expression data for up to any ten mature miRNAs across species and organs. FishmiRNA was specifically designed for ease of use to reach a wide audience.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | - Philippe Bardou
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, F-31326, France
| | | | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | - Cervin Guyomar
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, F-31326, France
| | - Simon George
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
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10
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Kraberger S, Austin C, Farkas K, Desvignes T, Postlethwait JH, Fontenele RS, Schmidlin K, Bradley RW, Warzybok P, Van Doorslaer K, Davison W, Buck CB, Varsani A. Discovery of novel fish papillomaviruses: From the Antarctic to the commercial fish market. Virology 2022; 565:65-72. [PMID: 34739918 PMCID: PMC8713439 DOI: 10.1016/j.virol.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
Fish papillomaviruses form a newly discovered group broadly recognized as the Secondpapillomavirinae subfamily. This study expands the documented genomes of the fish papillomaviruses from six to 16, including one from the Antarctic emerald notothen, seven from commercial market fishes, one from data mining of sea bream sequence data, and one from a western gull cloacal swab that is likely diet derived. The genomes of secondpapillomaviruses are ∼6 kilobasepairs (kb), which is substantially smaller than the ∼8 kb of terrestrial vertebrate papillomaviruses. Each genome encodes a clear homolog of the four canonical papillomavirus genes, E1, E2, L1, and L2. In addition, we identified open reading frames (ORFs) with short linear peptide motifs reminiscent of E6/E7 oncoproteins. Fish papillomaviruses are extremely diverse and phylogenetically distant from other papillomaviruses suggesting a model in which terrestrial vertebrate-infecting papillomaviruses arose after an evolutionary bottleneck event, possibly during the water-to-land transition.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | | | - Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Russell W. Bradley
- Santa Rosa Island Research Station, California State University Channel Islands, Camarillo CA 93012, USA
| | - Pete Warzybok
- Point Blue Conservation Science, Petaluma, California, CA 94954, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute; Department of Immunobiology; Cancer Biology Graduate Interdisciplinary Program; UA Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - William Davison
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Christopher B. Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA,corresponding authors Christopher B. Buck, Arvind Varsani
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa,corresponding authors Christopher B. Buck, Arvind Varsani
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11
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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12
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Cardona E, Guyomar C, Desvignes T, Montfort J, Guendouz S, Postlethwait JH, Skiba-Cassy S, Bobe J. Circulating miRNA repertoire as a biomarker of metabolic and reproductive states in rainbow trout. BMC Biol 2021; 19:235. [PMID: 34781956 PMCID: PMC8594080 DOI: 10.1186/s12915-021-01163-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
Background Circulating miRNAs (c-miRNAs) are found in most, if not all, biological fluids and are becoming well-established non-invasive biomarkers of many human pathologies. However, their features in non-pathological contexts and whether their expression profiles reflect normal life history events have received little attention, especially in non-mammalian species. The aim of the present study was to investigate the potential of c-miRNAs to serve as biomarkers of reproductive and metabolic states in fish. Results The blood plasma was sampled throughout the reproductive cycle of female rainbow trout subjected to two different feeding regimes that triggered contrasting metabolic states. In addition, ovarian fluid was sampled at ovulation, and all samples were subjected to small RNA-seq analysis, leading to the establishment of a comprehensive miRNA repertoire (i.e., miRNAome) and enabling subsequent comparative analyses to a panel of RNA-seq libraries from a wide variety of tissues and organs. We showed that biological fluid miRNAomes are complex and encompass a high proportion of the overall rainbow trout miRNAome. While sharing a high proportion of common miRNAs, the blood plasma and ovarian fluid miRNAomes exhibited strong fluid-specific signatures. We further revealed that the blood plasma miRNAome significantly changed depending on metabolic and reproductive states. We subsequently identified three evolutionarily conserved muscle-specific miRNAs or myomiRs (miR-1-1/2-3p, miR-133a-1/2-3p, and miR-206-3p) that accumulated in the blood plasma in response to high feeding rates, making these myomiRs strong candidate biomarkers of active myogenesis. We also identified miR-202-5p as a candidate biomarker for reproductive success that could be used to predict ovulation and/or egg quality. Conclusions Together, these promising results reveal the high potential of c-miRNAs, including evolutionarily conserved myomiRs, as physiologically relevant biomarker candidates and pave the way for the use of c-miRNAs for non-invasive phenotyping in various fish species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01163-5.
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Affiliation(s)
- Emilie Cardona
- INRAE, LPGP, Fish Physiology and Genomics, F-35000, Rennes, France.,INRAE, Univ. Pau & Pays Adour, E2S UPPA, NUMEA, 64310, Saint-Pée-sur-Nivelle, France
| | - Cervin Guyomar
- INRAE, LPGP, Fish Physiology and Genomics, F-35000, Rennes, France.,GenPhySE, University of Toulouse, INRAE, ENVT, F-31326, Castanet-Tolosan, France
| | - Thomas Desvignes
- Institute of Neurosciences, University of Oregon, Eugene, OR, 97403, USA
| | - Jérôme Montfort
- INRAE, LPGP, Fish Physiology and Genomics, F-35000, Rennes, France
| | - Samia Guendouz
- Institute of Functional Genomics, MGX, UMR 5203 CNRS - U1191 INSERM, F-34094, Montpellier, France
| | | | - Sandrine Skiba-Cassy
- INRAE, Univ. Pau & Pays Adour, E2S UPPA, NUMEA, 64310, Saint-Pée-sur-Nivelle, France
| | - Julien Bobe
- INRAE, LPGP, Fish Physiology and Genomics, F-35000, Rennes, France.
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13
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Yan YL, Titus T, Desvignes T, BreMiller R, Batzel P, Sydes J, Farnsworth D, Dillon D, Wegner J, Phillips JB, Peirce J, Dowd J, Buck CL, Miller A, Westerfield M, Postlethwait JH. A fish with no sex: gonadal and adrenal functions partition between zebrafish NR5A1 co-orthologs. Genetics 2021; 217:6043928. [PMID: 33724412 DOI: 10.1093/genetics/iyaa030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
People with NR5A1 mutations experience testicular dysgenesis, ovotestes, or adrenal insufficiency, but we do not completely understand the origin of this phenotypic diversity. NR5A1 is expressed in gonadal soma precursor cells before expression of the sex-determining gene SRY. Many fish have two co-orthologs of NR5A1 that likely partitioned ancestral gene subfunctions between them. To explore ancestral roles of NR5A1, we knocked out nr5a1a and nr5a1b in zebrafish. Single-cell RNA-seq identified nr5a1a-expressing cells that co-expressed genes for steroid biosynthesis and the chemokine receptor Cxcl12a in 1-day postfertilization (dpf) embryos, as does the mammalian adrenal-gonadal (interrenal-gonadal) primordium. In 2dpf embryos, nr5a1a was expressed stronger in the interrenal-gonadal primordium than in the early hypothalamus but nr5a1b showed the reverse. Adult Leydig cells expressed both ohnologs and granulosa cells expressed nr5a1a stronger than nr5a1b. Mutants for nr5a1a lacked the interrenal, formed incompletely differentiated testes, had no Leydig cells, and grew far larger than normal fish. Mutants for nr5a1b formed a disorganized interrenal and their gonads completely disappeared. All homozygous mutant genotypes lacked secondary sex characteristics, including male breeding tubercles and female sex papillae, and had exceedingly low levels of estradiol, 11-ketotestosterone, and cortisol. RNA-seq showed that at 21dpf, some animals were developing as females and others were not, independent of nr5a1 genotype. By 35dpf, all mutant genotypes greatly under-expressed ovary-biased genes. Because adult nr5a1a mutants form gonads but lack an interrenal and conversely, adult nr5a1b mutants lack a gonad but have an interrenal, the adrenal, and gonadal functions of the ancestral nr5a1 gene partitioned between ohnologs after the teleost genome duplication, likely owing to reciprocal loss of ancestral tissue-specific regulatory elements. Identifying such elements could provide hints to otherwise unexplained cases of Differences in Sex Development.
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Affiliation(s)
- Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ruth BreMiller
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Dylan Farnsworth
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Danielle Dillon
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jeremy Wegner
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | | | - Judy Peirce
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - John Dowd
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | | | - Charles Loren Buck
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam Miller
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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14
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Ashique AM, Atake OJ, Ovens K, Guo R, Pratt IV, Detrich HW, Cooper DML, Desvignes T, Postlethwait JH, Eames BF. Bone microstructure and bone mineral density are not systemically different in Antarctic icefishes and related Antarctic notothenioids. J Anat 2021; 240:34-49. [PMID: 34423431 PMCID: PMC8655173 DOI: 10.1111/joa.13537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Ancestors of the Antarctic icefishes (family Channichthyidae) were benthic and had no swim bladder, making it energetically expensive to rise from the ocean floor. To exploit the water column, benthopelagic icefishes were hypothesized to have evolved a skeleton with “reduced bone,” which gross anatomical data supported. Here, we tested the hypothesis that changes to icefish bones also occurred below the level of gross anatomy. Histology and micro‐CT imaging of representative craniofacial bones (i.e., ceratohyal, frontal, dentary, and articular) of extant Antarctic fish species specifically evaluated two features that might cause the appearance of “reduced bone”: bone microstructure (e.g., bone volume fraction and structure linear density) and bone mineral density (BMD, or mass of mineral per volume of bone). Measures of bone microstructure were not consistently different in bones from the icefishes Chaenocephalus aceratus and Champsocephalus gunnari, compared to the related benthic notothenioids Notothenia coriiceps and Gobionotothen gibberifrons. Some quantitative measures, such as bone volume fraction and structure linear density, were significantly increased in some icefish bones compared to homologous bones of non‐icefish. However, such differences were rare, and no microstructural measures were consistently different in icefishes across all bones and species analyzed. Furthermore, BMD was similar among homologous bones of icefish and non‐icefish Antarctic notothenioids. In summary, “reduced bone” in icefishes was not due to systemic changes in bone microstructure or BMD, raising the prospect that “reduced bone” in icefish occurs only at the gross anatomic level (i.e., smaller or fewer bones). Given that icefishes exhibit delayed skeletal development compared to non‐icefish Antarctic fishes, combining these phenotypic data with genomic data might clarify genetic changes driving skeletal heterochrony.
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Affiliation(s)
- Amir M Ashique
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oghenevwogaga J Atake
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Katie Ovens
- Augmented Intelligence & Precision Health Laboratory (AIPHL), McGill University, Montreal, Quebec, Canada
| | - Ruiyi Guo
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Isaac V Pratt
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - H William Detrich
- Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - David M L Cooper
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | | | - B Frank Eames
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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15
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Caccavo JA, Christiansen H, Constable AJ, Ghigliotti L, Trebilco R, Brooks CM, Cotte C, Desvignes T, Dornan T, Jones CD, Koubbi P, Saunders RA, Strobel A, Vacchi M, van de Putte AP, Walters A, Waluda CM, Woods BL, Xavier JC. Productivity and Change in Fish and Squid in the Southern Ocean. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.624918] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern Ocean ecosystems are globally important and vulnerable to global drivers of change, yet they remain challenging to study. Fish and squid make up a significant portion of the biomass within the Southern Ocean, filling key roles in food webs from forage to mid-trophic species and top predators. They comprise a diverse array of species uniquely adapted to the extreme habitats of the region. Adaptations such as antifreeze glycoproteins, lipid-retention, extended larval phases, delayed senescence, and energy-conserving life strategies equip Antarctic fish and squid to withstand the dark winters and yearlong subzero temperatures experienced in much of the Southern Ocean. In addition to krill exploitation, the comparatively high commercial value of Antarctic fish, particularly the lucrative toothfish, drives fisheries interests, which has included illegal fishing. Uncertainty about the population dynamics of target species and ecosystem structure and function more broadly has necessitated a precautionary, ecosystem approach to managing these stocks and enabling the recovery of depleted species. Fisheries currently remain the major local driver of change in Southern Ocean fish productivity, but global climate change presents an even greater challenge to assessing future changes. Parts of the Southern Ocean are experiencing ocean-warming, such as the West Antarctic Peninsula, while other areas, such as the Ross Sea shelf, have undergone cooling in recent years. These trends are expected to result in a redistribution of species based on their tolerances to different temperature regimes. Climate variability may impair the migratory response of these species to environmental change, while imposing increased pressures on recruitment. Fisheries and climate change, coupled with related local and global drivers such as pollution and sea ice change, have the potential to produce synergistic impacts that compound the risks to Antarctic fish and squid species. The uncertainty surrounding how different species will respond to these challenges, given their varying life histories, environmental dependencies, and resiliencies, necessitates regular assessment to inform conservation and management decisions. Urgent attention is needed to determine whether the current management strategies are suitably precautionary to achieve conservation objectives in light of the impending changes to the ecosystem.
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16
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Abstract
MicroRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole-genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the teleost genome duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than nonclustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3'-complementary regions, compared with minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multispecies analysis of the mechanisms influencing metazoan miRNA evolution after whole-genome duplication.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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17
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Yan YL, Titus T, Desvignes T, BreMiller R, Batzel P, Sydes J, Farnsworth D, Dillon D, Wegner J, Phillips JB, Peirce J, Dowd J, Buck CL, Miller A, Westerfield M, Postlethwait JH. Erratum to: A fish with no sex: gonadal and adrenal functions partition between zebrafish NR5A1 co-orthologs. Genetics 2021; 218:6214480. [PMID: 33826717 DOI: 10.1093/genetics/iyab051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Feron R, Pan Q, Wen M, Imarazene B, Jouanno E, Anderson J, Herpin A, Journot L, Parrinello H, Klopp C, Kottler VA, Roco AS, Du K, Kneitz S, Adolfi M, Wilson CA, McCluskey B, Amores A, Desvignes T, Goetz FW, Takanashi A, Kawaguchi M, Detrich HW, Oliveira MA, Nóbrega RH, Sakamoto T, Nakamoto M, Wargelius A, Karlsen Ø, Wang Z, Stöck M, Waterhouse RM, Braasch I, Postlethwait JH, Schartl M, Guiguen Y. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data. Mol Ecol Resour 2021; 21:1715-1731. [PMID: 33590960 DOI: 10.1111/1755-0998.13360] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
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Affiliation(s)
- Romain Feron
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Qiaowei Pan
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ming Wen
- INRAE, LPGP, Rennes, France.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Jennifer Anderson
- INRAE, LPGP, Rennes, France.,Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Christophe Klopp
- SIGENAE, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
| | - Verena A Kottler
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Alvaro S Roco
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Kang Du
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mateus Adolfi
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | | | | | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Frederick W Goetz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Ato Takanashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Harry William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, MA, USA
| | - Marcos A Oliveira
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Rafael H Nóbrega
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Takashi Sakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Masatoshi Nakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | | | - Zhongwei Wang
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ingo Braasch
- Department of Integrative Biology, Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | | | - Manfred Schartl
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
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19
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Kelley JL, Desvignes T, McGowan KL, Perez M, Rodriguez LA, Brown AP, Culumber Z, Tobler M. microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide. J Evol Biol 2020; 34:977-988. [PMID: 33124163 DOI: 10.1111/jeb.13727] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/18/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022]
Abstract
microRNAs (miRNAs) are post-transcriptional regulators of gene expression and can play an important role in modulating organismal development and physiology in response to environmental stress. However, the role of miRNAs in mediating adaptation to diverse environments in natural study systems remains largely unexplored. Here, we characterized miRNAs and their expression in Poecilia mexicana, a species of small fish that inhabits both normal streams and extreme environments in the form of springs rich in toxic hydrogen sulphide (H2 S). We found that P. mexicana has a similar number of miRNA genes as other teleosts. In addition, we identified a large population of mature miRNAs that were differentially expressed between locally adapted populations in contrasting habitats, indicating that miRNAs may contribute to P. mexicana adaptation to sulphidic environments. In silico identification of differentially expressed miRNA-mRNA pairs revealed, in the sulphidic environment, the downregulation of miRNAs predicted to target mRNAs involved in sulphide detoxification and cellular homeostasis, which are pathways essential for life in H2 S-rich springs. In addition, we found that predicted targets of upregulated miRNAs act in the mitochondria (16.6% of predicted annotated targets), which is the main site of H2 S toxicity and detoxification, possibly modulating mitochondrial function. Together, the differential regulation of miRNAs between these natural populations suggests that miRNAs may be involved in H2 S adaptation by promoting functions needed for survival and reducing functions affected by H2 S. This study lays the groundwork for further research to directly demonstrate the role of miRNAs in adaptation to H2 S. Overall, this study provides a critical stepping-stone towards a comprehensive understanding of the regulatory mechanisms underlying the adaptive variation in gene expression in a natural system.
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Affiliation(s)
- Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Marcos Perez
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Lenin Arias Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, México
| | - Anthony P Brown
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Zach Culumber
- Biological Sciences Department, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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20
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Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Bofill-De Ros X, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano L. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics 2020; 36:698-703. [PMID: 31504201 DOI: 10.1093/bioinformatics/btz675] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/17/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION MicroRNAs (miRNAs) are small RNA molecules (∼22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. RESULTS To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification. AVAILABILITY AND IMPLEMENTATION https://github.com/miRTop/mirGFF3/ and https://github.com/miRTop/mirtop. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Karen Eilbeck
- University of Utah, Biomedical Informatics, Salt Lake City, UT 84108, USA
| | - Jeffery Ma
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Gianvito Urgese
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10129, Italy
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 114 18, Sweden
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ernesto Aparicio-Puerta
- Computational Epigenomics Laboratory, Genetics Department and Biotechnology Institute and Biosanitary Institute, University of Granada, Granada 18002, Spain
| | - Victor Barrera
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Roderic Espín
- Universitat Oberta de Catalunya, Barcelona 08018, Spain
| | - Florian Thibord
- Sorbonne Université, Pierre Louis Doctoral School of Public Health, Paris 75006, France.,Institut National pour la Santé et la Recherche Médicale (INSERM) Unité Mixte de Recherche en Santé (UMR_S), University of Bordeaux, Bordeaux 33076, France
| | - Xavier Bofill-De Ros
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Eric Londin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, Torino 10129, Italy
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm 114 18, Sweden
| | | | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Michael Hackenberg
- Computational Epigenomics Laboratory, Genetics Department and Biotechnology Institute and Biosanitary Institute, University of Granada, Granada 18002, Spain
| | - Ioannis S Vlachos
- Non-coding Research Lab, Department of Pathology, Cancer Research Institute, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lorena Pantano
- Bioinformatics Core, The Picower Institute for Learning and Memory, Cambridge, MA 02139, USA
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21
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Bista I, McCarthy SA, Wood J, Ning Z, Detrich III HW, Desvignes T, Postlethwait J, Chow W, Howe K, Torrance J, Smith M, Oliver K, Miska EA, Durbin R. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861). Wellcome Open Res 2020; 5:148. [PMID: 33195818 PMCID: PMC7649722 DOI: 10.12688/wellcomeopenres.16012.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2020] [Indexed: 01/06/2023] Open
Abstract
We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes.
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Affiliation(s)
- Iliana Bista
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Shane A. McCarthy
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - H. William Detrich III
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Massachusetts, MA 01908, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - William Chow
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | | | | | - Karen Oliver
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Vertebrate Genomes Project Consortium
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Massachusetts, MA 01908, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Eric A. Miska
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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22
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Damsgaard C, Lauridsen H, Funder AM, Thomsen JS, Desvignes T, Crossley DA, Møller PR, Huong DT, Phuong NT, Detrich HW, Brüel A, Wilkens H, Warrant E, Wang T, Nyengaard JR, Berenbrink M, Bayley M. Retinal oxygen supply shaped the functional evolution of the vertebrate eye. eLife 2019; 8:52153. [PMID: 31820735 PMCID: PMC6904217 DOI: 10.7554/elife.52153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/19/2019] [Indexed: 11/13/2022] Open
Abstract
The retina has a very high energy demand but lacks an internal blood supply in most vertebrates. Here we explore the hypothesis that oxygen diffusion limited the evolution of retinal morphology by reconstructing the evolution of retinal thickness and the various mechanisms for retinal oxygen supply, including capillarization and acid-induced haemoglobin oxygen unloading. We show that a common ancestor of bony fishes likely had a thin retina without additional retinal oxygen supply mechanisms and that three different types of retinal capillaries were gained and lost independently multiple times during the radiation of vertebrates, and that these were invariably associated with parallel changes in retinal thickness. Since retinal thickness confers multiple advantages to vision, we propose that insufficient retinal oxygen supply constrained the functional evolution of the eye in early vertebrates, and that recurrent origins of additional retinal oxygen supply mechanisms facilitated the phenotypic evolution of improved functional eye morphology.
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Affiliation(s)
- Christian Damsgaard
- Section for Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Henrik Lauridsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Meinig School of Biomedical Engineering, Cornell University, Ithaca, United States
| | - Anette Md Funder
- Department of Forensic Medicine, Aarhus University, Aarhus, Denmark
| | | | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, United States
| | - Dane A Crossley
- Department of Biological Sciences, University of North Texas, Denton, United States
| | - Peter R Møller
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Do Tt Huong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho, Viet Nam
| | - Nguyen T Phuong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho, Viet Nam
| | - H William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, United States
| | - Annemarie Brüel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Horst Wilkens
- Zoological Institute and Zoological Museum, University of Hamburg, Hamburg, Germany
| | - Eric Warrant
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Wang
- Section for Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Jens R Nyengaard
- Core Center for Molecular Morphology, Section for Stereology and Microscopy, Centre for Stochastic Geometry and Advanced Bioimaging, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Berenbrink
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mark Bayley
- Section for Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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23
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Yan YL, Batzel P, Titus T, Sydes J, Desvignes T, BreMiller R, Draper B, Postlethwait JH. A Hormone That Lost Its Receptor: Anti-Müllerian Hormone (AMH) in Zebrafish Gonad Development and Sex Determination. Genetics 2019; 213:529-553. [PMID: 31399485 PMCID: PMC6781894 DOI: 10.1534/genetics.119.302365] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/04/2019] [Indexed: 12/26/2022] Open
Abstract
Fetal mammalian testes secrete Anti-Müllerian hormone (Amh), which inhibits female reproductive tract (Müllerian duct) development. Amh also derives from mature mammalian ovarian follicles, which marks oocyte reserve and characterizes polycystic ovarian syndrome. Zebrafish (Danio rerio) lacks Müllerian ducts and the Amh receptor gene amhr2 but, curiously, retains amh To discover the roles of Amh in the absence of Müllerian ducts and the ancestral receptor gene, we made amh null alleles in zebrafish. Results showed that normal amh prevents female-biased sex ratios. Adult male amh mutants had enormous testes, half of which contained immature oocytes, demonstrating that Amh regulates male germ cell accumulation and inhibits oocyte development or survival. Mutant males formed sperm ducts and some produced a few offspring. Young female mutants laid a few fertile eggs, so they also had functional sex ducts. Older amh mutants accumulated nonvitellogenic follicles in exceedingly large but sterile ovaries, showing that Amh helps control ovarian follicle maturation and proliferation. RNA-sequencing data partitioned juveniles at 21 days postfertilization (dpf) into two groups that each contained mutant and wild-type fish. Group21-1 upregulated ovary genes compared to Group21-2, which were likely developing as males. By 35 dpf, transcriptomes distinguished males from females and, within each sex, mutants from wild types. In adult mutants, ovaries greatly underexpressed granulosa and theca genes, and testes underexpressed Leydig cell genes. These results show that ancestral Amh functions included development of the gonadal soma in ovaries and testes and regulation of gamete proliferation and maturation. A major gap in our understanding is the identity of the gene encoding a zebrafish Amh receptor; we show here that the loss of amhr2 is associated with the breakpoint of a chromosome rearrangement shared among cyprinid fishes.
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Affiliation(s)
- Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Ruth BreMiller
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Bruce Draper
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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24
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Cytrynbaum EG, Small CM, Kwon RY, Hung B, Kent D, Yan YL, Knope ML, Bremiller RA, Desvignes T, Kimmel CB. Developmental tuning of mineralization drives morphological diversity of gill cover bones in sculpins and their relatives. Evol Lett 2019; 3:374-391. [PMID: 31388447 PMCID: PMC6675512 DOI: 10.1002/evl3.128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 06/17/2019] [Accepted: 06/22/2019] [Indexed: 12/21/2022] Open
Abstract
The role of osteoblast placement in skeletal morphological variation is relatively well understood, but alternative developmental mechanisms affecting bone shape remain largely unknown. Specifically, very little attention has been paid to variation in later mineralization stages of intramembranous ossification as a driver of morphological diversity. We discover the occurrence of specific, sometimes large, regions of nonmineralized osteoid within bones that also contain mineralized tissue. We show through a variety of histological, molecular, and tomographic tests that this “extended” osteoid material is most likely nonmineralized bone matrix. This tissue type is a significant determinant of gill cover bone shape in the teleostean suborder Cottoidei. We demonstrate repeated evolution of extended osteoid in Cottoidei through ancestral state reconstruction and test for an association between extended osteoid variation and habitat differences among species. Through measurement of extended osteoid at various stages of gill cover development in species across the phylogeny, we gain insight into possible evolutionary developmental origins of the trait. We conclude that this fine‐tuned developmental regulation of bone matrix mineralization reflects heterochrony at multiple biological levels and is a novel mechanism for the evolution of diversity in skeletal morphology. This research lays the groundwork for a new model in which to study bone mineralization and evolutionary developmental processes, particularly as they may relate to adaptation during a prominent evolutionary radiation of fishes.
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Affiliation(s)
- Eli G Cytrynbaum
- Institute of Neuroscience University of Oregon Eugene Oregon 97403
| | - Clayton M Small
- Institute of Ecology and Evolution University of Oregon Eugene Oregon 97403
| | - Ronald Y Kwon
- Department of Orthopedics and Sports Medicine University of Washington Seattle Washington 98104.,Institute for Stem Cell and Regenerative Medicine University of Washington Seattle Washington 98104.,Department of Mechanical Engineering University of Washington Seattle Washington 98104
| | - Boaz Hung
- Vancouver Aquarium Ocean Wise Vancouver BC V6G 3E2 Canada
| | - Danny Kent
- Vancouver Aquarium Ocean Wise Vancouver BC V6G 3E2 Canada
| | - Yi-Lin Yan
- Institute of Neuroscience University of Oregon Eugene Oregon 97403
| | - Matthew L Knope
- Department of Biology University of Hawai'i at Hilo Hilo Hawaii 96720
| | - Ruth A Bremiller
- Institute of Neuroscience University of Oregon Eugene Oregon 97403
| | - Thomas Desvignes
- Institute of Neuroscience University of Oregon Eugene Oregon 97403
| | - Charles B Kimmel
- Institute of Neuroscience University of Oregon Eugene Oregon 97403
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25
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Lauridsen H, Desvignes T, Damsgaard C, Funder AMD, Thomsen JS, Postlethwait JH, Møller PR, Detrich HW. PO
2
Profiles in the Retina of the Hemoglobin‐less Icefishes. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.lb413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Lauridsen H, Desvignes T, Damsgaard C, Thomsen JS, Stenum TS, Ringgaard S, Hansen K, Funder AMD, Andersen TL, Boel LWT, Rejnmark L, Postlethwait JH, Møller PR, Detrich HW. Bone Mineral Density Reduction Explains Buoyancy Adaptations in Notothenioids. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.lb146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Desvignes T, Batzel P, Sydes J, Eames BF, Postlethwait JH. miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish. Sci Rep 2019; 9:3913. [PMID: 30850632 PMCID: PMC6408482 DOI: 10.1038/s41598-019-40361-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/15/2019] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) can have organ-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variation. It remains unclear, however, which mechanisms of miRNA production or modification are organ-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, helps quantify mature miRNAs, accounts for post-transcriptional processing, such as nucleotide editing, and identifies mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Our results provided evidence for the existence of 286 miRNA genes and 382 unique mature miRNAs (excluding mir430 gene duplicates and the vaultRNA-derived mir733), which doesn't represent a miRNAome larger than other teleost miRNomes. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, many of which are evolutionarily-conserved in the brain and heart in both species. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms may regulate post-transcriptional variations in miRNA sequence. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide changes in the seed sequence with organ specific editing rates, highest in the brain. In summary, Prost! is a new tool to identify and understand small RNAs, to help clarify a species' miRNA biology as shown here for an important model for the evolution of developmental mechanisms, and to provide insight into organ-enriched expression and the evolutionary conservation of miRNA post-transcriptional modifications.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA.
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | - B Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
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28
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Kim BM, Amores A, Kang S, Ahn DH, Kim JH, Kim IC, Lee JH, Lee SG, Lee H, Lee J, Kim HW, Desvignes T, Batzel P, Sydes J, Titus T, Wilson CA, Catchen JM, Warren WC, Schartl M, Detrich HW, Postlethwait JH, Park H. Antarctic blackfin icefish genome reveals adaptations to extreme environments. Nat Ecol Evol 2019; 3:469-478. [PMID: 30804520 PMCID: PMC7307600 DOI: 10.1038/s41559-019-0812-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 01/15/2019] [Indexed: 11/09/2022]
Abstract
Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we report a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus, highlighting evolved genomic features for its unique physiology. Phylogenomic analysis revealed that Antarctic fish of the teleost suborder Notothenioidei, including icefishes, diverged from the stickleback lineage about 77 million years ago and subsequently evolved cold-adapted phenotypes as the Southern Ocean cooled to sub-zero temperatures. Our results show that genes involved in protection from ice damage, including genes encoding antifreeze glycoprotein and zona pellucida proteins, are highly expanded in the icefish genome. Furthermore, genes that encode enzymes that help to control cellular redox state, including members of the sod3 and nqo1 gene families, are expanded, probably as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. In contrast, some crucial regulators of circadian homeostasis (cry and per genes) are absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment. The availability of the icefish genome sequence will accelerate our understanding of adaptation to extreme Antarctic environments.
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Affiliation(s)
- Bo-Mi Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Do-Hwan Ahn
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Jin-Hyoung Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea
| | - Il-Chan Kim
- Department of Polar Life Science, Korea Polar Research Institute, Incheon, Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Sung Gu Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Jungeun Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Han-Woo Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.,Polar Science, University of Science and Technology, Daejeon, Korea
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Julian M Catchen
- Department of Animal Biology, University of Illinois, Champaign, IL, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Manfred Schartl
- Department of Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany. .,Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA. .,Department of Biology, Texas A&M University, College Station, TX, USA.
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
| | | | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea. .,Polar Science, University of Science and Technology, Daejeon, Korea.
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Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? Genome Biol Evol 2019; 11:220-231. [PMID: 30496401 PMCID: PMC6336007 DOI: 10.1093/gbe/evy262] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/25/2022] Open
Abstract
The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whereas successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding, and degrading proteins at their ambient temperatures of -1.86 °C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold. The exception was the significant overrepresentation of positions where leucine in temperate fish proteins was replaced by methionine in the notothenioid orthologues. We hypothesize that these extra methionines have been preferentially assimilated into the genome to act as redox sensors in the highly oxygenated waters of the Southern Ocean. This redox hypothesis is supported by analyses of notothenioids showing enrichment of genes associated with responses to environmental stress, particularly reactive oxygen species. So overall, although notothenioid fish show cold-associated problems with protein homeostasis, they may have modified only a selected number of biochemical pathways to work efficiently below 0 °C. Even a slight warming of the Southern Ocean might disrupt the critical functions of this handful of key pathways with considerable impacts for the functioning of this ecosystem in the future.
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Affiliation(s)
- Camille Berthelot
- Laboratoire Dynamique et Organisation des Génomes (Dyogen), Institut de Biologie de l'Ecole Normale Supérieure – UMR 8197, INSERM U1024, Paris Cedex 05, France
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, United Kingdom
| | | | - H William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Michael Peters
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | | | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
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Desvignes T, Carey A, Postlethwait JH. Evolution of caudal fin ray development and caudal fin hypural diastema complex in spotted gar, teleosts, and other neopterygian fishes. Dev Dyn 2018; 247:832-853. [PMID: 29569346 PMCID: PMC5980753 DOI: 10.1002/dvdy.24630] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/05/2018] [Accepted: 03/09/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The caudal fin of actinopterygians transitioned from a heterocercal dorsoventrally asymmetrical fin to a homocercal externally symmetrical fin in teleosts through poorly understood evolutionary developmental mechanisms. We studied the caudal skeleton of major living actinopterygian lineages, including polypteriformes, acipenseriformes, Holostei (gars and bowfin), and teleosts, compared with reports of extinct neopterygians and basal teleosteans. We focused on the hypural diastema complex, which includes (1) a gap between hypurals 2 and 3, that (2) separates two plates of connective tissue at (3) the branching of caudal vasculature; these features had been considered as a shared, derived trait of teleosts, a synapomorphy. RESULTS These studies revealed that gars and teleosts share all three features of the hypural diastema complex. Absence of a complex with these features from bowfin, fossil Holostei, and stem Teleostei argues in favor of repetitive, independent emergence in several neopterygian and basal Teleostei lineages, or less likely, many independent losses. We further observed that, in gars and teleosts, the earliest developing lepidotrichia align with the horizontal adult body axis, thus participating in external symmetry. CONCLUSIONS These results suggest that the hypural diastema complex in teleosts and gars represents a homoplasy among neopterygians and that it emerged repeatedly by parallel evolution due to shared inherited underlying genetic and developmental programs (latent homology). Because the hypural diastema complex exists in gars with heterocercal tails, this complex is independent of homocercality. Developmental Dynamics 247:832-853, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | - Andrew Carey
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
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31
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Desvignes T, Carey A, Braasch I, Enright T, Postlethwait JH. Skeletal development in the heterocercal caudal fin of spotted gar (lepisosteus oculatus) and other lepisosteiformes. Dev Dyn 2018; 247:724-740. [PMID: 29330942 PMCID: PMC5902655 DOI: 10.1002/dvdy.24617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/06/2017] [Accepted: 12/27/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The caudal fin of actinopterygians experienced substantial morphological changes during evolution. In basal actinopterygians, the caudal fin skeleton supports an asymmetrical heterocercal caudal fin, while most teleosts have a symmetrical homocercal caudal fin. The transition from the ancestral heterocercal form to the derived homocercal caudal fin remains poorly understood. Few developmental studies provide an understanding of derived and ancestral characters among basal actinopterygians. To fill this gap, we examined the development of the caudal fin of spotted gar Lepisosteus oculatus, one of only eight living species of Holostei, the sister group to the teleosts. RESULTS Our observations of animals from fertilization to more than a year old provide the most detailed description of the development of caudal fin skeletal elements in any Holostean species. We observed two different types of distal caudal radials replacing two transient plates of connective tissue, identifying two hypaxial ensembles separated by a space between hypurals 2 and 3. These features have not been described in any gar species, but can be observed in other gar species, and thus represent anatomical structures common to lepisosteiformes. CONCLUSIONS The present work highlights the power and importance of ontogenic studies and provides bases for future evolutionary and morphological investigations on actinopterygians fins. Developmental Dynamics 247:724-740, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 9733, USA
| | - Andrew Carey
- Institute of Neuroscience, University of Oregon, Eugene OR 9733, USA
| | | | - Trevor Enright
- Institute of Neuroscience, University of Oregon, Eugene OR 9733, USA
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Desvignes T, Bourjon P, Chanet B. [Reproductive behavior of the green birdmouth wrasse Gomphosus caeruleus on a Reunion Island reef: Mode of reproduction, environmental factors and reproductive strategy alternation]. C R Biol 2017; 341:43-60. [PMID: 29276130 DOI: 10.1016/j.crvi.2017.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
Abstract
The green birdmouth wrasse Gomphosus caeruleus is present all year round on the coral reefs of Reunion Island (Indian Ocean). A group of individuals was followed on one of these reefs with the objective of studying the reproduction mode of the species, the influence of environmental factors, and social behaviors on the control of reproduction. Our observations revealed that G. caeruleus is, like many Labridae, a protogynous hermaphrodite species, probably diandric, that the reproduction of G. caeruleus is, like in other reef fish species, influenced by the lunar cycle with a peak of reproductive activity during waxing gibbous phase, and that G. caeruleus displays social behavior leading to alternating haremic mating system on a single territory and lek-like mating systems without aggressions between males. These observations enhanced our knowledge of the reproduction of Labridae and reef species.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, 97401-1254 OR, États-Unis.
| | - Philippe Bourjon
- Réseau d'observateurs sous-marins « Les Sentinelles du Récif » (Réserve nationale marine de la-Réunion), 26, rue des Bengalis, Plateau-Caillou, 97640 Saint-Paul, la-Réunion.
| | - Bruno Chanet
- ISYEB, UMR 7205 CNRS-MNHN-UPMC-EPHE, département "Systématique et Évolution", Muséum national d'histoire naturelle, CP50, 57, rue Cuvier, 75005 Paris, France.
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33
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Yan YL, Desvignes T, Bremiller R, Wilson C, Dillon D, High S, Draper B, Buck CL, Postlethwait J. Gonadal soma controls ovarian follicle proliferation through Gsdf in zebrafish. Dev Dyn 2017; 246:925-945. [PMID: 28856758 PMCID: PMC5761338 DOI: 10.1002/dvdy.24579] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/20/2017] [Accepted: 08/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Aberrant signaling between germ cells and somatic cells can lead to reproductive disease and depends on diffusible signals, including transforming growth factor-beta (TGFB) -family proteins. The TGFB-family protein Gsdf (gonadal soma derived factor) controls sex determination in some fish and is a candidate for mediating germ cell/soma signaling. RESULTS Zebrafish expressed gsdf in somatic cells of bipotential gonads and expression continued in ovarian granulosa cells and testicular Sertoli cells. Homozygous gsdf knockout mutants delayed leaving the bipotential gonad state, but then became a male or a female. Mutant females ovulated a few oocytes, then became sterile, accumulating immature follicles. Female mutants stored excess lipid and down-regulated aromatase, gata4, insulin receptor, estrogen receptor, and genes for lipid metabolism, vitellogenin, and steroid biosynthesis. Mutant females contained less estrogen and more androgen than wild-types. Mutant males were fertile. Genomic analysis suggests that Gsdf, Bmp15, and Gdf9, originated as paralogs in vertebrate genome duplication events. CONCLUSIONS In zebrafish, gsdf regulates ovarian follicle maturation and expression of genes for steroid biosynthesis, obesity, diabetes, and female fertility, leading to ovarian and extra-ovarian phenotypes that mimic human polycystic ovarian syndrome (PCOS), suggesting a role for a related TGFB signaling molecule in the etiology of PCOS. Developmental Dynamics 246:925-945, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Ruth Bremiller
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Danielle Dillon
- Center for Bioengineering Innovation, Northern Arizona University, Flagstaff, Arizona
| | - Samantha High
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | - Bruce Draper
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California
| | - Charles Loren Buck
- Center for Bioengineering Innovation, Northern Arizona University, Flagstaff, Arizona
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona
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34
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Le François NR, Sheehan E, Desvignes T, Belzile C, Postlethwait JH, Detrich HW. Characterization and husbandry of wild broodstock of the blackfin icefish Chaenocephalus aceratus (Lönnberg 1906) from the Palmer Archipelago (Southern Ocean) for breeding purposes. Polar Biol 2017. [DOI: 10.1007/s00300-017-2161-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Nucleoside triphosphate (NTP)s, like ATP (adenosine 5'-triphosphate) and GTP (guanosine 5'-triphosphate), have long been considered sufficiently concentrated and diffusible to fuel all cellular ATPases (adenosine triphosphatases) and GTPases (guanosine triphosphatases) in an energetically healthy cell without becoming limiting for function. However, increasing evidence for the importance of local ATP and GTP pools, synthesised in close proximity to ATP- or GTP-consuming reactions, has fundamentally challenged our view of energy metabolism. It has become evident that cellular energy metabolism occurs in many specialised 'microcompartments', where energy in the form of NTPs is transferred preferentially from NTP-generating modules directly to NTP-consuming modules. Such energy channeling occurs when diffusion through the cytosol is limited, where these modules are physically close and, in particular, if the NTP-consuming reaction has a very high turnover, i.e. is very processive. Here, we summarise the evidence for these conclusions and describe new insights into the physiological importance and molecular mechanisms of energy channeling gained from recent studies. In particular, we describe the role of glycolytic enzymes for axonal vesicle transport and nucleoside diphosphate kinases for the functions of dynamins and dynamin-related GTPases.
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Affiliation(s)
- Diana Zala
- ESPCI - Paris, PSL Research University, Paris, F-75005, France.,CNRS, UMR8249, Paris, F-75005, France
| | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA), and SFR Environmental and Systems Biology (BEeSy), U1055, University Grenoble Alpes, Grenoble, 38058, France.,Inserm-U1055, Grenoble, F-38058, France
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97401, USA
| | - Julien Bobe
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, F-35000, France
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, CH-1211, Switzerland.,Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, CH-1211, Switzerland
| | - Philippe Chavrier
- Institut Curie, Paris, F-75248, France.,PSL Research University, Paris, F-75005, France.,CNRS, UMR144, Paris, F-75248, France
| | - Mathieu Boissan
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMRS938, Saint-Antoine Research Center, Paris, F-75012, France.,AP-HP, Hospital Tenon, Service de Biochimie et Hormonologie, Paris, F-75020, France
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36
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Abstract
Nucleoside triphosphate (NTP)s, like ATP (adenosine 5'-triphosphate) and GTP (guanosine 5'-triphosphate), have long been considered sufficiently concentrated and diffusible to fuel all cellular ATPases (adenosine triphosphatases) and GTPases (guanosine triphosphatases) in an energetically healthy cell without becoming limiting for function. However, increasing evidence for the importance of local ATP and GTP pools, synthesised in close proximity to ATP- or GTP-consuming reactions, has fundamentally challenged our view of energy metabolism. It has become evident that cellular energy metabolism occurs in many specialised 'microcompartments', where energy in the form of NTPs is transferred preferentially from NTP-generating modules directly to NTP-consuming modules. Such energy channeling occurs when diffusion through the cytosol is limited, where these modules are physically close and, in particular, if the NTP-consuming reaction has a very high turnover, i.e. is very processive. Here, we summarise the evidence for these conclusions and describe new insights into the physiological importance and molecular mechanisms of energy channeling gained from recent studies. In particular, we describe the role of glycolytic enzymes for axonal vesicle transport and nucleoside diphosphate kinases for the functions of dynamins and dynamin-related GTPases.
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Affiliation(s)
- Diana Zala
- ESPCI - Paris, PSL Research University, Paris, F-75005, France.,CNRS, UMR8249, Paris, F-75005, France
| | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA), and SFR Environmental and Systems Biology (BEeSy), U1055, University Grenoble Alpes, Grenoble, 38058, France.,Inserm-U1055, Grenoble, F-38058, France
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97401, USA
| | - Julien Bobe
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, F-35000, France
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, CH-1211, Switzerland.,Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, CH-1211, Switzerland
| | - Philippe Chavrier
- Institut Curie, Paris, F-75248, France.,PSL Research University, Paris, F-75005, France.,CNRS, UMR144, Paris, F-75248, France
| | - Mathieu Boissan
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMRS938, Saint-Antoine Research Center, Paris, F-75012, France.,AP-HP, Hospital Tenon, Service de Biochimie et Hormonologie, Paris, F-75020, France
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Desvignes T, Detrich HW, Postlethwait JH. Genomic conservation of erythropoietic microRNAs (erythromiRs) in white-blooded Antarctic icefish. Mar Genomics 2016; 30:27-34. [PMID: 27189439 PMCID: PMC5108692 DOI: 10.1016/j.margen.2016.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/27/2016] [Accepted: 04/27/2016] [Indexed: 01/03/2023]
Abstract
White-blooded Antarctic crocodile icefish are the only vertebrates known to lack functional hemoglobin genes and red blood cells throughout their lives. We do not yet know, however, whether extinction of hemoglobin genes preceded loss of red blood cells or vice versa, nor whether erythropoiesis regulators disappeared along with hemoglobin genes in this erythrocyte-null clade. Several microRNAs, which we here call erythromiRs, are expressed primarily in developing red blood cells in zebrafish, mouse, and humans. Abrogating some erythromiRs, like mir144 and mir451a, leads to profound anemia, demonstrating a functional role in erythropoiesis. Here, we tested two not mutually exclusive hypotheses: 1) that the loss of one or more erythromiR genes extinguished the erythropoietic program of icefish and/or led to the loss of globin gene expression through pseudogenization; and 2) that some erythromiR genes were secondarily lost after the loss of functional hemoglobin and red blood cells in icefish. We explored small RNA transcriptomes generated from the hematopoietic kidney marrow of four Antarctic notothenioids: two red-blooded species (bullhead notothen Notothenia coriiceps and emerald notothen Trematomus bernacchii) and two white-blooded icefish (blackfin icefish Chaenocephalus aceratus and hooknose icefish Chionodraco hamatus). The N. coriiceps genome assembly anchored analyses. Results showed that, like the two red-blooded species, the blackfin icefish genome possessed and the marrow expressed all known erythromiRs. This result indicates that loss of hemoglobin and red blood cells in icefish was not caused by loss of known erythromiR genes. Furthermore, expression of only one erythromiR, mir96, appears to have been lost after the loss of red blood cells and hemoglobin-expression was not detected in the erythropoietic organ of hooknose icefish but was present in blackfin icefish. All other erythromiRs investigated, including mir144 and mir451a, were expressed by all four species and thus are present in the genomes of at least the two white-blooded icefish. Our results rule out the hypothesis that genomic loss of any known erythromiRs extinguished erythropoiesis in icefish, and suggest that after the loss of red blood cells, few erythromiRs experienced secondary loss. Results suggest that functions independent of erythropoiesis maintained erythromiRs, thereby highlighting the evolutionary resilience of miRNA genes in vertebrate genomes.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA.
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, 01908, USA.
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38
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Postlethwait JH, Yan YL, Desvignes T, Allard C, Titus T, Le François NR, Detrich HW. Embryogenesis and early skeletogenesis in the antarctic bullhead notothen, Notothenia coriiceps. Dev Dyn 2016; 245:1066-1080. [PMID: 27507212 DOI: 10.1002/dvdy.24437] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Environmental temperature influences rates of embryonic development, but a detailed staging series for vertebrate embryos developing in the subzero cold of Antarctic waters is not yet available from fertilization to hatching. Given projected warming of the Southern Ocean, it is imperative to establish a baseline to evaluate potential effects of changing climate on fish developmental dynamics. RESULTS We studied the Bullhead notothen (Notothenia coriiceps), a notothenioid fish inhabiting waters between -1.9 and +2 °C. In vitro fertilization produced embryos that progressed through cleavage, epiboly, gastrulation, segmentation, organogenesis, and hatching. We compared morphogenesis spatially and temporally to Zebrafish and medaka. Experimental animals hatched after about 6 months to early larval stages. To help understand skeletogenesis, we analyzed late embryos for expression of sox9 and runx2, which regulate chondrogenesis, osteogenesis, and eye development. Results revealed that, despite their prolonged developmental time course, N. coriiceps embryos developed similarly to those of other teleosts with large yolk cells. CONCLUSIONS Our studies set the stage for future molecular analyses of development in these extremophile fish. Results provide a foundation for understanding the impact of ocean warming on embryonic development and larval recruitment of notothenioid fish, which are key factors in the marine trophic system. Developmental Dynamics 245:1066-1080, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Corey Allard
- Biodôme de Montréal, Division des collections vivantes et recherche, Montréal, Quebec, Canada
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | - Nathalie R Le François
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
| | - H William Detrich
- Biodôme de Montréal, Division des collections vivantes et recherche, Montréal, Quebec, Canada
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Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo¨ldi J, Lindblad-Toh K, Postlethwait JH. Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:700. [DOI: 10.1038/ng0616-700c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH. miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends Genet 2015; 31:613-626. [PMID: 26453491 DOI: 10.1016/j.tig.2015.09.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/10/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of alternative mature miRNA-like RNA fragments and propose a revised definition of miRNAs to encompass this diversity. We then review nomenclature guidelines for miRNAs and propose to extend nomenclature conventions to align with those for protein-coding genes established by international consortia. Finally, we suggest a system to encompass the full complexity of sequence variations (i.e., isomiRs) in the analysis of small RNA sequencing experiments.
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Affiliation(s)
- T Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - P Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - E Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - K Eilbeck
- Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - J T Eppig
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - M S McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - A Singer
- ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA
| | - J H Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
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Desvignes T, Nguyen T, Chesnel F, Bouleau A, Fauvel C, Bobe J. X-Linked Retinitis Pigmentosa 2 Is a Novel Maternal-Effect Gene Required for Left-Right Asymmetry in Zebrafish. Biol Reprod 2015; 93:42. [PMID: 26134862 DOI: 10.1095/biolreprod.115.130575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/10/2015] [Indexed: 01/05/2023] Open
Abstract
Retinitis pigmentosa 2 (RP2) gene is responsible for up to 20% of X-linked retinitis pigmentosa, a severe heterogeneous genetic disorder resulting in progressive retinal degeneration in humans. In vertebrates, several bodies of evidence have clearly established the role of Rp2 protein in cilia genesis and/or function. Unexpectedly, some observations in zebrafish have suggested the oocyte-predominant expression of the rp2 gene, a typical feature of maternal-effect genes. In the present study, we investigate the maternal inheritance of rp2 gene products in zebrafish eggs in order to address whether rp2 could be a novel maternal-effect gene required for normal development. Although both rp2 mRNA and corresponding protein are expressed during oogenesis, rp2 mRNA is maternally inherited, in contrast to Rp2 protein. A knockdown of the protein transcribed from both rp2 maternal and zygotic mRNA results in delayed epiboly and severe developmental defects, including eye malformations, that were not observed when only the protein from zygotic origin was knocked down. Moreover, the knockdown of maternal and zygotic Rp2 revealed a high incidence of left-right asymmetry establishment defects compared to only zygotic knockdown. Here we show that rp2 is a novel maternal-effect gene exclusively expressed in oocytes within the zebrafish ovary and demonstrate that maternal rp2 mRNA is essential for successful embryonic development and thus contributes to egg developmental competence. Our observations also reveal that Rp2 protein translated from maternal mRNA is important to allow normal heart loop formation, thus providing evidence of a direct maternal contribution to left-right asymmetry establishment.
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Affiliation(s)
- Thomas Desvignes
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas Les Flots, France
| | - Thaovi Nguyen
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France
| | | | - Aurélien Bouleau
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas Les Flots, France
| | | | - Julien Bobe
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. J Exp Zool B Mol Dev Evol 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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Desvignes T, Beam MJ, Batzel P, Sydes J, Postlethwait JH. Expanding the annotation of zebrafish microRNAs based on small RNA sequencing. Gene 2014; 546:386-9. [PMID: 24835514 PMCID: PMC4130647 DOI: 10.1016/j.gene.2014.05.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/29/2014] [Accepted: 05/14/2014] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. Because of their role in the regulation of gene expression, miRs are essential players in development by acting on cell fate determination and progression towards cell differentiation and are increasingly relevant to human health and disease. Although the zebrafish Danio rerio is a major model for studies of development, genetics, physiology, evolution, and human biology, the annotation of zebrafish miR-producing genes remains limited. In the present work, we report deep sequencing data of zebrafish small RNAs from brain, heart, testis, and ovary. Results provide evidence for the expression of 56 un-annotated mir genes and 248 un-annotated mature strands, increasing the number of zebrafish mir genes over those already deposited in miRBase by 16% and the number of mature sequences by 63%. We also describe the existence of three pairs of mirror-mir genes and two mirtron genes, genetic features previously undescribed in non-mammalian vertebrates. This report provides information that substantially increases our knowledge of the zebrafish miRNome and will benefit the entire miR community.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
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Bouleau A, Desvignes T, Traverso JM, Nguyen T, Chesnel F, Fauvel C, Bobe J. Maternally inherited npm2 mRNA is crucial for egg developmental competence in zebrafish. Biol Reprod 2014; 91:43. [PMID: 25009208 DOI: 10.1095/biolreprod.114.119925] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The molecular mechanisms underlying and determining egg developmental competence remain poorly understood in vertebrates. Nucleoplasmin (Npm2) is one of the few known maternal effect genes in mammals, but this maternal effect has never been demonstrated in nonmammalian species. A link between developmental competence and the abundance of npm2 maternal mRNA in the egg was previously established using a teleost fish model for egg quality. The importance of maternal npm2 mRNA for egg developmental competence remains unknown in any vertebrate species. In the present study, we aimed to characterize the contribution of npm2 maternal mRNA to early developmental success in zebrafish using a knockdown strategy. We report here the oocyte-specific expression of npm2 and maternal inheritance of npm2 mRNA in zebrafish eggs. The knockdown of the protein translated from this maternal mRNA results in developmental arrest before the onset of epiboly and subsequent embryonic death, a phenotype also observed in embryos lacking zygotic transcription. Npm2 knockdown also results in impaired transcription of the first-wave zygotic genes. Our results show that npm2 is also a maternal effect gene in a nonmammalian vertebrate species and that maternally inherited npm2 mRNA is crucial for egg developmental competence. We also show that de novo protein synthesis from npm2 maternal mRNA is critical for developmental success beyond the blastula stage and required for zygotic genome activation. Finally, our results suggest that npm2 maternal mRNA is an important molecular factor of egg quality in fish and possibly in all vertebrates.
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Affiliation(s)
- Aurélien Bouleau
- INRA, LPGP UR1037 Sex differentiation and oogenesis group, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas-Les-Flots, France
| | - Thomas Desvignes
- INRA, LPGP UR1037 Sex differentiation and oogenesis group, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas-Les-Flots, France
| | - Juan Martin Traverso
- INRA, LPGP UR1037 Sex differentiation and oogenesis group, Campus de Beaulieu, Rennes, France
| | - Thaovi Nguyen
- INRA, LPGP UR1037 Sex differentiation and oogenesis group, Campus de Beaulieu, Rennes, France
| | | | | | - Julien Bobe
- INRA, LPGP UR1037 Sex differentiation and oogenesis group, Campus de Beaulieu, Rennes, France
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Desvignes T, Contreras A, Postlethwait JH. Evolution of the miR199-214 cluster and vertebrate skeletal development. RNA Biol 2014; 11:281-94. [PMID: 24643020 PMCID: PMC4075512 DOI: 10.4161/rna.28141] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/19/2014] [Accepted: 02/07/2014] [Indexed: 02/07/2023] Open
Abstract
MicroRNA (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. MicroRNAs are transcribed from miR genes and primary miR transcripts are processed to approximately 22 nucleotide single strand mature forms that function as repressors of transcript translation when bound to the 3'UTR of protein coding transcripts in association with the RISC. Because of their role in the regulation of gene expression, miRs are essential players in development by acting on cell fate determination and progression toward cell differentiation. The miR199 and miR214 genes occupy an intronic cluster located on the opposite strand of the Dynamin3 gene. These miRNAs play major roles in a broad variety of developmental processes and diseases, including skeletal development and several types of cancer. In the work reported here, we first deciphered the origin of the miR199 and miR214 families by following evolution of miR paralogs and their host Dynamin paralogs. We then examined the expression patterns of miR199 and miR214 in developing zebrafish embryos and demonstrated their regulation through a common primary transcript. Results suggest an evolutionarily conserved regulation across vertebrate lineages. Our expression study showed predominant expression patterns for both miR in tissues surrounding developing craniofacial skeletal elements consistent with expression data in mouse and human, thus indicating a conserved role of miR199 and miR214 in vertebrate skeletogenesis.
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Affiliation(s)
| | - Adam Contreras
- Institute of Neuroscience; University of Oregon; Eugene, OR USA
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Abstract
The Nme gene family, also known as Nm23 or NDPK, is a very ancient gene family that can be found in all kingdoms of life. In the late eighties, a gene of the Nme family, NME1, was identified as the first metastatic suppressor gene, resulting in a major interest for this family. Due to the complexity of the family, the need for a unified and evolutionary-supported gene nomenclature was recently stressed by the scientific community. Based on a complete evolutionary history study of the gene family in metazoans and vertebrates, a unified nomenclature was recently proposed and accepted by gene nomenclature consortia. In addition to its well-documented role in tumor metastasis, members of the Nme family are also involved in a wide variety of cellular and physiological processes. Available data in non-mammalian species remain, however, scarce with the noticeable exception of Drosophila in which a major role in development was reported. In fish, very few studies have specifically investigated the role of nme genes. Several transcriptomic and proteomic studies have, however, revealed the expression of nme genes in various fish organs and tissues, in mature oocytes, and during embryonic development. Altogether, interest for the Nme gene family in fish is growing and new functions/roles in fish biology are expected to be discovered in the forthcoming years. Here, we briefly review the current knowledge of the Nme family in fish.
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Affiliation(s)
- T Desvignes
- Fish Physiology and Genomics, INRA, UR1037 LPGP, Campus de Beaulieu, 35042, Rennes, France
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Desvignes T, Fauvel C, Bobe J. The NME gene family in zebrafish oogenesis and early development. Naunyn Schmiedebergs Arch Pharmacol 2011; 384:439-49. [PMID: 21394481 DOI: 10.1007/s00210-011-0619-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/26/2011] [Indexed: 01/31/2023]
Abstract
After the recent report of the expression of several nme genes in the zebrafish gonads, the present study aimed at further analyzing the expression of nme genes in the ovary with special attention for the nme transcripts that are maternally inherited and could thus participate in the determination of oocyte developmental competence. The expression levels of all groups I and II nme genes were characterized by QPCR in a panel of zebrafish tissues. The nme genes exhibiting an ovarian expression were subsequently monitored throughout oogenesis and early development, and their expression sites characterized using in situ hybridization. Here, we show that nme2b1, nme3, nme4, and nme6 are highly expressed in the ovary and present in the zebrafish oocyte throughout oogenesis. While the four transcripts are maternally inherited, nme3 and nme6 display a typical maternal profile and are detected in the zebrafish early embryo. In contrast to nme3, nme6, abundance exhibits a sharp decrease during early embryogenesis. After zygotic genome activation, we observed an increased expression of nme2b1, nme2b2, nme3, and nme6. The present study provides a comprehensive overview of the expression of nme family members during zebrafish oogenesis and early development. In addition, the maternal origin of two nme transcripts in the early embryo is reported here for the first time in any vertebrate species. Together, our observations suggest an important role of the nme family in oocyte and embryo development in vertebrates.
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Affiliation(s)
- T Desvignes
- INRA, UR1037 SCRIBE, Campus de Beaulieu, 35042, Rennes, France
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Desvignes T, Pontarotti P, Bobe J. Nme gene family evolutionary history reveals pre-metazoan origins and high conservation between humans and the sea anemone, Nematostella vectensis. PLoS One 2010; 5:e15506. [PMID: 21085602 PMCID: PMC2978717 DOI: 10.1371/journal.pone.0015506] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 10/05/2010] [Indexed: 11/19/2022] Open
Abstract
Background The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. Methodology/Principal Findings Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. Conclusion/Significance Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of key developmental and cellular processes.
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Affiliation(s)
- Thomas Desvignes
- UMR 6632/IFR48, Université de Provence Aix Marseille 1/CNRS, F-13000, Marseille, France
- IFREMER, LALR, F-34250, Palavas les flots, France
| | - Pierre Pontarotti
- UMR 6632/IFR48, Université de Provence Aix Marseille 1/CNRS, F-13000, Marseille, France
| | - Julien Bobe
- UMR 6632/IFR48, Université de Provence Aix Marseille 1/CNRS, F-13000, Marseille, France
- * E-mail:
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Abstract
BACKGROUND The Nme family, previously known as Nm23 or NDPK, is involved in various molecular processes including tumor metastasis and some members of the family, but not all, exhibit a Nucleoside Diphosphate Kinase (NDPK) activity. Ten genes are known in humans, in which some members have been extensively studied. In non-mammalian species, the Nme protein family has received, in contrast, far less attention. The picture of the vertebrate Nme family remains thus incomplete and orthology relationships with mammalian counterparts were only partially characterized. The present study therefore aimed at characterizing the Nme gene repertoire in vertebrates with special interest for teleosts, and providing a comprehensive overview of the Nme gene family evolutionary history in vertebrates. RESULTS In the present study, we present the evolutionary history of the Nme family in vertebrates and characterize the gene family repertoire for the first time in several non-mammalian species. Our observations show that vertebrate Nme genes can be separated in two evolutionary distinct groups. Nme1, Nme2, Nme3, and Nme4 belong to Group I while vertebrate Nme5, Nme6, Nme7, Nme8, and Nme9 belong to Group II. The position of Nme10 is in contrast more debatable due to its very specific evolutionary history. The present study clearly indicates that Nme5, Nme6, Nme7, and Nme8 originate from duplication events that occurred before the chordate radiation. In contrast, Nme genes of the Group I have a very different evolutionary history as our results suggest that they all arise from a common gene present in the chordate ancestor. In addition, expression patterns of all zebrafish nme transcripts were studied in a broad range of tissues by quantitative PCR and discussed in the light of the function of their mammalian counterparts. CONCLUSION This work offers an evolutionary framework that will pave the way for future studies on vertebrate Nme proteins and provides a unified vertebrate Nme nomenclature that is consistent with the nomenclature in use in mammals. Based on protein structure and expression data, we also provide new insight into molecular functions of Nme proteins among vertebrates and raise intriguing questions on the roles of Nme proteins in gonads.
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Affiliation(s)
- Thomas Desvignes
- INRA, UR1037 SCRIBE, IFR140, Ouest-Genopole, F-35000 Rennes, France
- IFREMER, LALR, F-34250 Palavas Les Flots, France
| | - Pierre Pontarotti
- UMR 6632/IFR48 Université de Aix Marseille/CNRS. Equipe Evolution biologique et Modélisation, case 19, 3 place Victor Hugo, 13331 Marseille Cedex 03, France
| | | | - Julien Bobe
- INRA, UR1037 SCRIBE, IFR140, Ouest-Genopole, F-35000 Rennes, France
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