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Wangler MF, Yamamoto S, Chao HT, Posey JE, Westerfield M, Postlethwait J, Hieter P, Boycott KM, Campeau PM, Bellen HJ. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research. Genetics 2017; 207:9-27. [PMID: 28874452 PMCID: PMC5586389 DOI: 10.1534/genetics.117.203067] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions. Here, we review the current state of research into undiagnosed diseases, highlighting large efforts in North America and internationally, including the Undiagnosed Diseases Network (UDN) (Supplemental Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM). We discuss how merging human genetics with model organism research guides experimental studies to solve these medical mysteries, gain new insights into disease pathogenesis, and uncover new therapeutic strategies.
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Affiliation(s)
- Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Hsiao-Tuan Chao
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4C, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario K1H 8L1, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Quebec H3T 1C5, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
- Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, Texas 77030
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52
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Le François NR, Sheehan E, Desvignes T, Belzile C, Postlethwait JH, Detrich HW. Characterization and husbandry of wild broodstock of the blackfin icefish Chaenocephalus aceratus (Lönnberg 1906) from the Palmer Archipelago (Southern Ocean) for breeding purposes. Polar Biol 2017. [DOI: 10.1007/s00300-017-2161-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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53
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Broeckhoven C, de Kock C, Mouton PLFN. Sexual dimorphism in osteoderm expression and the role of male intrasexual aggression. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Lu Y, Klimovich CM, Robeson KZ, Boswell W, Ríos-Cardenas O, Walter RB, Morris MR. Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fish Xiphophorus multilineatus. PeerJ 2017; 5:e3275. [PMID: 28480144 PMCID: PMC5417068 DOI: 10.7717/peerj.3275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 04/04/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanisms of nutritional programming. The live-bearing fish Xiphophorus multilineatus has the potential to be a new model for understanding these mechanisms, given prior evidence of nutritional programming influencing behavior and juvenile growth rate. We tested the hypotheses that nutritional programming would influence behaviors involved in energy homeostasis as well gene expression in X. multilineatus. METHODS We first examined the influence of both juvenile environment (varied in nutrition and density) and adult environment (varied in nutrition) on behaviors involved in energy acquisition and energy expenditure in adult male X. multilineatus. We also compared the behavioral responses across the genetically influenced size classes of males. Males stop growing at sexual maturity, and the size classes of can be identified based on phenotypes (adult size and pigment patterns). To study the molecular signatures of nutritional programming, we assembled a de novo transcriptome for X. multilineatus using RNA from brain, liver, skin, testis and gonad tissues, and used RNA-Seq to profile gene expression in the brains of males reared in low quality (reduced food, increased density) and high quality (increased food, decreased density) juvenile environments. RESULTS We found that both the juvenile and adult environments influenced the energy intake behavior, while only the adult environment influenced energy expenditure. In addition, there were significant interactions between the genetically influenced size classes and the environments that influenced energy intake and energy expenditure, with males from one of the four size classes (Y-II) responding in the opposite direction as compared to the other males examined. When we compared the brains of males of the Y-II size class reared in a low quality juvenile environment to males from the same size class reared in high quality juvenile environment, 131 genes were differentially expressed, including metabolism and appetite master regulator agrp gene. DISCUSSION Our study provides evidence for nutritional programming in X. multilineatus, with variation across size classes of males in how juvenile environment and adult diet influences behaviors involved in energy homeostasis. In addition, we provide the first transcriptome of X. multilineatus, and identify a group of candidate genes involved in nutritional programming.
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Affiliation(s)
- Yuan Lu
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | | | - Kalen Z Robeson
- Department of Biological Sciences, Ohio University, Athens, OH, USA
| | - William Boswell
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Oscar Ríos-Cardenas
- Red de Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Mexico
| | - Ronald B Walter
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Molly R Morris
- Department of Biological Sciences, Ohio University, Athens, OH, USA
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55
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Opazo JC, Zavala K, Krall P, Arias RA. Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants. PeerJ 2017; 5:e2901. [PMID: 28149683 PMCID: PMC5274524 DOI: 10.7717/peerj.2901] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022] Open
Abstract
Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile , Valdivia , Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile , Valdivia , Chile
| | - Paola Krall
- Unidad de Nefrología, Universidad Austral de Chile , Valdivia , Chile
| | - Rodrigo A Arias
- Instituto de Producción Animal, Universidad Austral de Chile , Valdivia , Chile
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56
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Krishnan J, Rohner N. Cavefish and the basis for eye loss. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150487. [PMID: 27994128 PMCID: PMC5182419 DOI: 10.1098/rstb.2015.0487] [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] [Accepted: 06/08/2016] [Indexed: 11/12/2022] Open
Abstract
Animals have colonized the entire world from rather moderate to the harshest environments, some of these so extreme that only few animals are able to survive. Cave environments present such a challenge and obligate cave animals have adapted to perpetual darkness by evolving a multitude of traits. The most common and most studied cave characteristics are the regression of eyes and the overall reduction in pigmentation. Studying these traits can provide important insights into how evolutionary forces drive convergent and regressive adaptation. The blind Mexican cavefish (Astyanax mexicanus) has emerged as a useful model to study cave evolution owing to the availability of genetic and genomic resources, and the amenability of embryonic development as the different populations remain fertile with each other. In this review, we give an overview of our current knowledge underlying the process of regressive and convergent evolution using eye degeneration in cavefish as an example.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Jaya Krishnan
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
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57
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Schartl M, Walter RB. Xiphophorus and Medaka Cancer Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:531-52. [PMID: 27165369 DOI: 10.1007/978-3-319-30654-4_23] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Besides recently developed zebrafish cancer models, other fish species have been employed for many years as cancer models in laboratory studies. Two models, namely in Xiphophorus and medaka have proven useful in providing important clues to cancer etiology. Medaka is a complementary model to zebrafish in many areas of research since it offers similar resources and experimental tools. Xiphophorus provides the advantages of a natural ("evolutionary mutant") model with established genetics. Xiphophorus hybrids can develop spontaneous and radiation or carcinogen induced cancers. This chapter describes the tumor models in both species, which mainly focus on melanoma, and summarizes the main findings and future research directions.
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Affiliation(s)
- Manfred Schartl
- Physiologische Chemie, Universität Würzburg, Biozentrum, Am Hubland, D-97074, Würzburg, Germany. .,Texas Institute for Advanced Study and Department of Biology, Texas A&M University, 100 Butler Hall, College Station, Texas, 77843-3258, USA.
| | - Ronald B Walter
- Chemistry and Biochemistry, 419A Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX, 78666-4616, USA
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58
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Postlethwait JH, Yan YL, Desvignes T, Allard C, Titus T, Le François NR, Detrich HW. Embryogenesis and early skeletogenesis in the antarctic bullhead notothen, Notothenia coriiceps. Dev Dyn 2016; 245:1066-1080. [PMID: 27507212 DOI: 10.1002/dvdy.24437] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Environmental temperature influences rates of embryonic development, but a detailed staging series for vertebrate embryos developing in the subzero cold of Antarctic waters is not yet available from fertilization to hatching. Given projected warming of the Southern Ocean, it is imperative to establish a baseline to evaluate potential effects of changing climate on fish developmental dynamics. RESULTS We studied the Bullhead notothen (Notothenia coriiceps), a notothenioid fish inhabiting waters between -1.9 and +2 °C. In vitro fertilization produced embryos that progressed through cleavage, epiboly, gastrulation, segmentation, organogenesis, and hatching. We compared morphogenesis spatially and temporally to Zebrafish and medaka. Experimental animals hatched after about 6 months to early larval stages. To help understand skeletogenesis, we analyzed late embryos for expression of sox9 and runx2, which regulate chondrogenesis, osteogenesis, and eye development. Results revealed that, despite their prolonged developmental time course, N. coriiceps embryos developed similarly to those of other teleosts with large yolk cells. CONCLUSIONS Our studies set the stage for future molecular analyses of development in these extremophile fish. Results provide a foundation for understanding the impact of ocean warming on embryonic development and larval recruitment of notothenioid fish, which are key factors in the marine trophic system. Developmental Dynamics 245:1066-1080, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Corey Allard
- Biodôme de Montréal, Division des collections vivantes et recherche, Montréal, Quebec, Canada
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | - Nathalie R Le François
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
| | - H William Detrich
- Biodôme de Montréal, Division des collections vivantes et recherche, Montréal, Quebec, Canada
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59
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Powder KE, Albertson RC. Cichlid fishes as a model to understand normal and clinical craniofacial variation. Dev Biol 2016; 415:338-346. [PMID: 26719128 PMCID: PMC4914429 DOI: 10.1016/j.ydbio.2015.12.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 01/26/2023]
Abstract
We have made great strides towards understanding the etiology of craniofacial disorders, especially for 'simple' Mendelian traits. However, the facial skeleton is a complex trait, and the full spectrum of genetic, developmental, and environmental factors that contribute to its final geometry remain unresolved. Forward genetic screens are constrained with respect to complex traits due to the types of genes and alleles commonly identified, developmental pleiotropy, and limited information about the impact of environmental interactions. Here, we discuss how studies in an evolutionary model - African cichlid fishes - can complement traditional approaches to understand the genetic and developmental origins of complex shape. Cichlids exhibit an unparalleled range of natural craniofacial morphologies that model normal human variation, and in certain instances mimic human facial dysmorphologies. Moreover, the evolutionary history and genomic architecture of cichlids make them an ideal system to identify the genetic basis of these phenotypes via quantitative trait loci (QTL) mapping and population genomics. Given the molecular conservation of developmental genes and pathways, insights from cichlids are applicable to human facial variation and disease. We review recent work in this system, which has identified lbh as a novel regulator of neural crest cell migration, determined the Wnt and Hedgehog pathways mediate species-specific bone morphologies, and examined how plastic responses to diet modulate adult facial shapes. These studies have not only revealed new roles for existing pathways in craniofacial development, but have identified new genes and mechanisms involved in shaping the craniofacial skeleton. In all, we suggest that combining work in traditional laboratory and evolutionary models offers significant potential to provide a more complete and comprehensive picture of the myriad factors that are involved in the development of complex traits.
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Affiliation(s)
- Kara E Powder
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
| | - R Craig Albertson
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
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60
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Petersen AM, Earp NC, Redmond ME, Postlethwait JH, von Hippel FA, Buck CL, Cresko WA. Perchlorate Exposure Reduces Primordial Germ Cell Number in Female Threespine Stickleback. PLoS One 2016; 11:e0157792. [PMID: 27383240 PMCID: PMC4934864 DOI: 10.1371/journal.pone.0157792] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/03/2016] [Indexed: 11/18/2022] Open
Abstract
Perchlorate is a common aquatic contaminant that has long been known to affect thyroid function in vertebrates, including humans. More recently perchlorate has been shown to affect primordial sexual differentiation in the aquatic model fishes zebrafish and threespine stickleback, but the mechanism has been unclear. Stickleback exposed to perchlorate from fertilization have increased androgen levels in the embryo and disrupted reproductive morphologies as adults, suggesting that perchlorate could disrupt the earliest stages of primordial sexual differentiation when primordial germ cells (PGCs) begin to form the gonad. Female stickleback have three to four times the number of PGCs as males during the first weeks of development. We hypothesized that perchlorate exposure affects primordial sexual differentiation by reducing the number of germ cells in the gonad during an important window of stickleback sex determination at 14-18 days post fertilization (dpf). We tested this hypothesis by quantifying the number of PGCs at 16 dpf in control and 100 mg/L perchlorate-treated male and female stickleback. Perchlorate exposure from the time of fertilization resulted in significantly reduced PGC number only in genotypic females, suggesting that the masculinizing effects of perchlorate observed in adult stickleback may result from early changes to the number of PGCs at a time critical for sex determination. To our knowledge, this is the first evidence of a connection between an endocrine disruptor and reduction in PGC number prior to the first meiosis during sex determination. These findings suggest that a mode of action of perchlorate on adult reproductive phenotypes in vertebrates, including humans, such as altered fecundity and sex reversal or intersex gonads, may stem from early changes to germ cell development.
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Affiliation(s)
- Ann M. Petersen
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, 97403, United States of America
- Department of Integrative Biology, Oregon State University Cascades, Bend, Oregon 97703, United States of America
| | - Nathanial C. Earp
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Mandy E. Redmond
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - John H. Postlethwait
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Frank A. von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86001, United States of America
| | - C. Loren Buck
- Department of Biological Sciences & Center for Bioengineering Innovation, Northern Arizona University, Flagstaff, Arizona, 86001, United States of America
| | - William A. Cresko
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon, 97403, United States of America
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61
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Abstract
The Genetics Society of America’s George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers and who exemplify the qualities of its namesake as a respected academic, administrator, and public servant. The 2015 recipient is John Postlethwait. He has made groundbreaking contributions in developing the zebrafish as a molecular genetic model and in understanding the evolution of new gene functions in vertebrates. He built the first zebrafish genetic map and showed that its genome, along with that of distantly related teleost fish, had been duplicated. Postlethwait played an integral role in the zebrafish genome-sequencing project and elucidated the genomic organization of several fish species. Postlethwait is also honored for his active involvement with the zebrafish community, advocacy for zebrafish as a model system, and commitment to driving the field forward.
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62
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Sun Y, Huang Y, Li X, Baldwin CC, Zhou Z, Yan Z, Crandall KA, Zhang Y, Zhao X, Wang M, Wong A, Fang C, Zhang X, Huang H, Lopez JV, Kilfoyle K, Zhang Y, Ortí G, Venkatesh B, Shi Q. Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies. Gigascience 2016; 5:18. [PMID: 27144000 PMCID: PMC4853854 DOI: 10.1186/s13742-016-0124-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/14/2016] [Indexed: 11/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in ‘omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the “Transcriptomes of 1,000 Fishes” (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far.
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Affiliation(s)
- Ying Sun
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China ; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China
| | - Xiaofeng Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China
| | - Carole C Baldwin
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560 USA
| | | | | | - Keith A Crandall
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA
| | - Yong Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China
| | - Xiaomeng Zhao
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China
| | - Min Wang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China ; BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000 China
| | - Alex Wong
- BGI-Hong Kong, Hong Kong, 999077 China
| | - Chao Fang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China
| | - Hai Huang
- Sanya Science and Technology Academy for Crop Winter Multiplication, Hainan, 572000 China
| | - Jose V Lopez
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale, 33004 USA
| | - Kirk Kilfoyle
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale, 33004 USA
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, ASTAR, Singapore, 138673 Singapore
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China ; BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000 China ; College of Life Sciences, Shenzhen University, Shenzhen, 518060 China
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63
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Abstract
The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
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64
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Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:427-37. [PMID: 26950095 PMCID: PMC4817229 DOI: 10.1038/ng.3526] [Citation(s) in RCA: 403] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022]
Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Andrew R Gehrke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Jeremy Pasquier
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Aaron M Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S Campbell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, UK
| | - John F Mulley
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Vydianathan Ravi
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Alison P Lee
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Tetsuya Nakamura
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Shaohua Fan
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dustin Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Cristian Cañestro
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Felix E G Beaudry
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Yi Sun
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Mikio Ishiyama
- Department of Dental Hygiene, Nippon Dental University College at Niigata, Niigata, Japan
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steffi Kehr
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Marcia Lara
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John H Letaw
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Masato Mikami
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Hayama, Japan
| | - Nil Ratan Saha
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Louise Williams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - John S Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Brazil
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
- International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | - Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Yann Guiguen
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Julien Bobe
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Neil H Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | | | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Developmental basis of phenotypic integration in two Lake Malawi cichlids. EvoDevo 2016; 7:3. [PMID: 26798449 PMCID: PMC4721197 DOI: 10.1186/s13227-016-0040-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023] Open
Abstract
Background Cichlid fishes from the Rift Lakes of East Africa have undergone the most spectacular adaptive radiations in vertebrate history. Eco-morphological adaptations in lakes Victoria, Malawi and Tanganyika have resulted in a vast array of skull shapes and sizes, yet primary axes of morphological variation are conserved in all three radiations, prominently including the size of the preorbital region of the skull. This conserved pattern suggests that development may constrain the trajectories of cichlid head morphological evolution. Results Here, we (1) present a comparative analysis of adult head morphology in two sand-dweller cichlids from Lake Malawi with preorbital size differences representative of the main axis of variation among the three lakes and (2) analyze the ontogeny of shape and size differences by focusing on known developmental modules throughout the head. We find that (1) developmental differences between the two species correlate with known developmental modules; (2) differences in embryonic cartilage development result in phenotypically integrated changes among all bones derived from a single cartilage, while differences in dermal bone development tend to influence isolated regions within a bone; and lastly (3) species-specific morphologies appear in the embryo as subtle differences, which become progressively amplified throughout ontogeny. We propose that this amplification takes place at skeletal growth zones, the locations and shapes of which are patterned during embryogenesis. Conclusions This study is the most anatomically comprehensive analysis of the developmental differences underlying cichlid skull evolution in the Rift Lakes of East Africa. The scale of our analysis reveals previously unnoticed correlations between developmental modules and patterns of phenotypic integration. We propose that the primary axes of morphological variation among East African cichlid adaptive radiations are constrained by the hierarchical modularity of the teleost head skeleton.
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Gross JB, Stahl BA, Powers AK, Carlson BM. Natural bone fragmentation in the blind cave-dwelling fish, Astyanax mexicanus: candidate gene identification through integrative comparative genomics. Evol Dev 2016; 18:7-18. [PMID: 26153732 PMCID: PMC5226847 DOI: 10.1111/ede.12131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Animals that colonize dark and nutrient-poor subterranean environments evolve numerous extreme phenotypes. These include dramatic changes to the craniofacial complex, many of which are under genetic control. These phenotypes can demonstrate asymmetric genetic signals wherein a QTL is detected on one side of the face but not the other. The causative gene(s) underlying QTL are difficult to identify with limited genomic resources. We approached this task by searching for candidate genes mediating fragmentation of the third suborbital bone (SO3) directly inferior to the orbit of the eye. We integrated positional genomic information using emerging Astyanax resources, and linked these intervals to homologous (syntenic) regions of the Danio rerio genome. We identified a discrete, approximately 6 Mb, conserved region wherein the gene causing SO3 fragmentation likely resides. We interrogated this interval for genes demonstrating significant differential expression using mRNA-seq analysis of cave and surface morphs across life history. We then assessed genes with known roles in craniofacial evolution and development based on GO term annotation. Finally, we screened coding sequence alterations in this region, identifying two key genes: transforming growth factor β3 (tgfb3) and bone morphogenetic protein 4 (bmp4). Of these candidates, tgfb3 is most promising as it demonstrates significant differential expression across multiple stages of development, maps close (<1 Mb) to the fragmentation critical locus, and is implicated in a variety of other animal systems (including humans) in non-syndromic clefting and malformations of the cranial sutures. Both abnormalities are analogous to the failure-to-fuse phenotype that we observe in SO3 fragmentation. This integrative approach will enable discovery of the causative genetic lesions leading to complex craniofacial features analogous to human craniofacial disorders. This work underscores the value of cave-dwelling fish as a powerful evolutionary model of craniofacial disease, and demonstrates the power of integrative system-level studies for informing the genetic basis of craniofacial aberrations in nature.
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Affiliation(s)
- Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Bethany A. Stahl
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Amanda K. Powers
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Brian M. Carlson
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
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Milligan-Myhre K, Small CM, Mittge EK, Agarwal M, Currey M, Cresko WA, Guillemin K. Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations. Dis Model Mech 2015; 9:187-98. [PMID: 26681746 PMCID: PMC4770144 DOI: 10.1242/dmm.021881] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 12/04/2015] [Indexed: 12/19/2022] Open
Abstract
Animal hosts must co-exist with beneficial microbes while simultaneously being able to mount rapid, non-specific, innate immune responses to pathogenic microbes. How this balance is achieved is not fully understood, and disruption of this relationship can lead to disease. Excessive inflammatory responses to resident microbes are characteristic of certain gastrointestinal pathologies such as inflammatory bowel disease (IBD). The immune dysregulation of IBD has complex genetic underpinnings that cannot be fully recapitulated with single-gene-knockout models. A deeper understanding of the genetic regulation of innate immune responses to resident microbes requires the ability to measure immune responses in the presence and absence of the microbiota using vertebrate models with complex genetic variation. Here, we describe a new gnotobiotic vertebrate model to explore the natural genetic variation that contributes to differences in innate immune responses to microbiota. Threespine stickleback, Gasterosteus aculeatus, has been used to study the developmental genetics of complex traits during the repeated evolution from ancestral oceanic to derived freshwater forms. We established methods to rear germ-free stickleback larvae and gnotobiotic animals monoassociated with single bacterial isolates. We characterized the innate immune response of these fish to resident gut microbes by quantifying the neutrophil cells in conventionally reared monoassociated or germ-free stickleback from both oceanic and freshwater populations grown in a common intermediate salinity environment. We found that oceanic and freshwater fish in the wild and in the laboratory share many intestinal microbial community members. However, oceanic fish mount a strong immune response to residential microbiota, whereas freshwater fish frequently do not. A strong innate immune response was uniformly observed across oceanic families, but this response varied among families of freshwater fish. The gnotobiotic stickleback model that we have developed therefore provides a platform for future studies mapping the natural genetic basis of the variation in immune response to microbes. Summary: We developed a gnotobiotic threespine stickleback system to identify the cellular and genetic bases for variation in inflammatory responses to microbiota.
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Affiliation(s)
- Kathryn Milligan-Myhre
- Biology Department, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA Biology Department, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
| | - Clayton M Small
- Biology Department, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Erika K Mittge
- Biology Department, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Meghna Agarwal
- Biology Department, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Mark Currey
- Biology Department, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Biology Department, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Karen Guillemin
- Biology Department, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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Hassinen M, Haverinen J, Vornanen M. Molecular basis and drug sensitivity of the delayed rectifier (IKr) in the fish heart. Comp Biochem Physiol C Toxicol Pharmacol 2015. [PMID: 26215639 DOI: 10.1016/j.cbpc.2015.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fishes are increasingly used as models for human cardiac diseases, creating a need for a better understanding of the molecular basis of fish cardiac ion currents. To this end we cloned KCNH6 channel of the crucian carp (Carassius carassius) that produces the rapid component of the delayed rectifier K(+) current (IKr), the main repolarising current of the fish heart. KCNH6 (ccErg2) was the main isoform of the Kv11 potassium channel family with relative transcript levels of 98.9% and 99.6% in crucian carp atrium and ventricle, respectively. KCNH2 (ccErg1), an orthologue to human cardiac Erg (Herg) channel, was only slightly expressed in the crucian carp heart. The native atrial IKr and the cloned ccErg2 were inhibited by similar concentrations of verapamil, terfenadine and KB-R7943 (P>0.05), while the atrial IKr was about an order of magnitude more sensitive to E-4031 than ccErg2 (P<0.05) suggesting that some accessory β-subunits may be involved. Sensitivity of the crucian carp atrial IKr to E-4031, terfenadine and KB-R7943 was similar to what has been reported for the Herg channel. In contrast, the sensitivity of the crucian carp IKr to verapamil was approximately 30 times higher than the previously reported values for the Herg current. In conclusion, the cardiac IKr is produced by non-orthologous gene products in fish (Erg2) and mammalian hearts (Erg1) and some marked differences exist in drug sensitivity between fish and mammalian Erg1/2 which need to be taken into account when using fish heart as a model for human heart.
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Affiliation(s)
- Minna Hassinen
- University of Eastern Finland, Department of Biology, P.O. Box 111, 80101 Joensuu, Finland.
| | - Jaakko Haverinen
- University of Eastern Finland, Department of Biology, P.O. Box 111, 80101 Joensuu, Finland
| | - Matti Vornanen
- University of Eastern Finland, Department of Biology, P.O. Box 111, 80101 Joensuu, Finland
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Johanson Z, Boisvert C, Maksimenko A, Currie P, Trinajstic K. Development of the Synarcual in the Elephant Sharks (Holocephali; Chondrichthyes): Implications for Vertebral Formation and Fusion. PLoS One 2015; 10:e0135138. [PMID: 26339918 PMCID: PMC4560447 DOI: 10.1371/journal.pone.0135138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/17/2015] [Indexed: 01/03/2023] Open
Abstract
The synarcual is a structure incorporating multiple elements of two or more anterior vertebrae of the axial skeleton, forming immediately posterior to the cranium. It has been convergently acquired in the fossil group ‘Placodermi’, in Chondrichthyes (Holocephali, Batoidea), within the teleost group Syngnathiformes, and to varying degrees in a range of mammalian taxa. In addition, cervical vertebral fusion presents as an abnormal pathology in a variety of human disorders. Vertebrae develop from axially arranged somites, so that fusion could result from a failure of somite segmentation early in development, or from later heterotopic development of intervertebral bone or cartilage. Examination of early developmental stages indicates that in the Batoidea and the ‘Placodermi’, individual vertebrae developed normally and only later become incorporated into the synarcual, implying regular somite segmentation and vertebral development. Here we show that in the holocephalan Callorhinchus milii, uniform and regular vertebral segmentation also occurs, with anterior individual vertebra developing separately with subsequent fusion into a synarcual. Vertebral elements forming directly behind the synarcual continue to be incorporated into the synarcual through growth. This appears to be a common pattern through the Vertebrata. Research into human disorders, presenting as cervical fusion at birth, focuses on gene misexpression studies in humans and other mammals such as the mouse. However, in chondrichthyans, vertebral fusion represents the normal morphology, moreover, taxa such Leucoraja (Batoidea) and Callorhinchus (Holocephali) are increasingly used as laboratory animals, and the Callorhinchus genome has been sequenced and is available for study. Our observations on synarcual development in three major groups of early jawed vertebrates indicate that fusion involves heterotopic cartilage and perichondral bone/mineralised cartilage developing outside the regular skeleton. We suggest that chondrichthyans have potential as ideal extant models for identifying the genes involved in these processes, for application to human skeletal heterotopic disorders.
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Affiliation(s)
- Zerina Johanson
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- * E-mail:
| | - Catherine Boisvert
- Australian Regenerative Medicine Institute (ARMI), EMBL Australia Building 75, Level 1 Monash University, Clayton, Victoria, 3800, Australia
| | - Anton Maksimenko
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, 3168, Australia
| | - Peter Currie
- Australian Regenerative Medicine Institute (ARMI), EMBL Australia Building 75, Level 1 Monash University, Clayton, Victoria, 3800, Australia
| | - Kate Trinajstic
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6845, Australia, and Department of Earth and Planetary Sciences, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia, 6106, Australia
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Gross JB, Meyer B, Perkins M. The rise of Astyanax cavefish. Dev Dyn 2015; 244:1031-1038. [PMID: 25601346 PMCID: PMC4508244 DOI: 10.1002/dvdy.24253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/08/2015] [Accepted: 01/10/2015] [Indexed: 01/01/2023] Open
Abstract
Numerous animals have invaded subterranean caverns and evolved remarkably similar features. These features include loss of vision and pigmentation, and gains in nonvisual sensation. This broad convergence echoes smaller-scale convergence, in which members of the same species repeatedly evolve the same cave-associated phenotypes. The blind Mexican tetra of the Sierra de El Abra region of northeastern Mexico has a complex origin, having recurrently colonized subterranean environments through numerous invasions of surface-dwelling fish. These colonizations likely occurred ∼1-5 MYa. Despite evidence of historical and contemporary gene flow between cave and surface forms, the cave-associated phenotype appears to remain quite stable in nature. This model system has provided insight to the mechanisms of phenotypic regression, the genetic basis for constructive trait evolution, and the origin of behavioral novelties. Here, we document the rise of this model system from its discovery by a Mexican surveyor in 1936, to a powerful system for cave biology and contemporary genetic research. The recently sequenced genome provides exciting opportunities for future research, and will help resolve several long-standing biological problems. Developmental Dynamics 244:1031-1038, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Joshua B Gross
- University of Cincinnati, Department of Biological Sciences, Cincinnati Ohio
| | - Bradley Meyer
- University of Cincinnati, Department of Biological Sciences, Cincinnati Ohio
| | - Molly Perkins
- University of Cincinnati, Department of Biological Sciences, Cincinnati Ohio
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Wang G, Yang E, Smith KJ, Zeng Y, Ji G, Connon R, Fangue NA, Cai JJ. Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Front Genet 2014; 5:312. [PMID: 25309574 PMCID: PMC4160998 DOI: 10.3389/fgene.2014.00312] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/20/2014] [Indexed: 01/11/2023] Open
Abstract
Despite recent success with genome-wide association studies (GWAS), identifying hypertension (HTN)-susceptibility loci in the general population remains difficult. Here, we present a novel strategy to address this challenge by studying salinity adaptation in the threespine stickleback, a fish species with diverse salt-handling ecotypes. We acclimated native freshwater (FW) and anadromous saltwater (SW) threespine sticklebacks to fresh, brackish, and sea water for 30 days, and applied RNA sequencing to determine the gene expression in fish kidneys. We identified 1844 salt-responsive genes that were differentially expressed between FW sticklebacks acclimated to different salinities and/or between SW and FW sticklebacks acclimated to full-strength sea water. Significant overlap between stickleback salt-responsive genes and human genes implicated in HTN was detected (P < 10−7, hypergeometric test), suggesting a possible similarity in genetic mechanisms of salt handling between threespine sticklebacks and humans. The overlapping genes included a newly discovered HTN gene—MAP3K15, whose expression in FW stickleback kidneys decreases with salinity. These also included genes located in the GWAS loci such as AGTRAP-PLOD1 and CYP1A1-ULK3, which contain multiple potentially causative genes contributing to HTN susceptibility that need to be prioritized for study. Taken together, we show that stickleback salt-responsive genes provide valuable information facilitating the identification of human HTN genes. Thus, threespine sticklebacks may be used as a model, complementary to existing animal models, in human HTN research.
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Affiliation(s)
- Gang Wang
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA
| | - Ence Yang
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA
| | - Kerri J Smith
- Interdisciplinary Program in Genetics, Texas A&M University College Station, TX, USA
| | - Yong Zeng
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA ; Department of Automation, Xiamen University Xiamen, China
| | - Guoli Ji
- Department of Automation, Xiamen University Xiamen, China
| | - Richard Connon
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, CA, USA
| | - Nann A Fangue
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, CA, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University College Station, TX, USA ; Interdisciplinary Program in Genetics, Texas A&M University College Station, TX, USA
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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73
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Eastman JT, Witmer LM, Ridgely RC, Kuhn KL. Divergence in skeletal mass and bone morphology in antarctic notothenioid fishes. J Morphol 2014; 275:841-61. [PMID: 24590921 DOI: 10.1002/jmor.20258] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/03/2014] [Accepted: 01/26/2014] [Indexed: 11/10/2022]
Abstract
Although notothenioid fishes lack swim bladders, some species live temporarily or permanently in the water column. Given its relatively high density, skeletal mass is a key determinant of buoyancy. Notothenioids have reduced skeletal ossification, but there is little quantitative data on the phylogenetic distribution of this trait. We obtained dry skeletal masses for 54 specimens representing 20 species from six notothenioid families. Although comparative data are sparse, notothenioid skeletons comprise a smaller percentage of body mass, <3.5%, than those of three non-notothenioid perciforms. With relatively high skeletal mass, the non-Antarctic Bovichtus diacanthus is similar in skeletal mass to some non-notothenioids. Eleginops maclovinus, the non-Antarctic sister group of the Antarctic clade, has a relatively light skeleton (<2% of body mass) similar to many species in the Antarctic clade. Low skeletal mass is therefore a synapomorphy shared by Eleginops plus the Antarctic clade. We provide gross, histological, and micro-CT documentation of the structure and location of bone and cartilage in skulls, pectoral girdles, and vertebrae, with emphasis on the bovichtid B. diacanthus, the eleginopsid E. maclovinus, and the channichthyid Chaenodraco wilsoni. In Eleginops and the Antarctic clade, most bone is spongy and most species have persisting cartilage in the skull and appendicular skeleton. We also measured the relative size of the notochordal canal in adult vertebral centra of 38 species representing all eight families. There is considerable interspecific variation in this pedomorphic trait and all species show an ontogenetic reduction in the relative size of the canal. However, large persisting canals are present in adults of the Antarctic clade, especially in the nototheniids Pleuragramma and Aethotaxis and in a number of bathydraconid and channichthyid genera.
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Affiliation(s)
- Joseph T Eastman
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, 45701-2979
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Brennan PLR, Irschick DJ, Johnson N, Craig Albertson R. Oddball Science: Why Studies of Unusual Evolutionary Phenomena Are Crucial. Bioscience 2014. [DOI: 10.1093/biosci/bit039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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75
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Affiliation(s)
- Jessica A. Bolker
- Department of Biological Sciences; University of New Hampshire; Durham NH 03824 USA
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76
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Bolker JA. Models in Context: Biological and Epistemological Niches. HISTORY, PHILOSOPHY AND THEORY OF THE LIFE SCIENCES 2014. [DOI: 10.1007/978-94-007-7067-6_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Abstract
In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research.
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Affiliation(s)
- Manfred Schartl
- Department Physiological Chemistry, Biocenter, University of Würzburg, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97078 Würzburg, Germany
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78
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Cooper WJ, Wirgau RM, Sweet EM, Albertson RC. Deficiency of zebrafish fgf20a results in aberrant skull remodeling that mimics both human cranial disease and evolutionarily important fish skull morphologies. Evol Dev 2013; 15:426-41. [PMID: 24261444 PMCID: PMC3890419 DOI: 10.1111/ede.12052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The processes that direct skull remodeling are of interest to both human-oriented studies of cranial dysplasia and evolutionary studies of skull divergence. There is increasing awareness that these two fields can be mutually informative when natural variation mimics pathology. Here we describe a zebrafish mutant line, devoid of blastema (dob), which does not have a functional fgf20a protein, and which also presents cranial defects similar to both adaptive and clinical variation. We used geometric morphometric methods to provide quantitative descriptions of the effects of the dob mutation on skull morphogenesis. In combination with "whole-mount in situ hybridization" labeling of normal fgf20a expression and assays for osteoblast and osteoclast activity, the results of these analyses indicate that cranial dysmorphologies in dob zebrafish are generated by aberrations in post-embryonic skull remodeling via decreased osteoblasotgenesis and increased osteoclastogenesis. Mutational effects include altered skull vault geometries and midfacial hypoplasia that are consistent with key diagnostic signs for multiple human craniofacial syndromes. These phenotypic shifts also mimic changes in the functional morphology of fish skulls that have arisen repeatedly in several highly successful radiations (e.g., damselfishes and East-African rift-lake cichlids). Our results offer the dob/fgf20a mutant as an experimentally tractable model with which to examine post-embryonic skull development as it relates to human disease and vertebrate evolution.
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Affiliation(s)
- W. James Cooper
- School of Biological Sciences, Washington State University Tri-cities, Richland, WA 99354, USA
| | - Rachel M. Wirgau
- School of Biological Sciences, Washington State University Tri-cities, Richland, WA 99354, USA
| | - Elly M. Sweet
- School of Biological Sciences, Washington State University Tri-cities, Richland, WA 99354, USA
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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79
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Hu Y, Parsons KJ, Albertson RC. Evolvability of the Cichlid Jaw: New Tools Provide Insights into the Genetic Basis of Phenotypic Integration. Evol Biol 2013. [DOI: 10.1007/s11692-013-9254-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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80
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Meng F, Braasch I, Phillips JB, Lin X, Titus T, Zhang C, Postlethwait JH. Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish. Mol Biol Evol 2013; 30:1527-43. [PMID: 23612715 PMCID: PMC3684860 DOI: 10.1093/molbev/mst079] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and evolve alternatives for exploring their environments. Although troglodyte features evolved independently many times in cavefish, we do not yet know whether independent evolution of these characters involves common genetic mechanisms. Surface-dwelling and many cave-dwelling species make the freshwater teleost genus Sinocyclocheilus an excellent model for studying the evolution of adaptations to life in constant darkness. We compared the mature retinal histology of surface and cave species in Sinocyclocheilus and found that adult cavefish showed a reduction in the number and length of photoreceptor cells. To identify genes and genetic pathways that evolved in constant darkness, we used RNA-seq to compare eyes of surface and cave species. De novo transcriptome assemblies were developed for both species, and contigs were annotated with gene ontology. Results from cave-dwelling Sinocyclocheilus revealed reduced transcription of phototransduction and other genes important for retinal function. In contrast to the blind Mexican tetra cavefish Astyanax mexicanus, our results on morphologies and gene expression suggest that evolved retinal reduction in cave-dwelling Sinocyclocheilus occurs in a lens-independent fashion by the reduced proliferation and downregulation of transcriptional factors shown to have direct roles in retinal development and maintenance, including cone-rod homeobox (crx) and Wnt pathway members. These results show that the independent evolution of retinal degeneration in cavefish can occur by different developmental genetic mechanisms.
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Affiliation(s)
- Fanwei Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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81
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O'Quin KE, Yoshizawa M, Doshi P, Jeffery WR. Quantitative genetic analysis of retinal degeneration in the blind cavefish Astyanax mexicanus. PLoS One 2013; 8:e57281. [PMID: 23437360 PMCID: PMC3577753 DOI: 10.1371/journal.pone.0057281] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/22/2013] [Indexed: 01/26/2023] Open
Abstract
The retina is the light-sensitive tissue of the eye that facilitates vision. Mutations within genes affecting eye development and retinal function cause a host of degenerative visual diseases, including retinitis pigmentosa and anophthalmia/microphthalmia. The characin fish Astyanax mexicanus includes both eyed (surface fish) and eyeless (cavefish) morphs that initially develop eyes with normal retina; however, early in development, the eyes of cavefish degenerate. Since both surface and cave morphs are members of the same species, they serve as excellent evolutionary mutant models with which to identify genes causing retinal degeneration. In this study, we crossed the eyed and eyeless forms of A. mexicanus and quantified the thickness of individual retinal layers among 115 F2 hybrid progeny. We used next generation sequencing (RAD-seq) and microsatellite mapping to construct a dense genetic map of the Astyanax genome, scan for quantitative trait loci (QTL) affecting retinal thickness, and identify candidate genes within these QTL regions. The map we constructed for Astyanax includes nearly 700 markers assembled into 25 linkage groups. Based on our scans with this map, we identified four QTL, one each associated with the thickness of the ganglion, inner nuclear, outer plexiform, and outer nuclear layers of the retina. For all but one QTL, cavefish alleles resulted in a clear reduction in the thickness of the affected layer. Comparative mapping of genetic markers within each QTL revealed that each QTL corresponds to an approximately 35 Mb region of the zebrafish genome. Within each region, we identified several candidate genes associated with the function of each affected retinal layer. Our study is the first to examine Astyanax retinal degeneration in the context of QTL mapping. The regions we identify serve as a starting point for future studies on the genetics of retinal degeneration and eye disease using the evolutionary mutant model Astyanax.
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Affiliation(s)
- Kelly E O'Quin
- Department of Biology, University of Maryland, College Park, Maryland, United States of America.
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82
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Crews D, Gore AC. Epigenetic synthesis: a need for a new paradigm for evolution in a contaminated world. F1000 BIOLOGY REPORTS 2012; 4:18. [PMID: 22991583 PMCID: PMC3434969 DOI: 10.3410/b4-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Epigenetics is a perspective, not a set of techniques. Molecular biology and genetics are the dominant disciplines in biology today, but practitioners of these fields have only recently ‘rediscovered’ the importance of the environment. This has led to increasing research into molecular epigenetics and the interface between the environment and gene regulation. Beyond the study of epigenetic mechanisms at the level of the gene, more investigation of epigenetic outcomes at the level of both the individual organism and the evolution of the population is needed.
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Affiliation(s)
- David Crews
- Section of Integrative Biology, The University of Texas at Austin Austin, TX 78712 USA ; Institute for Cellular and Molecular Biology, The University of Texas at Austin Austin, TX 78712 USA
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83
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Stanca L, Petrache SN, Radu M, Serban AI, Munteanu MC, Teodorescu D, Staicu AC, Sima C, Costache M, Grigoriu C, Zarnescu O, Dinischiotu A. Impact of silicon-based quantum dots on the antioxidative system in white muscle of Carassius auratus gibelio. FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:963-975. [PMID: 22139144 DOI: 10.1007/s10695-011-9582-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 11/22/2011] [Indexed: 05/31/2023]
Abstract
Silicon-based quantum dots were intraperitoneally injected in individuals of Carassius auratus gibelio. Their effects on white muscle were investigated by following their distribution and impact on the antioxidative system. The GSH level significantly increased after 1 and 3 days of exposure by, respectively, 85.3 and 25.4%. Seven days later, GSH levels were similar to control concentrations. MDA concentration rose after three days by 46.9% and remained at the same level after 7 days. Protein thiol levels significantly decreased by 6.7 and 8.1% after 3 and 7 days, whereas advanced oxidation protein products increased by 12.7, respectively, 28.1% in the same time intervals. The protein reactive carbonyl groups were raised only after the first day of exposure and returned to the control level later on. SOD specific activity increased up to 48% after 7 days, while CAT activity increased by 328, 176, and 26% after 1, 3, and 7 days of treatment. GST specific activity was up-regulated by 87, 18, and 9%, while GR activity increased by 68, 34, and 9%. G6PD activity was up-regulated by 12, 22, and 50%, whereas GPx activity raised by 75 and 109% compared to control after, respectively, 1, 3, and 7 days. Our results suggest that oxidative stress induced by silicon-based quantum dots was not strong enough to cause permanent damage in the white muscle of crucian carp.
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Affiliation(s)
- Loredana Stanca
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Sorina Nicoleta Petrache
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Mihaela Radu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Andreea Iren Serban
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, 105 Splaiul Independetei, 050097, Bucharest, Romania
| | - Maria Cristina Munteanu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Daniela Teodorescu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Andreea Cristina Staicu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Cornelia Sima
- Laser Department, National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor, 077125, Bucharest-Magurele, Romania
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Constantin Grigoriu
- Laser Department, National Institute of Laser, Plasma and Radiation Physics, 409 Atomistilor, 077125, Bucharest-Magurele, Romania
| | - Otilia Zarnescu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania
| | - Anca Dinischiotu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independetei, 050095, Bucharest, Romania.
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84
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Intestinal synthesis and secretion of bile salts as an adaptation to developmental biliary atresia in the sea lamprey. Proc Natl Acad Sci U S A 2012; 109:11419-24. [PMID: 22733776 DOI: 10.1073/pnas.1203008109] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Bile salt synthesis is a specialized liver function in vertebrates. Bile salts play diverse roles in digestion and signaling, and their homeostasis is maintained by controlling input (biosynthesis) and intestinal conservation. Patients with biliary atresia (i.e., obliteration of the biliary tree) suffer liver fibrosis and cirrhosis. In contrast, sea lamprey thrives despite developmental biliary atresia. We discovered that the sea lamprey adapts to biliary atresia through a unique mechanism of de novo synthesis and secretion of bile salts in intestine after developmental biliary atresia, in addition to known mechanisms, such as the reduction of bile salt synthesis in liver. During and after developmental biliary atresia, expression of cyp7a1 in intestine increased by more than 100-fold (P < 0.001), whereas in liver it decreased by the same magnitude (P < 0.001). Concurrently, bile salt pools changed in similar patterns and magnitudes in these two organs and the composition shifted from C24 bile alcohol sulfates to taurine-conjugated C24 bile acids. In addition, both in vivo and ex vivo experiments showed that aductular sea lamprey secreted taurocholic acid into its intestinal lumen. Our results indicate that the sea lamprey, a jawless vertebrate, may be in an evolutionarily transitional state where bile salt synthesis occurs in both liver and intestine. Understanding the molecular basis of these mechanisms may shed light on the evolution of bile salt synthesis and possible therapy for infant biliary atresia.
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85
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Mehinto AC, Martyniuk CJ, Spade DJ, Denslow ND. Applications for next-generation sequencing in fish ecotoxicogenomics. Front Genet 2012; 3:62. [PMID: 22539934 PMCID: PMC3336092 DOI: 10.3389/fgene.2012.00062] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/02/2012] [Indexed: 01/23/2023] Open
Abstract
The new technologies for next-generation sequencing (NGS) and global gene expression analyses that are widely used in molecular medicine are increasingly applied to the field of fish biology. This has facilitated new directions to address research areas that could not be previously considered due to the lack of molecular information for ecologically relevant species. Over the past decade, the cost of NGS has decreased significantly, making it possible to use non-model fish species to investigate emerging environmental issues. NGS technologies have permitted researchers to obtain large amounts of raw data in short periods of time. There have also been significant improvements in bioinformatics to assemble the sequences and annotate the genes, thus facilitating the management of these large datasets.The combination of DNA sequencing and bioinformatics has improved our abilities to design custom microarrays and study the genome and transcriptome of a wide variety of organisms. Despite the promising results obtained using these techniques in fish studies, NGS technologies are currently underused in ecotoxicogenomics and few studies have employed these methods. These issues should be addressed in order to exploit the full potential of NGS in ecotoxicological studies and expand our understanding of the biology of non-model organisms.
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Affiliation(s)
- Alvine C Mehinto
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
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86
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Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics 2011; 188:799-808. [PMID: 21828280 PMCID: PMC3176089 DOI: 10.1534/genetics.111.127324] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F(1) offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F(1) dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing.
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87
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Nicodemus-Johnson J, Silic S, Ghigliotti L, Pisano E, Cheng CHC. Assembly of the antifreeze glycoprotein/trypsinogen-like protease genomic locus in the Antarctic toothfish Dissostichus mawsoni (Norman). Genomics 2011; 98:194-201. [DOI: 10.1016/j.ygeno.2011.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/02/2011] [Indexed: 10/18/2022]
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Whitehead A, Pilcher W, Champlin D, Nacci D. Common mechanism underlies repeated evolution of extreme pollution tolerance. Proc Biol Sci 2011; 279:427-33. [PMID: 21733895 DOI: 10.1098/rspb.2011.0847] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human alterations to the environment can exert strong evolutionary pressures, yet contemporary adaptation to human-mediated stressors is rarely documented in wildlife populations. A common-garden experimental design was coupled with comparative transcriptomics to discover evolved mechanisms enabling three populations of killifish resident in urban estuaries to survive normally lethal pollution exposure during development, and to test whether mechanisms are unique or common across populations. We show that killifish populations from these polluted sites have independently converged on a common adaptive mechanism, despite variation in contaminant profiles among sites. These populations are united by a similarly profound desensitization of aryl-hydrocarbon receptor-mediated transcriptional activation, which is associated with extreme tolerance to the lethal effects of toxic dioxin-like pollutants. The rapid, repeated, heritable and convergent nature of evolved tolerance suggests that ancestral killifish populations harboured genotypes that enabled adaptation to twentieth-century industrial pollutants.
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Affiliation(s)
- Andrew Whitehead
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
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Parsons KJ, Andreeva V, James Cooper W, Yelick PC, Craig Albertson R. Morphogenesis of the zebrafish jaw: development beyond the embryo. Methods Cell Biol 2011; 101:225-48. [PMID: 21550447 DOI: 10.1016/b978-0-12-387036-0.00011-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The zebrafish has emerged as an important model for vertebrate development as it relates to human health and disease. Work in this system has provided significant insights into the variety of genetic signals that direct the cellular activities and tissue interactions necessary for proper assembly of the pharyngeal skeleton. Unfortunately our understanding of craniofacial development beyond embryonic stages is far less complete. Stated another way, we know a great deal about the early patterning of the skull, but we know comparatively little about how mature craniofacial shape is determined and maintained over time. Here we propose ways to expand the current molecular genetic paradigm beyond the embryo to gain an understanding of the processes and mechanisms that guide growth and remodeling of mineralized craniofacial, skeletal, and dental tissues. First, we discuss sources of adult mutant phenotypes that can be used to study of postembryonic development. Next, we review salient quantitative methods that are necessary to define complex adult phenotypes. We also discuss how other organismal systems can be used to inform and complement studies in zebrafish. We conclude by discussing the implications for such studies within the context of furthering an understanding of the etiology and pathophysiology of human craniofacial malformations, as well as informing an understanding of adaptive craniofacial variation among natural populations.
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Affiliation(s)
- Kevin J Parsons
- Department of Biology, Syracuse University, Syracuse, NY, USA
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90
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DETRICH HWILLIAM, STUART ANDREW, SCHOENBORN MICHAEL, PARKER SANDRAK, METHÉ BARBARAA, AMEMIYA CHRIST. Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 representative taxa. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:369-81. [PMID: 20235119 PMCID: PMC3631310 DOI: 10.1002/jez.b.21341] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species flock in the cold Southern Ocean surrounding Antarctica. To enable genome-level studies of these psychrophilic fishes, we estimated the sizes of the genomes of 11 Antarctic species and generated high-quality BAC libraries for 2, the notothen Notothenia coriiceps and the icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families, [e.g., the icefishes (Channichthyidae)], was accompanied by genome expansion. Species (n=6) of the basal family Nototheniidae had C values that ranged between 0.98 and 1.20 pg, whereas those of the icefishes, the notothenioid crown group, were 1.66-1.83 pg (n=4 species). The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprised 12X and 10X coverage of the respective genomes and had average insert sizes of 138 and 168 kb. Greater than 60% of paired BAC ends sampled from each library ( approximately 0.1% of each genome) contained repetitive sequences, and the repetitive element landscapes of the 2 genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The representation and depth of coverage of the libraries were verified by identification of multiple Hox gene contigs: six discrete Hox clusters were found in N. coriiceps and at least five Hox clusters were found in C. aceratus. Given the unusual anatomical and physiological adaptations of the notothenioids, the availability of these BAC libraries sets the stage for expanded analysis of the psychrophilic mode of life.
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Affiliation(s)
| | - ANDREW STUART
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | | | - SANDRA K. PARKER
- Department of Biology, Northeastern University, Boston, Massachusetts
| | | | - CHRIS T. AMEMIYA
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
- Department of Biology, University of Washington, Seattle, Washington
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Detrich HW, Amemiya CT. Antarctic notothenioid fishes: genomic resources and strategies for analyzing an adaptive radiation. Integr Comp Biol 2010; 50:1009-17. [PMID: 21082069 DOI: 10.1093/icb/icq071] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species-flock in the cold Southern Ocean that surrounds Antarctica. To facilitate genome-level studies of the diversification of these fishes, we present estimates of the genome sizes of 11 Antarctic species and describe the production of high-quality bacterial artificial chromosome (BAC) libraries for two, the red-blooded notothen Notothenia coriiceps and the white-blooded icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families (e.g., the crown group Channichthyidae [icefishes]), was accompanied by genome expansion. Six species from the basal family Nototheniidae had C-values between 0.98 and 1.20 pg, a range that is consistent with the genome sizes of proposed outgroups (e.g., percids) of the notothenioid suborder. In contrast, four icefishes had C-values in the range 1.66-1.83 pg. The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprise 12× and 10× coverage of the respective genomes and have average insert sizes of 138 and 168 kb. Paired BAC-end reads representing ∼0.1% of each genome showed that the repetitive element landscapes of the two genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The availability of these high-quality and well-characterized BAC libraries sets the stage for targeted genomic analyses of the unusual anatomical and physiological adaptations of the notothenioids, some of which mimic human diseases. Here we consider the evolution of secondary pelagicism by various taxa of the group and illustrate the utility of Antarctic icefishes as an evolutionary-mutant model of human osteopenia (low-mineral density of bones).
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Affiliation(s)
- H W Detrich
- Department of Biology, Northeastern University, Boston, MA 02115, USA.
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Albertson RC, Yan YL, Titus TA, Pisano E, Vacchi M, Yelick PC, Detrich HW, Postlethwait JH. Molecular pedomorphism underlies craniofacial skeletal evolution in Antarctic notothenioid fishes. BMC Evol Biol 2010; 10:4. [PMID: 20053275 PMCID: PMC2824663 DOI: 10.1186/1471-2148-10-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 01/06/2010] [Indexed: 11/20/2022] Open
Abstract
Background Pedomorphism is the retention of ancestrally juvenile traits by adults in a descendant taxon. Despite its importance for evolutionary change, there are few examples of a molecular basis for this phenomenon. Notothenioids represent one of the best described species flocks among marine fishes, but their diversity is currently threatened by the rapidly changing Antarctic climate. Notothenioid evolutionary history is characterized by parallel radiations from a benthic ancestor to pelagic predators, which was accompanied by the appearance of several pedomorphic traits, including the reduction of skeletal mineralization that resulted in increased buoyancy. Results We compared craniofacial skeletal development in two pelagic notothenioids, Chaenocephalus aceratus and Pleuragramma antarcticum, to that in a benthic species, Notothenia coriiceps, and two outgroups, the threespine stickleback and the zebrafish. Relative to these other species, pelagic notothenioids exhibited a delay in pharyngeal bone development, which was associated with discrete heterochronic shifts in skeletal gene expression that were consistent with persistence of the chondrogenic program and a delay in the osteogenic program during larval development. Morphological analysis also revealed a bias toward the development of anterior and ventral elements of the notothenioid pharyngeal skeleton relative to dorsal and posterior elements. Conclusions Our data support the hypothesis that early shifts in the relative timing of craniofacial skeletal gene expression may have had a significant impact on the adaptive radiation of Antarctic notothenioids into pelagic habitats.
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Affiliation(s)
- R Craig Albertson
- Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA.
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Parsons KJ, Albertson RC. Roles for Bmp4 and CaM1 in Shaping the Jaw: Evo-Devo and Beyond. Annu Rev Genet 2009; 43:369-88. [DOI: 10.1146/annurev-genet-102808-114917] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kevin J. Parsons
- Department of Biology, Syracuse University, Syracuse, New York 13244;
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Navratilova P, Becker TS. Genomic regulatory blocks in vertebrates and implications in human disease. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:333-42. [DOI: 10.1093/bfgp/elp019] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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