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Baer L, Barthelson K, Postlethwait JH, Adelson DL, Pederson SM, Lardelli M. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. PLoS Comput Biol 2024; 20:e1011868. [PMID: 38346074 PMCID: PMC10890730 DOI: 10.1371/journal.pcbi.1011868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 02/23/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when the effects of homozygosity for recessive mutations are studied in non-isogenic backgrounds, genes located proximal to the mutation on the same chromosome often appear over-represented among those genes identified as differentially expressed (DE). One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect functional responses to the mutation but, instead, result from an unequal distribution of expression quantitative trait loci (eQTLs) between sample groups of mutant or wild-type genotypes. This is problematic because eQTL expression differences are difficult to distinguish from genes that are DE due to functional responses to a mutation. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) are also observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between those sample groups subjected to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting-based approaches. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. Our method for DAR analysis requires only RNA-sequencing data, facilitating its application across new and existing datasets.
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Affiliation(s)
- Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - John H. Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen M. Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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2
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Baer L, Barthelson K, Postlethwait J, Adelson D, Pederson S, Lardelli M. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530865. [PMID: 36945478 PMCID: PMC10028786 DOI: 10.1101/2023.03.02.530865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when homozygous mutations are studied in non-isogenic backgrounds, genes from the same chromosome as a mutation often appear over-represented among differentially expressed (DE) genes. One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect true biological responses to the mutation but, instead, result from differences in representation of expression quantitative trait loci (eQTLs) between sample groups selected on the basis of mutant or wild-type genotype. This is problematic when inclusion of spurious DE genes in a functional enrichment study results in incorrect inferences of mutation effect. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) can also be observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between groups of samples subject to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting of gene-level rankings. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. The DAR metric provides a solid foundation for addressing the eQTL issue in new and existing datasets because it relies solely on RNA-sequencing data.
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Affiliation(s)
- Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | | | - David Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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3
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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4
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Bisazza A, Santacà M. Zebrafish excel in number discrimination under an operant conditioning paradigm. Anim Cogn 2022; 25:917-933. [PMID: 35179665 PMCID: PMC9334370 DOI: 10.1007/s10071-022-01602-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/23/2022] [Indexed: 12/26/2022]
Abstract
Numerical discrimination is widespread in vertebrates, but this capacity varies enormously between the different species examined. The guppy (Poecilia reticulata), the only teleost examined following procedures that allow a comparison with the other vertebrates, outperforms amphibians, reptiles and many warm-blooded vertebrates, but it is unclear whether this is a feature shared with the other teleosts or represents a peculiarity of this species. We trained zebrafish (Danio rerio) to discriminate between numbers differing by one unit, varying task difficulty from 2 versus 3 to 5 versus 6 items. Non-numerical variables that covary with number, such as density or area, did not affect performance. Most fish reached learning criterion on all tasks up to 4 versus 5 discrimination with no sex difference in accuracy. Although no individual reached learning criterion in the 5 versus 6 task, performance was significant at the group level, suggesting that this may represent the discrimination threshold for zebrafish. Numerosity discrimination abilities of zebrafish compare to those of guppy, being higher than in some warm-blooded vertebrates, such as dogs, horses and domestic fowl, though lower than in parrots, corvids and primates. Learning rate was similar in a control group trained to discriminate between different-sized shapes, but zebrafish were slightly more accurate when discriminating areas than numbers and males were more accurate than females. At the end of the experiment, fish trained on numbers and controls trained on areas generalized to the reciprocal set of stimuli, indicating they had used a relational strategy to solve these tasks.
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Affiliation(s)
- Angelo Bisazza
- Department of General Psychology, University of Padova, Padua, Italy.,Padua Neuroscience Center, University of Padova, Padua, Italy
| | - Maria Santacà
- Department of Biology, University of Padova, Viale Giuseppe Colombo 3-Via Ugo Bassi 58/B, 35131, Padua, Italy.
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5
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Woo SJ, Chung JK. Cytochrome P450 1 enzymes in black rockfish, Sebastes schlegelii: Molecular characterization and expression patterns after exposure to benzo[a]pyrene. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 226:105566. [PMID: 32682194 DOI: 10.1016/j.aquatox.2020.105566] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 07/02/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Cytochrome P450 (CYP) enzymes play important roles in the detoxification and bioactivation of environmental contaminants and are involved in the responses to pollution in fish. In this study, we cloned four new CYP1 genes, CYP1A, CYP1B, CYP1C1, and CYP1C2, from black rockfish (Sebastes schlegelii), a dominant and economically important fish species in Korea. This species is at a significant risk of exposure to petrohydrocarbons, such as benzo[a]pyrene(B[a]P), due to frequent oil spills along the Korean coast. Quantitative PCR analysis of CYP1 gene transcription in 12 organs of the fish revealed tissue-specific expression patterns. CYP1A was significantly expressed in the liver, heart, kidneys, and muscle, and CYP1B was significantly expressed in the gills, muscle, and heart. CYP1C1 and CYP1C2 showed similar tissue expression patterns, with the highest levels in the muscle. Furthermore, exposure to an aryl hydrocarbon receptor (AHR) agonist, B[a]P, at 2, 20, and 200 mg/kg body weight showed significant dysregulation of the CYP1A, CYP1B, CYP1C1, and CYP1C2 expression levels in the gills, liver, kidneys, and spleen. The mRNA expression levels of CYP1A and CYP1B were upregulated by 450- and 17-fold, respectively, in the spleen. Compared with their levels in the control, CYP1C1 increased by 45-fold, while CYP1C2 remained unchanged in the gills, indicating differential effects of the polycyclic aromatic hydrocarbon on CYP1 expression in different fish organs. The results suggested that expression profiles of inducible CYP1 enzymes in S. schlegelii might be used as indicators for assessing aquatic contamination by AHR agonists. Determination of the basal and induced expression levels, as well as substrate specificity, of the four CYP1 enzymes may contribute to a better understanding of their roles in the metabolization of toxicants or drugs.
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Affiliation(s)
- Soo Ji Woo
- Department of Aquatic Life Medicine, Pukyong National University, Busan 48513, South Korea; Pathology Division, National Instititue of Fisheries Science, Busan 46083, South Korea
| | - Joon Ki Chung
- Department of Aquatic Life Medicine, Pukyong National University, Busan 48513, South Korea.
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6
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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: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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7
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Lucon-Xiccato T, Montalbano G, Bertolucci C. Personality traits covary with individual differences in inhibitory abilities in 2 species of fish. Curr Zool 2020; 66:187-195. [PMID: 32440277 PMCID: PMC7233618 DOI: 10.1093/cz/zoz039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/03/2019] [Indexed: 12/21/2022] Open
Abstract
In a number of animal species, individuals differ in their ability to solve cognitive tasks. However, the mechanisms underlying this variability remain unclear. It has been proposed that individual differences in cognition may be related to individual differences in behavior (i.e., personality); a hypothesis that has received mixed support. In this study, we investigated whether personality correlates with the cognitive ability that allows inhibiting behavior in 2 teleost fish species, the zebrafish Danio rerio and the guppy Poecilia reticulata. In both species, individuals that were bolder in a standard personality assay, the open-field test, showed greater inhibitory abilities in the tube task, which required them to inhibit foraging behavior toward live prey sealed into a transparent tube. This finding reveals a relationship between boldness and inhibitory abilities in fish and lends support to the hypothesis of a link between personality and cognition. Moreover, this study suggests that species separated by a relatively large phylogenetic distance may show the same link between personality and cognition, when tested on the same tasks.
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Affiliation(s)
- Tyrone Lucon-Xiccato
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - Giulia Montalbano
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
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8
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Ji LQ, Rao YZ, Zhang Y, Chen R, Tao YX. Regulation of melanocortin-1 receptor pharmacology by melanocortin receptor accessory protein 2 in orange-spotted grouper (Epinephelus coioides). Gen Comp Endocrinol 2020; 285:113291. [PMID: 31568758 DOI: 10.1016/j.ygcen.2019.113291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023]
Abstract
Melanocortin-1 receptor (MC1R) has important roles in regulating pigmentation and inflammation. Melanocortin receptor accessory protein 2 (MRAP2) modulates trafficking, ligand binding, and signaling of mammalian melanocortin receptors. However, the effect of MRAP2 on fish MC1R has not been extensively studied. Herein, we cloned the orange-spotted grouper (Epinephelus coioides) mc1r, which had a 972 bp open reading frame encoding a putative protein of 323 amino acids. Grouper mc1r was mainly expressed in the brain, skin, testis, spleen, head kidney, and kidney. EcoMC1R showed high constitutive activities in both Gs-cAMP and ERK1/2 pathways, which could be differentially modulated by grouper MRAP2 (EcoMRAP2). Three agonists, including α-melanocyte-stimulating hormone (MSH), β-MSH, and ACTH, could bind to EcoMC1R and dose-dependently increase intracellular cAMP production. EcoMRAP2 had no effect on the IC50 in binding assay or EC50 in cAMP assay; however, it dose-dependently decreased the cell surface expression and maximal response to the three agonists. EcoMRAP2 increased basal ERK1/2 activation but did not alter α-MSH-stimulated ERK1/2 activation. This study extends the knowledge base of fish MC1R pharmacology and its regulation by MRAP2.
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Affiliation(s)
- Li-Qin Ji
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ying-Zhu Rao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States; Institute of Applied Biotechnology, Life Science and Technology School, Lingnan Normal University, Zhanjiang 524048, Guangdong, China
| | - Yong Zhang
- Southern Laboratory of Ocean Science and Engineering (Zhuhai, Guangdong), Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Zhuhai 51900, China
| | - Rong Chen
- Institute of Applied Biotechnology, Life Science and Technology School, Lingnan Normal University, Zhanjiang 524048, Guangdong, China
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States.
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9
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Boothby TC. Mechanisms and evolution of resistance to environmental extremes in animals. EvoDevo 2019; 10:30. [PMID: 31827759 PMCID: PMC6862762 DOI: 10.1186/s13227-019-0143-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 11/02/2019] [Indexed: 11/25/2022] Open
Abstract
When animals are exposed to an extreme environmental stress, one of three possible outcomes takes place: the animal dies, the animal avoids the environmental stress and survives, or the animal tolerates the environmental stress and survives. This review is concerned with the third possibility, and will look at mechanisms that rare animals use to survive extreme environmental stresses including freezing, desiccation, intense heat, irradiation, and low-oxygen conditions (hypoxia). In addition, an increasing understanding of the molecular mechanisms involved in environmental stress tolerance allows us to speculate on how these tolerances arose. Uncovering the mechanisms of extreme environmental stress tolerance and how they evolve has broad implications for our understanding of the evolution of early life on this planet, colonization of new environments, and the search for novel forms of life both on Earth and elsewhere, as well as a number of agricultural and health-related applications.
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Affiliation(s)
- Thomas C Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY USA
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10
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Santacà M, Busatta M, Lucon-Xiccato T, Bisazza A. Sensory differences mediate species variation in detour task performance. Anim Behav 2019. [DOI: 10.1016/j.anbehav.2019.05.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Kaitetzidou E, Katsiadaki I, Lagnel J, Antonopoulou E, Sarropoulou E. Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis. Sci Rep 2019; 9:3752. [PMID: 30842559 PMCID: PMC6403355 DOI: 10.1038/s41598-019-40127-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/08/2019] [Indexed: 12/24/2022] Open
Abstract
Development requires the implementation of a plethora of molecular mechanisms, involving a large set of genes to ensure proper cell differentiation, morphogenesis of tissues and organs as well as the growth of the organism. Genome duplication and resulting paralogs are considered to provide the raw genetic materials important for new adaptation opportunities and boosting evolutionary innovation. The present study investigated paralogous genes, involved in three-spined stickleback (Gasterosteus aculeatus) development. Therefore, the transcriptomes of five early stages comprising developmental leaps were explored. Obtained expression profiles reflected the embryo's needs at different stages. Early stages, such as the morula stage comprised transcripts mainly involved in energy requirements while later stages were mostly associated with GO terms relevant to organ development and morphogenesis. The generated transcriptome profiles were further explored for differential expression of known and new paralogous genes. Special attention was given to hox genes, with hoxa13a being of particular interest and to pigmentation genes where itgb1, involved in the melanophore development, displayed a complementary expression pattern throughout studied stages. Knowledge obtained by untangling specific paralogous gene functions during development might not only significantly contribute to the understanding of teleost ontogenesis but might also shed light on paralogous gene evolution.
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Affiliation(s)
- Elisavet Kaitetzidou
- Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Institute for Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ioanna Katsiadaki
- Centre for Environment Fisheries and Aquaculture Science, (Cefas), Weymouth, UK
| | - Jacques Lagnel
- Institute for Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece.,Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GALF), Montfavet Cedex, France
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elena Sarropoulou
- Institute for Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece.
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12
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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] [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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13
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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: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [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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14
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Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Mol Phylogenet Evol 2017; 113:33-48. [PMID: 28487262 DOI: 10.1016/j.ympev.2017.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/23/2022]
Abstract
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.
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15
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Yang L, Zhang Z, He S. Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes. Genome Biol Evol 2016; 8:3433-3445. [PMID: 27742722 PMCID: PMC5203780 DOI: 10.1093/gbe/evw239] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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16
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Vivien CJ, Hudson JE, Porrello ER. Evolution, comparative biology and ontogeny of vertebrate heart regeneration. NPJ Regen Med 2016; 1:16012. [PMID: 29302337 PMCID: PMC5744704 DOI: 10.1038/npjregenmed.2016.12] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/01/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022] Open
Abstract
There are 64,000 living species of vertebrates on our planet and all of them have a heart. Comparative analyses devoted to understanding the regenerative potential of the myocardium have been performed in a dozen vertebrate species with the aim of developing regenerative therapies for human heart disease. Based on this relatively small selection of animal models, important insights into the evolutionary conservation of regenerative mechanisms have been gained. In this review, we survey cardiac regeneration studies in diverse species to provide an evolutionary context for the lack of regenerative capacity in the adult mammalian heart. Our analyses highlight the importance of cardiac adaptations that have occurred over hundreds of millions of years during the transition from aquatic to terrestrial life, as well as during the transition from the womb to an oxygen-rich environment at birth. We also discuss the evolution and ontogeny of cardiac morphological, physiological and metabolic adaptations in the context of heart regeneration. Taken together, our findings suggest that cardiac regenerative potential correlates with a low-metabolic state, the inability to regulate body temperature, low heart pressure, hypoxia, immature cardiomyocyte structure and an immature immune system. A more complete understanding of the evolutionary context and developmental mechanisms governing cardiac regenerative capacity would provide stronger scientific foundations for the translation of cardiac regeneration therapies into the clinic.
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Affiliation(s)
- Celine J Vivien
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD, Australia
| | - James E Hudson
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD, Australia
| | - Enzo R Porrello
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD, Australia
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17
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Abstract
The mangrove killifish Kryptolebias marmoratus, and its close relative Kryptolebias hermaphroditus, are the only vertebrate species known to reproduce by self-fertilization due to functional ovotestis development. To improve our understanding of their genomes, we constructed a genetic map. First, a single F1 fish was made by artificial fertilization between K. marmoratus and K. hermaphroditus strains. F2 progeny were then obtained by self-fertilization of the F1 fish. We used RAD-seq to query genomic DNAs from the two parental strains, the F1 individual and 49 F2 progeny. Results identified 9904 polymorphic RAD-tags (DNA markers) that mapped to 24 linkage groups, corresponding to the haploid chromosome number of these species. The total length of the map was 1248 cM, indicating that about one recombination occurred for each of the 24 homologous chromosome pairs in each meiosis. Markers were not evenly distributed along the chromosomes: in all chromosomes, many markers (> 8% of the total markers for each chromosome) mapped to chromosome tips. Centromeres suppress recombination, and this uneven distribution is probably due to the species’ acrocentric chromosomes. Mapped marker sequences were compared to genomic sequences of medaka and platyfish, the next most closely related species with sequenced genomes that are anchored to genetic maps. Results showed that each mangrove killifish chromosome corresponds to a single chromosome of both platyfish and medaka, suggesting strong conservation of chromosomes over 100 million years of evolution. Our genetic map provides a framework for the K. marmoratus/K. hermaphroditus genome sequence and an important resource for understanding the biology of hermaphroditism.
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18
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Davis A, Reubens MC, Stellwag EJ. Functional and Comparative Genomics of Hoxa2 Gene cis-Regulatory Elements: Evidence for Evolutionary Modification of Ancestral Core Element Activity. J Dev Biol 2016; 4:jdb4020015. [PMID: 29615583 PMCID: PMC5831782 DOI: 10.3390/jdb4020015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Hoxa2 is an evolutionarily conserved developmental regulatory gene that functions to specify rhombomere (r) and pharyngeal arch (PA) identities throughout the Osteichthyes. Japanese medaka (Oryzias latipes) hoxa2a, like orthologous Hoxa2 genes from other osteichthyans, is expressed during embryogenesis in r2–7 and PA2-7, whereas the paralogous medaka pseudogene, ψhoxa2b, is expressed in noncanonical Hoxa2 domains, including the pectoral fin buds. To understand the evolution of cis-regulatory element (CRE) control of gene expression, we conducted eGFP reporter gene expression studies with extensive functional mapping of several conserved CREs upstream of medaka hoxa2a and ψhoxa2b in transient and stable-line transgenic medaka embryos. The CREs tested were previously shown to contribute to directing mouse Hoxa2 gene expression in r3, r5, and PA2-4. Our results reveal the presence of sequence elements embedded in the medaka hoxa2a and ψhoxa2b upstream enhancer regions (UERs) that mediate expression in r4 and the PAs (hoxa2a r4/CNCC element) or in r3–7 and the PAs ψhoxa2b r3–7/CNCC element), respectively. Further, these elements were shown to be highly conserved among osteichthyans, which suggests that the r4 specifying element embedded in the UER of Hoxa2 is a deeply rooted rhombomere specifying element and the activity of this element has been modified by the evolution of flanking sequences that redirect its activity to alternative developmental compartments.
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Affiliation(s)
- Adam Davis
- Department of Biology and Physical Sciences, Gordon State College, Barnesville, GA 30204, USA.
| | - Michael C Reubens
- The Scripps Research Institute, 10550 N, Torrey Pines Road, MB3, La Jolla, CA 92037, USA.
| | - Edmund J Stellwag
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA.
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19
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Walter RB, Obara T. Workshop report: The medaka model for comparative assessment of human disease mechanisms. Comp Biochem Physiol C Toxicol Pharmacol 2015; 178:156-162. [PMID: 26099189 PMCID: PMC4662895 DOI: 10.1016/j.cbpc.2015.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 11/29/2022]
Abstract
Results of recent studies showing the utility of medaka as a model of various human disease states were presented at the 7th Aquatic Models of Human Disease Conference (December 13-18, 2014, Austin, TX). This conference brought together many of the most highly regarded national and international scientists that employ the medaka model in their investigations. To take advantage of this opportunity, a cohort of established medaka researchers were asked to stay an extra day and represent the medaka scientific community in a workshop entitled "The Medaka Model for Comparative Assessment of Human Disease Mechanisms." The central purpose of this medaka workshop was to assess current use and project the future resource needs of the American medaka research community. The workshop sought to spur discussions of issues that would promote more informative comparative disease model studies. Finally, workshop attendees met together to propose, discuss, and agree on recommendations regarding the most effective research resources needed to enable US scientists to perform experiments leading to impacting experimental results that directly translate to human disease. Consistent with this central purpose, the workshop was divided into two sessions of invited speakers having expertise and experience in the session topics. The workshop hosted 20 scientific participants (Appendices 1 and 2), and of these, nine scientists presented formal talks. Here, we present a summary report stemming from workshop presentations and subsequent round table discussions and forward recommendations from this group that we believe represent views of the overall medaka research community.
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Affiliation(s)
- Ronald B Walter
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 419 Centennial Hall, San Marcos, TX 78666, USA.
| | - Tomoko Obara
- Department of Cell Biology, University of Oklahoma Health Sciences Center, BRC Room 256, 975 N.E. 10th St., Oklahoma City, OK 73104-5419, USA.
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20
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AlMomin S, Kumar V, Al-Amad S, Al-Hussaini M, Dashti T, Al-Enezi K, Akbar A. Draft genome sequence of the silver pomfret fish, Pampus argenteus. Genome 2015; 59:51-8. [PMID: 26692342 DOI: 10.1139/gen-2015-0056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.
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Affiliation(s)
- Sabah AlMomin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Vinod Kumar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Sami Al-Amad
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Mohsen Al-Hussaini
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Talal Dashti
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Khaznah Al-Enezi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Abrar Akbar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
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21
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Edmunds RC, Su B, Balhoff JP, Eames BF, Dahdul WM, Lapp H, Lundberg JG, Vision TJ, Dunham RA, Mabee PM, Westerfield M. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. Mol Biol Evol 2015; 33:13-24. [PMID: 26500251 PMCID: PMC4693980 DOI: 10.1093/molbev/msv223] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.
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Affiliation(s)
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University
| | | | - B Frank Eames
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wasila M Dahdul
- National Evolutionary Synthesis Center, Durham, NC Department of Biology, University of South Dakota
| | - Hilmar Lapp
- National Evolutionary Synthesis Center, Durham, NC
| | - John G Lundberg
- Department of Ichthyology, The Academy of Natural Sciences, Philadelphia, Philadelphia, PA
| | - Todd J Vision
- National Evolutionary Synthesis Center, Durham, NC Department of Biology, University of North Carolina, Chapel Hill
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University
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22
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Pinto DP, Chivittz CC, Ferreira RS, Sopezki MS, Zanette J. Beta-naphthoflavone-inducedCYP1A expression in the guppy Jenynsia multidentata: Time-dependent response, anesthetic MS-222 effect and fin analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 113:38-44. [PMID: 25483370 DOI: 10.1016/j.ecoenv.2014.11.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/20/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
Cytochrome P450 1A (CYP1A) expression in fish is used as a biomarker of exposure to organic contaminants, such PAHs, PCBs and dioxins, in the aquatic environment. South American guppy fish Jenynsia multidentata were exposed to the prototypical aryl hydrocarbon receptor (AHR) agonist beta-naphthoflavone (BNF; 1μM) and the fins were biopsied to characterize different aspects of CYP1A induction. RTq-PCR was used to quantify CYP1A mRNA levels in fish tissues. CYP1A induction in the gill, liver and anal fin (gonopodium) occurred within the first hour of waterborne exposure to BNF and persisted throughout 2, 4, 8, 24, 48 and 96h compared to controls (DMSO vehicle; p<0.05). The organ-specific temporal pattern of induction was marked by mRNA levels consistently augment as duration of exposure increases and tend to a sustained induction from 24h to 96h for gill and liver (∼15-fold and ∼50-fold over control, respectively). In gonopodium, there was a maximum CYP1A mRNA level at 4h (∼34-fold over control). Basal CYP1A mRNA levels and its induction following BNF exposure were not affected by administration of a chemical anesthetic (fish immersion in 100mgl(-1) MS-222 for 2-5min) in the gill, liver, gonopodium, dorsal or tail fin (p<0.05). In an ex vivo assay, in which small pieces of biopsied fins were exposed to BNF for 4h, high CYP1A induction was observed in the tail and gonopodium (∼49-fold and ∼69-fold, respectively) but not in the dorsal fin compared to controls. To our knowledge, this is the first study to show that a 1h waterborne exposure to an AHR agonist is sufficient to cause CYP1A induction in fish organs and fins. The present study added new information to the field regarding the use of MS-222 as an anesthetic on fish and the analysis of biopsied fins as an alternative non-lethalex vivo assay for evaluating the CYP1A biomarker in fish. This observation could be useful for planning fish toxicological bioassays and biomonitoring studies on the aquatic environments in South America.
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Affiliation(s)
- Debora P Pinto
- Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS 96203-900, Brazil
| | - Cíntia C Chivittz
- Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS 96203-900, Brazil
| | - Roger S Ferreira
- Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS 96203-900, Brazil
| | - Mauricio S Sopezki
- Programa de Pós-graduação em Ciências Fisiológicas - Fisiologia Animal Comparada, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS 96203-900, Brazil
| | - Juliano Zanette
- Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS 96203-900, Brazil; Programa de Pós-graduação em Ciências Fisiológicas - Fisiologia Animal Comparada, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Rio Grande, RS 96203-900, Brazil.
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23
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Garcia de la Serrana D, Mareco EA, Johnston IA. Systematic variation in the pattern of gene paralog retention between the teleost superorders Ostariophysi and Acanthopterygii. Genome Biol Evol 2015; 6:981-7. [PMID: 24732281 PMCID: PMC4007551 DOI: 10.1093/gbe/evu074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Teleost fish underwent whole-genome duplication around 450 Ma followed by diploidization and loss of 80-85% of the duplicated genes. To identify a deep signature of this teleost-specific whole-genome duplication (TSGD), we searched for duplicated genes that were systematically and uniquely retained in one or other of the superorders Ostariophysi and Acanthopterygii. TSGD paralogs comprised 17-21% of total gene content. Some 2.6% (510) of TSGD paralogs were present as pairs in the Ostariophysi genomes of Danio rerio (Cypriniformes) and Astyanax mexicanus (Characiformes) but not in species from four orders of Acanthopterygii (Gasterosteiformes, Gasterosteus aculeatus; Tetraodontiformes, Tetraodon nigroviridis; Perciformes, Oreochromis niloticus; and Beloniformes, Oryzias latipes) where a single copy was identified. Similarly, 1.3% (418) of total gene number represented cases where TSGD paralogs pairs were systematically retained in the Acanthopterygian but conserved as a single copy in Ostariophysi genomes. We confirmed the generality of these results by phylogenetic and synteny analysis of 40 randomly selected linage-specific paralogs (LSPs) from each superorder and completed with the transcriptomes of three additional Ostariophysi species (Ictalurus punctatus [Siluriformes], Sinocyclocheilus species [Cypriniformes], and Piaractus mesopotamicus [Characiformes]). No chromosome bias was detected in TSGD paralog retention. Gene ontology (GO) analysis revealed significant enrichment of GO terms relative to the human GO SLIM database for "growth," "Cell differentiation," and "Embryo development" in Ostariophysi and for "Transport," "Signal Transduction," and "Vesicle mediated transport" in Acanthopterygii. The observed patterns of paralog retention are consistent with different diploidization outcomes having contributed to the evolution/diversification of each superorder.
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24
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Comparative mapping for bighead carp (Aristichthys nobilis) against model and non-model fishes provides insights into the genomic evolution of cyprinids. Mol Genet Genomics 2015; 290:1313-26. [PMID: 25627158 DOI: 10.1007/s00438-015-0992-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 01/09/2015] [Indexed: 02/03/2023]
Abstract
Comparative mapping provides an efficient method to connect genomes of non-model and model fishes. In this study, we used flanking sequences of the 659 microsatellites on a genetic map of bighead carp (Aristichthys nobilis) to comprehensively study syntenic relationships between bighead carp and nine model and non-model fishes. Of the five model and two food fishes with whole genome data, Cyprinus carpio showed the highest rate of positive BLAST hits (95.3 %) with bighead carp map, followed by Danio rerio (70.9 %), Oreochromis niloticus (21.7 %), Tetraodon nigroviridis (6.4 %), Gasterosteus aculeatus (5.2 %), Oryzias latipes (4.7 %) and Fugu rubripes (3.5 %). Chromosomal syntenic analyses showed that inversion was the basic chromosomal rearrangement during genomic evolution of cyprinids, and the extent of inversions and translocations was found to be positively correlated with evolutionary relationships among fishes studied. Among the five investigated cyprinids, linkage groups (LGs) of bighead carp, Hypophthalmichthys molitrix and Ctenopharyngodon idella exhibited a one-to-one relationship. Besides, LG 9 of bighead carp and homologous LGs of silver carp and grass carp all corresponded to the chromosomes 10 and 22 of zebrafish, suggesting that chromosomal fission may have occurred in the ancestor of zebrafish. On the other hand, LGs of bighead carp and common carp showed an approximate one-to-two relationship with extensive translocations, confirming the occurrence of a 4th whole genome duplication in common carp. This study provides insights into the understanding of genome evolution among cyprinids and would aid in transferring positional and functional information of genes from model fish like zebrafish to non-model fish like bighead carp.
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Yang L, Wang Y, Zhang Z, He S. Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus. Genome Biol Evol 2014; 7:251-61. [PMID: 25543049 PMCID: PMC4316632 DOI: 10.1093/gbe/evu279] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ying Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Ontario, Canada Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
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Sovrano VA, Albertazzi L, Rosa Salva O. The Ebbinghaus illusion in a fish (Xenotoca eiseni). Anim Cogn 2014; 18:533-42. [DOI: 10.1007/s10071-014-0821-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 11/10/2014] [Indexed: 12/31/2022]
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Gori S, Agrillo C, Dadda M, Bisazza A. Do fish perceive illusory motion? Sci Rep 2014; 4:6443. [PMID: 25246001 PMCID: PMC4171700 DOI: 10.1038/srep06443] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022] Open
Abstract
Motion illusion refers to a perception of motion that is absent or different in the physical stimulus. These illusions are a powerful non-invasive tool for understanding the neurobiology of vision because they tell us, indirectly, how we process motion. There is general agreement in ascribing motion illusion to higher-level processing in the visual cortex, but debate remains about the exact role of eye movements and cortical networks in triggering it. Surprisingly, there have been no studies investigating global illusory motion evoked by static patterns in animal species other than humans. Herein, we show that fish perceive one of the most studied motion illusions, the Rotating Snakes. Fish responded similarly to real and illusory motion. The demonstration that complex global illusory motion is not restricted to humans and can be found even in species that do not have a cortex paves the way to develop animal models to study the neurobiological bases of motion perception.
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Affiliation(s)
- Simone Gori
- 1] Developmental and Cognitive Neuroscience lab, Department of General Psychology, University of Padua [2] Developmental Neuropsychology Unit, Scientific Institute "E. Medea, " Bosisio Parini, Lecco
| | - Christian Agrillo
- Comparative Psychology Research Group, Department of General Psychology, University of Padua
| | - Marco Dadda
- Comparative Psychology Research Group, Department of General Psychology, University of Padua
| | - Angelo Bisazza
- Comparative Psychology Research Group, Department of General Psychology, University of Padua
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Berdan EL, Kozak GM, Ming R, Rayburn AL, Kiehart R, Fuller RC. Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion. G3 (BETHESDA, MD.) 2014; 4:1363-72. [PMID: 24898707 PMCID: PMC4132168 DOI: 10.1534/g3.114.012096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/20/2014] [Indexed: 01/31/2023]
Abstract
Linkage maps are important tools in evolutionary genetics and in studies of speciation. We performed a karyotyping study and constructed high-density linkage maps for two closely related killifish species, Lucania parva and L. goodei, that differ in salinity tolerance and still hybridize in their contact zone in Florida. Using SNPs from orthologous EST contigs, we compared synteny between the two species to determine how genomic architecture has shifted with divergence. Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes (1N) whereas L. parva possesses 23 chromosomes (1N), one of which is a large metacentric chromosome. Likewise, high-density single-nucleotide polymorphism-based linkage maps indicated 24 linkage groups for L. goodei and 23 linkage groups for L. parva. Synteny mapping revealed two linkage groups in L. goodei that were highly syntenic with the largest linkage group in L. parva. Together, this evidence points to the largest linkage group in L. parva being the result of a chromosomal fusion. We further compared synteny between Lucania with the genome of a more distant teleost relative medaka (Oryzias latipes) and found good conservation of synteny at the chromosomal level. Each Lucania LG had a single best match with each medaka chromosome. These results provide the groundwork for future studies on the genetic architecture of reproductive isolation and salinity tolerance in Lucania and other Fundulidae.
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Affiliation(s)
- Emma L Berdan
- Department of Animal Biology, University of Illinois, Champaign, Illinois 61820
| | - Genevieve M Kozak
- Department of Animal Biology, University of Illinois, Champaign, Illinois 61820
| | - Ray Ming
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| | - A Lane Rayburn
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Ryan Kiehart
- Department of Biology, Ursinus College, Collegeville, Pennsylvania 19426
| | - Rebecca C Fuller
- Department of Animal Biology, University of Illinois, Champaign, Illinois 61820
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29
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Amores A, Catchen J, Nanda I, Warren W, Walter R, Schartl M, Postlethwait JH. A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Genetics 2014; 197:625-41. [PMID: 24700104 PMCID: PMC4063920 DOI: 10.1534/genetics.114.164293] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 03/20/2014] [Indexed: 11/18/2022] Open
Abstract
Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, teleost fish genomes are stable (24-25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years.
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Affiliation(s)
- Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Indrajit Nanda
- Institute of Human Genetics, University of Würzburg, D-97074 Würzburg, Germany
| | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Ron Walter
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, and Comprehensive Cancer Center, University Clinic Würzburg, 97074 Würzburg, Germany
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Blewett TA, Chow TL, MacLatchy DL, Wood CM. A species comparison of 17-α-ethynylestradiol uptake and tissue-specific distribution in six teleost fish. Comp Biochem Physiol C Toxicol Pharmacol 2014; 161:33-40. [PMID: 24473066 DOI: 10.1016/j.cbpc.2014.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 11/22/2022]
Abstract
Differences exist among fish species in their sensitivity to endocrine disruptors such as 17-α-ethynylestradiol (EE2). We examined whether there were corresponding differences in EE2 uptake rates and short-term internal distribution patterns. Six freshwater species: Japanese ricefish (medaka, Oryzias latipes), goldfish (Carassius auratus), zebrafish (Danio rerio), fathead minnow (Pimephales promelas), Atlantic killifish (Fundulus heteroclitus) and rainbow trout (Oncorhynchus mykiss) were exposed to waterborne radiolabelled EE2 (100ng/L) for 2-h measurements of uptake, tissue accumulation and oxygen consumption rates (MO2). EE2 uptake rate and MO2 were relatively consistent among species (2.5-3.0 fold variation), with the only significant differences being a lower EE2 uptake rate in medaka, and lower MO2 in medaka, goldfish, and zebrafish relative to the other species. EE2 accumulation, however, exhibited two distinct patterns, suggesting differences in metabolic processing. In killifish and medaka, the highest accumulation (~50%) occurred in the liver and gallbladder, whereas in minnow, goldfish, zebrafish and trout, >50% accumulated in the carcass. No significant sex differences were found in killifish or minnow, apart from lower gill tissue EE2 accumulation in minnow females. This study demonstrated that metabolic processing of EE2 may be species-specific and tissue specific EE2 distribution profiles vary. These could be indicative of differences in overall EE2 sensitivity among species.
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Affiliation(s)
- Tamzin A Blewett
- Department of Biology, McMaster University, Hamilton, ON, Canada.
| | - Tiffany L Chow
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - Chris M Wood
- Department of Biology, McMaster University, Hamilton, ON, Canada
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31
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Sallan LC. Major issues in the origins of ray-finned fish (Actinopterygii) biodiversity. Biol Rev Camb Philos Soc 2014; 89:950-71. [DOI: 10.1111/brv.12086] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/02/2014] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Lauren C. Sallan
- Department of Organismal Biology and Anatomy; University of Chicago; Chicago IL 60637 U.S.A
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 U.S.A
- Michigan Society of Fellows; University of Michigan; Ann Arbor MI 48109 U.S.A
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Norman JD, Ferguson MM, Danzmann RG. Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes. Physiol Genomics 2013; 46:123-37. [PMID: 24368751 DOI: 10.1152/physiolgenomics.00105.2013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Osmoregulatory capabilities have played an important role in the evolution, dispersal, and diversification of vertebrates. To better understand the genetic architecture of hypo-osmoregulation in fishes and to determine which genes and biological processes affect intraspecific variation in salinity tolerance, we used mRNA sequence libraries from Arctic charr gill tissue to compare gene expression profiles in fish exhibiting divergent salinity tolerance quantitative trait locus (QTL) genotypes. We compared differentially expressed genes with QTL positions to gain insight about the nature of the underlying polymorphisms and examined gene expression within the context of genome organization to gain insight about the evolution of hypo-osmoregulation in fishes. mRNA sequencing of 18 gill tissue libraries produced 417 million reads, and the final reduced de novo transcriptome assembly consisted of 92,543 contigs. Families contained a similar number of differentially expressed contigs between high and low salinity tolerance capacity groups, and log2 expression ratios ranged from 10.4 to -8.6. We found that intraspecific variation in salinity tolerance capacity correlated with differential expression of immune response genes. Some differentially expressed genes formed clusters along linkage groups. Most clusters comprised gene pairs, though clusters of three, four, and eight genes were also observed. We postulated that conserved synteny of gene clusters on multiple ancestral and teleost chromosomes may have been preserved via purifying selection. Colocalization of QTL with differentially expressed genes suggests that polymorphisms in cis-regulatory elements are part of a majority of QTL.
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Affiliation(s)
- Joseph D Norman
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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33
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Graham LA, Hobbs RS, Fletcher GL, Davies PL. Helical antifreeze proteins have independently evolved in fishes on four occasions. PLoS One 2013; 8:e81285. [PMID: 24324684 PMCID: PMC3855684 DOI: 10.1371/journal.pone.0081285] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/21/2013] [Indexed: 12/25/2022] Open
Abstract
Alanine-rich α-helical (type I) antifreeze proteins (AFPs) are produced by a variety of fish species from three different orders to protect against freezing in icy seawater. Interspersed amongst and within these orders are fishes making AFPs that are completely different in both sequence and structure. The origin of this variety of types I, II, III and antifreeze glycoproteins (AFGPs) has been attributed to adaptation following sea-level glaciations that occurred after the divergence of most of the extant families of fish. The presence of similar types of AFPs in distantly related fishes has been ascribed to lateral gene transfer in the case of the structurally complex globular type II lectin-like AFPs and to convergent evolution for the AFGPs, which consist of a well-conserved tripeptide repeat. In this paper, we examine the genesis of the type I AFPs, which are intermediate in complexity. These predominantly α-helical peptides share many features, such as putative capping structures, Ala-richness and amphipathic character. We have added to the type I repertoire by cloning additional sequences from sculpin and have found that the similarities between the type I AFPs of the four distinct groups of fishes are not borne out at the nucleotide level. Both the non-coding sequences and the codon usage patterns are strikingly different. We propose that these AFPs arose via convergence from different progenitor helices with a weak affinity for ice and that their similarity is dictated by the propensity of specific amino acids to form helices and to align water on one side of the helix into an ice-like pattern.
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Affiliation(s)
- Laurie A. Graham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Rod S. Hobbs
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Garth L. Fletcher
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Peter L. Davies
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- * E-mail:
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Jiang Y, Gao X, Liu S, Zhang Y, Liu H, Sun F, Bao L, Waldbieser G, Liu Z. Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species. BMC Genomics 2013; 14:780. [PMID: 24215161 PMCID: PMC3840565 DOI: 10.1186/1471-2164-14-780] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 10/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative mapping is a powerful tool to study evolution of genomes. It allows transfer of genome information from the well-studied model species to non-model species. Catfish is an economically important aquaculture species in United States. A large amount of genome resources have been developed from catfish including genetic linkage maps, physical maps, BAC end sequences (BES), integrated linkage and physical maps using BES-derived markers, physical map contig-specific sequences, and draft genome sequences. Application of such genome resources should allow comparative analysis at the genome scale with several other model fish species. RESULTS In this study, we conducted whole genome comparative analysis between channel catfish and four model fish species with fully sequenced genomes, zebrafish, medaka, stickleback and Tetraodon. A total of 517 Mb draft genome sequences of catfish were anchored to its genetic linkage map, which accounted for 62% of the total draft genome sequences. Based on the location of homologous genes, homologous chromosomes were determined among catfish and the four model fish species. A large number of conserved syntenic blocks were identified. Analysis of the syntenic relationships between catfish and the four model fishes supported that the catfish genome is most similar to the genome of zebrafish. CONCLUSION The organization of the catfish genome is similar to that of the four teleost species, zebrafish, medaka, stickleback, and Tetraodon such that homologous chromosomes can be identified. Within each chromosome, extended syntenic blocks were evident, but the conserved syntenies at the chromosome level involve extensive inter-chromosomal and intra-chromosomal rearrangements. This whole genome comparative map should facilitate the whole genome assembly and annotation in catfish, and will be useful for genomic studies of various other fish species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, 203 Swingle Hall, Auburn University, Auburn, AL 36849, USA.
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Agrillo C, Miletto Petrazzini ME, Dadda M. Illusory patterns are fishy for fish, too. Front Neural Circuits 2013; 7:137. [PMID: 24009560 PMCID: PMC3755263 DOI: 10.3389/fncir.2013.00137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/07/2013] [Indexed: 11/17/2022] Open
Affiliation(s)
- Christian Agrillo
- Department of General Psychology, University of Padova Padova, Italy.
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36
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Wu J, Husile, Sun H, Wang F, Li Y, Zhao C, Zhang W. Adaptive evolution of Hoxc13 genes in the origin and diversification of the vertebrate integument. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:412-9. [PMID: 25961277 DOI: 10.1002/jez.b.22504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/07/2013] [Accepted: 04/01/2013] [Indexed: 11/06/2022]
Abstract
The problem of origination and diversification of integument derivatives in vertebrates is still a challenge. The homeobox (Hox) genes Hoxc13 control integument formation in vertebrate. Hoxc13 show strong expression in the integument development, are highly conserved across vertebrates, and show mutations that are associated with skin and appendages. To test whether the evolution of the integument is associated with positive selection or relaxation of Hoxc13, we obtained these genes in a wide range of vertebrates. In Hoxc13, we found evidence of diversifying selection after speciation during the origin of vertebrates. In addition, we found the glycine-rich regions in Hoxc13 protein in mammals, but not among non-mammalian taxa. Our results strongly implicate that Hoxc13 genes could have played an important role in the evolution of integument structure.
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Affiliation(s)
- Jianghong Wu
- Inner Mongolia Prataculture Research Center, Chinese Academy of Science, Hohhot, China.,Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
| | - Husile
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
| | - Hailian Sun
- Inner Mongolia Prataculture Research Center, Chinese Academy of Science, Hohhot, China
| | - Feng Wang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Yurong Li
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Cunfa Zhao
- Inner Mongolia Prataculture Research Center, Chinese Academy of Science, Hohhot, China.,Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Wenguang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
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The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet 2013; 45:567-72. [PMID: 23542700 PMCID: PMC3677569 DOI: 10.1038/ng.2604] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/01/2013] [Indexed: 01/23/2023]
Abstract
Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth, and malignant diseases like cancer, also appeared several times independently in so-called “lower” vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, Xiphophorus maculatus, offers a unique model to better understand the molecular biology of such traits. Herein we detail sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps uncovered that fish, in contrast to mammals, exhibit an unexpected evolutionary stability of chromosomes. Genes associated with viviparity show signatures of positive selection identifying new putative functional domains and rare cases of parallel evolution. We also discovered that genes implicated in cognition possess an unexpected high rate of duplicate gene retention after the teleost genome duplication suggesting a hypothesis for the evolution of the great behavioral complexity in fish, which exceeds that in amphibians and reptiles.
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38
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Ghysen A, Dambly-Chaudière C, Coves D, de la Gandara F, Ortega A. Developmental origin of a major difference in sensory patterning between zebrafish and bluefin tuna. Evol Dev 2013. [PMID: 23189756 PMCID: PMC3488297 DOI: 10.1111/j.1525-142x.2012.00529.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The posterior lateral line system (PLL) of teleost fish comprises a number of mechanosensory organs arranged in defined patterns on the body surface. Embryonic patterns are largely conserved among teleosts, yet adult patterns are highly diverse. Although changes in pattern modify the perceptual abilities of the system, their developmental origin remains unknown. Here we compare the processes that underlie the formation of the juvenile PLL pattern in Thunnus thynnus, the bluefin tuna, to the processes that were elucidated in Danio rerio, the zebrafish. In both cases, the embryonic PLL comprises five neuromasts regularly spaced along the horizontal myoseptum, but the juvenile PLL comprises four roughly parallel anteroposterior lines in zebrafish, whereas it is a simple dorsally arched line in tuna fish. We examined whether this difference involves evolutionary novelties, and show that the same mechanisms mediate the transition from embryonic to juvenile patterns in both species. We conclude that the marked difference in juveniles depends on a single change (dorsal vs. ventral migration of neuromasts) in the first days of larval life.
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Yoder JB, Briskine R, Mudge J, Farmer A, Paape T, Steele K, Weiblen GD, Bharti AK, Zhou P, May GD, Young ND, Tiffin P. Phylogenetic signal variation in the genomes of Medicago (Fabaceae). Syst Biol 2013; 62:424-38. [PMID: 23417680 DOI: 10.1093/sysbio/syt009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the Medicago truncatula reference genome to confidently identify 87 596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago species, to investigate the number of sites needed to provide robust phylogenetic estimates and to identify specific genomic regions supporting topologies in conflict with the genome-wide phylogeny. Our full genomic data set resolves relationships within the genus that were previously intractable. Subsampling the data reveals considerable variation in phylogenetic signal and power in smaller subsets of the data. Even when sampling 5000 sites, no random sample of the data supports a topology identical to that of the genome-wide phylogeny. Phylogenetic relationships estimated from 500-site sliding windows revealed genome regions supporting several alternative species relationships among recently diverged taxa, consistent with the expected effects of deep coalescence or introgression in the recent history of Medicago.
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Affiliation(s)
- Jeremy B Yoder
- Department of Plant Biology, University of Minnesota, Saint Paul MN 55108, USA
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Kuraku S. Impact of asymmetric gene repertoire between cyclostomes and gnathostomes. Semin Cell Dev Biol 2013; 24:119-27. [DOI: 10.1016/j.semcdb.2012.12.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 12/25/2012] [Indexed: 12/12/2022]
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A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq). G3-GENES GENOMES GENETICS 2013; 3:65-74. [PMID: 23316439 PMCID: PMC3538344 DOI: 10.1534/g3.112.003897] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/05/2012] [Indexed: 12/30/2022]
Abstract
Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F2 hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F2 offspring, we calculated a genome-wide mutation rate of 6.6 × 10−8 mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.
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Svingerud T, Solstad T, Sun B, Nyrud MLJ, Kileng Ø, Greiner-Tollersrud L, Robertsen B. Atlantic Salmon Type I IFN Subtypes Show Differences in Antiviral Activity and Cell-Dependent Expression: Evidence for High IFNb/IFNc–Producing Cells in Fish Lymphoid Tissues. THE JOURNAL OF IMMUNOLOGY 2012; 189:5912-23. [DOI: 10.4049/jimmunol.1201188] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Agrillo C, Miletto Petrazzini ME, Tagliapietra C, Bisazza A. Inter-specific differences in numerical abilities among teleost fish. Front Psychol 2012; 3:483. [PMID: 23162517 PMCID: PMC3498878 DOI: 10.3389/fpsyg.2012.00483] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 10/19/2012] [Indexed: 11/13/2022] Open
Abstract
Adults, infants and non-human primates are thought to possess similar non-verbal numerical systems, but there is considerable debate regarding whether all vertebrates share the same numerical abilities. Despite an abundance of studies, cross-species comparison remains difficult because the methodology employed and the context of species examination vary considerably across studies. To fill this gap, we used the same procedure, stimuli, and numerical contrasts to compare quantity abilities of five teleost fish: redtail splitfin, guppies, zebrafish, Siamese fighting fish, and angelfish. Subjects were trained to discriminate between two sets of geometrical figures using a food reward. Fish initially were trained on an easy numerical ratio (5 vs. 10 and 6 vs. 12). Once they reached the learning criterion, they were subjected to non-reinforced probe trials in which the set size was constant but numerical ratios varied (8 vs. 12 and 9 vs. 12). They also were subjected to probe trials in which the ratio was constant, but the total set size was increased (25 vs. 50) or decreased (2 vs. 4). Overall, fish generalized to numerosities with a 0.67 ratio, but failed with a 0.75 ratio; they generalized to a smaller set size, but not to a larger one. Only minor differences were observed among the five species. However, in one species, zebrafish, the proportion of individuals reaching the learning criterion was much smaller than in the others. In a control experiment, zebrafish showed a similar lower performance in shape discrimination, suggesting that the observed difference resulted from the zebrafish's difficulty in learning this procedure rather than from a cross-species variation in the numerical domain.
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Affiliation(s)
- Christian Agrillo
- Department of General Psychology, University of Padova Padova, Italy
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A window into domain amplification through Piccolo in teleost fish. G3-GENES GENOMES GENETICS 2012; 2:1325-39. [PMID: 23173084 PMCID: PMC3484663 DOI: 10.1534/g3.112.003624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/31/2012] [Indexed: 12/20/2022]
Abstract
I describe and characterize the extensive amplification of the zinc finger domain of Piccolo selectively in teleost fish. Piccolo and Bassoon are partially functionally redundant and play roles in regulating the pool of neurotransmitter-filled synaptic vesicles present at synapses. In mice, each protein contains two N-terminal zinc finger domains that have been implicated in interacting with synaptic vesicles. In all teleosts examined, both the Bassoon and Piccolo genes are duplicated. Both teleost bassoon genes and one piccolo gene show very similar domain structure and intron-exon organization to their mouse homologs. In contrast, in piccolo b a single exon that encodes a zinc finger domain is amplified 8 to 16 times in different teleost species. Analysis of the amplified exons suggests they were added and/or deleted from the gene as individual exons in rare events that are likely the result of unequal crossovers between homologous sequences. Surprisingly, the structure of the repeats from cod and zebrafish suggest that amplification of this exon has occurred independently multiple times in the teleost lineage. Based on the structure of the exons, I propose a model in which selection for high sequence similarity at the 5′ and 3′ ends of the exon drives amplification of the repeats and diversity in repeat length likely promotes the stability of the repeated exons by minimizing the likelihood of mispairing of adjacent repeat sequences. Further analysis of piccolo b in teleosts should provide a window through which to examine the process of domain amplification.
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Graham LA, Li J, Davidson WS, Davies PL. Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes. BMC Evol Biol 2012; 12:190. [PMID: 23009612 PMCID: PMC3499448 DOI: 10.1186/1471-2148-12-190] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/20/2012] [Indexed: 12/26/2022] Open
Abstract
Background Type II antifreeze protein (AFP) from the rainbow smelt, Osmerus mordax, is a calcium-dependent C-type lectin homolog, similar to the AFPs from herring and sea raven. While C-type lectins are ubiquitous, type II AFPs are only found in a few species in three widely separated branches of teleost fishes. Furthermore, several other non-homologous AFPs are found in intervening species. We have previously postulated that this sporadic distribution has resulted from lateral gene transfer. The alternative hypothesis, that the AFP evolved from a lectin present in a shared ancestor and that this gene was lost in most species, is not favored because both the exon and intron sequences are highly conserved. Results Here we have sequenced and annotated a 160 kb smelt BAC clone containing a centrally-located AFP gene along with 14 other genes. Quantitative PCR indicates that there is but a single copy of this gene within the smelt genome, which is atypical for fish AFP genes. The corresponding syntenic region has been identified and searched in a number of other species and found to be devoid of lectin or AFP sequences. Unlike the introns of the AFP gene, the intronic sequences of the flanking genes are not conserved between species. As well, the rate and pattern of mutation in the AFP gene are radically different from those seen in other smelt and herring genes. Conclusions These results provide stand-alone support for an example of lateral gene transfer between vertebrate species. They should further inform the debate about genetically modified organisms by showing that gene transfer between ‘higher’ eukaryotes can occur naturally. Analysis of the syntenic regions from several fishes strongly suggests that the smelt acquired the AFP gene from the herring.
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Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
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Zou M, Guo B, Tao W, Arratia G, He S. Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii). Sci Rep 2012; 2:665. [PMID: 22993690 PMCID: PMC3444750 DOI: 10.1038/srep00665] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/20/2012] [Indexed: 11/09/2022] Open
Abstract
The actinopterygians comprise nearly one-half of all extant vertebrate species and are very important for human well-being. However, the phylogenetic relationships among certain groups within the actinopterygians are still uncertain, and debates about these relationships have continued for a long time. Along with the progress achieved in sequencing technologies, phylogenetic analyses based on multi-gene sequences, termed phylogenomic approaches, are becoming increasingly common and often result in well-resolved and highly supported phylogenetic hypotheses. Based on the transcriptome sequences generated in this study and the extensive expression data currently available from public databases, we obtained alignments of 274 orthologue groups for 26 scientifically and commercially important actinopterygians, representing 17 out of 44 orders within the class Actinopterygii. Using these alignments and probabilistic methods, we recovered relationships between basal actinopterygians and teleosts, among teleosts within protacanthopterygians and related lineages, and also within acanthomorphs. These relationships were recovered with high confidence.
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Affiliation(s)
- Ming Zou
- The key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, PR China
| | - Baocheng Guo
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
| | - Wenjing Tao
- The key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, PR China
| | - Gloria Arratia
- Biodiversity Research Institute, The University of Kansas, Lawrence, Kansas 66045, U.S.A
| | - Shunping He
- The key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes from 371 Animalia: Updated structure-based alignment and detailed phylogenetic analysis. Mol Phylogenet Evol 2012; 64:603-17. [DOI: 10.1016/j.ympev.2012.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022]
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Kuraku S, Qiu H, Meyer A. Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys. Genome Biol Evol 2012; 4:929-36. [PMID: 22887124 PMCID: PMC3516227 DOI: 10.1093/gbe/evs069] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Horizontal gene transfer (HGT) has been recognized to be an important mechanism that shaped the evolution and genomes of prokaryotes and unicellular eukaryotes. However, HGT is regarded to be exceedingly rare among eukaryotes. We discovered massive transfers of a DNA transposon, a Tc1 element encoding a transposase, between multiple teleost fishes and lampreys that last shared a common ancestor over 500 Ma. Members of this group of Tc1 elements were found to exhibit a mosaic phylogenetic distribution, yet their sequences were highly similar even between distantly related lineages (95%-99% identity). Our molecular phylogenetic analyses suggested that horizontal transfers of this element happened repeatedly, involving multiple teleost fishes that are phylogenetically only distantly related. Interestingly, almost all the affected teleost lineages are also known to be subject to lamprey parasitism, suggesting that the horizontal transfers between vertebrates might have occurred through parasite-host interaction. The genomes of several northern hemisphere lamprey species, including that of the sea lamprey (Petromyzon marinus), were found to contain thousands of copies of the foreign elements. Impact of this event is discussed in relation to other peculiar genomic features of lampreys.
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Shen XX, Liang D, Zhang P. The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR. PLoS One 2012; 7:e39256. [PMID: 22720083 PMCID: PMC3375249 DOI: 10.1371/journal.pone.0039256] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/22/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics. METHODOLOGY/PRINCIPAL FINDINGS We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR. CONCLUSIONS/SIGNIFICANCE Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for phylogenetic questions of osteichthyans at different taxonomic levels.
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Affiliation(s)
- Xing-Xing Shen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Dan Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Peng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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Fan S, Elmer KR, Meyer A. Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages. Philos Trans R Soc Lond B Biol Sci 2012; 367:385-94. [PMID: 22201168 DOI: 10.1098/rstb.2011.0247] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cichlid fishes are remarkably phenotypically diverse and species-rich. Therefore, they provide an exciting opportunity for the study of the genetics of adaptation and speciation by natural and sexual selection. Here, we review advances in the genomics and transcriptomics of cichlids, particularly regarding ecologically relevant differences in body shape, trophic apparatus, coloration and patterning, and sex determination. Research conducted so far has focused almost exclusively on African cichlids. To analyse genomic diversity and selection in a Neotropical radiation, we conducted a comparative transcriptomic analysis between sympatric, ecologically divergent crater-lake Midas cichlids (Lake Xiloá Amphilophus amarillo and Amphilophus sagittae). We pyrosequenced (Roche 454) expressed sequence tag (EST) libraries and generated more than 178 000 000 ESTs and identified nine ESTs under positive selection between these sister species (Ka/Ks > 1). None of these ESTs were found to be under selection in African cichlids. Of 11 candidate genes for ecomorphological differentiation in African cichlids, none showed signs of selection between A. amarillo and A. sagittae. Although more population-level studies are now needed to thoroughly document patterns of divergence during speciation of cichlids, available information so far suggests that adaptive phenotypic diversification in Neotropical and African cichlids may be evolving through non-parallel genetic bases.
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Affiliation(s)
- Shaohua Fan
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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