1
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Eastment RV, Wong BBM, McGee MD. Convergent genomic signatures associated with vertebrate viviparity. BMC Biol 2024; 22:34. [PMID: 38331819 PMCID: PMC10854053 DOI: 10.1186/s12915-024-01837-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? RESULTS We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages. CONCLUSIONS Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.
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Affiliation(s)
- Rhiannon V Eastment
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
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2
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Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023; 33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten-Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA;
| | - Edward Rice
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Kremitzki Milin
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Ronald B Walter
- Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
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3
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Ren L, Gao X, Cui J, Zhang C, Dai H, Luo M, He S, Qin Q, Luo K, Tao M, Xiao J, Wang J, Zhang H, Zhang X, Zhou Y, Wang J, Zhao X, Liu G, Wang G, Huo L, Wang S, Hu F, Zhao R, Zhou R, Wang Y, Liu Q, Yan X, Wu C, Yang C, Tang C, Duan W, Liu S. Symmetric subgenomes and balanced homoeolog expression stabilize the establishment of allopolyploidy in cyprinid fish. BMC Biol 2022; 20:200. [PMID: 36100845 PMCID: PMC9472340 DOI: 10.1186/s12915-022-01401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. Results We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. Conclusions Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01401-4.
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Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Mengxue Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaofang He
- Wuhan Carbon Code Biotechnologies Corporation, Wuhan, 430070, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Hong Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jing Wang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xin Zhao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Linhe Huo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rong Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qinfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiaojing Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Wei Duan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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4
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Kirkpatrick M, Sardell JM, Pinto BJ, Dixon G, Peichel CL, Schartl M. Evolution of the canonical sex chromosomes of the guppy and its relatives. G3 (BETHESDA, MD.) 2022; 12:6472354. [PMID: 35100353 PMCID: PMC9335935 DOI: 10.1093/g3journal/jkab435] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/03/2021] [Indexed: 11/14/2022]
Abstract
The sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as humans and Drosophila melanogaster, and they carry many of the genes responsible for the males' dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here, we address these controversies by reviewing the evidence and reanalyzing data. We find no evidence of a nonrecombining sex-determining region or evolutionary strata in P. reticulata. Furthermore, we find that the data most strongly support the hypothesis that the sex-determining regions of 2 close relatives of the guppy, Poecilia wingei and Micropoecilia picta, evolved independently after their lineages diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.
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Affiliation(s)
- Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jason M Sardell
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Brendan J Pinto
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.,Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | - Groves Dixon
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Catherine L Peichel
- Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland
| | - Manfred Schartl
- Developmental Biochemistry, University of Würzburg, Würzburg97074, Germany.,Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
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5
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Charlesworth D, Graham C, Trivedi U, Gardner J, Bergero R. PromethION sequencing and assembly of the genome of Micropoecilia picta, a fish with a highly Degenerated Y chromosome. Genome Biol Evol 2021; 13:6326803. [PMID: 34297069 PMCID: PMC8449826 DOI: 10.1093/gbe/evab171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
We here describe sequencing and assembly of both the autosomes and the sex chromosome in M. picta, the closest related species to the guppy, Poecilia reticulata. Poecilia ()Micropoecilia) picta is a close outgroup for studying the guppy, an important organism for studies in evolutionary ecology and in sex chromosome evolution. The guppy XY pair (LG12) has long been studied as a test case for the importance of sexually antagonistic variants in selection for suppressed recombination between Y and X chromosomes. The guppy Y chromosome is not degenerated, but appears to carry functional copies of all genes that are present on its X counterpart. The X chromosomes of M. picta (and its relative M. parae) are homologous to the guppy XY pair, but their Y chromosomes are highly degenerated, and no genes can be identified in the fully Y-linked region. A complete genome sequence of a M. picta male may therefore contribute to understanding how the guppy Y evolved. These fish species' genomes are estimated to be about 750 Mb, with high densities of repetitive sequences, suggesting that long-read sequencing is needed. We evaluated several assembly approaches, and used our results to investigate the extent of Y chromosome degeneration in this species.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
| | - Chay Graham
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK.,University of Cambridge, Department of Biochemistry, Sanger Building, 80 Tennis Ct Rd, Cambridge, CB2 1GA, UK
| | - Urmi Trivedi
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
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6
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Safian D, Wiegertjes GF, Pollux BJA. The Fish Family Poeciliidae as a Model to Study the Evolution and Diversification of Regenerative Capacity in Vertebrates. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The capacity of regenerating a new structure after losing an old one is a major challenge in the animal kingdom. Fish have emerged as an interesting model to study regeneration due to their high and diverse regenerative capacity. To date, most efforts have focused on revealing the mechanisms underlying fin regeneration, but information on why and how this capacity evolves remains incomplete. Here, we propose the livebearing fish family Poeciliidae as a promising new model system to study the evolution of fin regeneration. First, we review the current state of knowledge on the evolution of regeneration in the animal kingdom, with a special emphasis on fish fins. Second, we summarize recent advances in our understanding of the mechanisms behind fin regeneration in fish. Third, we discuss potential evolutionary pressures that may modulate the regenerative capacity of fish fins and propose three new theories for how natural and sexual selection can lead to the evolution of fin regeneration: (1) signaling-driven fin regeneration, (2) predation-driven fin regeneration, and (3) matrotrophy-suppressed fin regeneration. Finally, we argue that fish from the family Poeciliidae are an excellent model system to test these theories, because they comprise of a large variety of species in a well-defined phylogenetic framework that inhabit very different environments and display remarkable variation in reproductive traits, allowing for comparative studies of fin regeneration among closely related species, among populations within species or among individuals within populations. This new model system has the potential to shed new light on the underlying genetic and molecular mechanisms driving the evolution and diversification of regeneration in vertebrates.
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7
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Powell DL, Payne C, Banerjee SM, Keegan M, Bashkirova E, Cui R, Andolfatto P, Rosenthal GG, Schumer M. The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations. Curr Biol 2021; 31:923-935.e11. [PMID: 33513352 DOI: 10.1016/j.cub.2020.12.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture and evolutionary loss of a sexually selected ornament, the "sword" fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species of Xiphophorus, we generated a mapping population and show that the sword ornament is polygenic-with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major-effect quantitative trait locus (QTL) that explains ~5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to several likely candidate genes, including genes involved in fin regeneration and growth. Furthermore, we find evidence of selection on ancestry at one of these candidates in four natural hybrid populations, consistent with selection against the sword in these populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA.
| | - Cheyenne Payne
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Mackenzie Keegan
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Elizaveta Bashkirova
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY 10032, USA
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA; Max Planck Institute for the Biology of Aging, Postfach 41 06 23, 50931 Cologne, Germany; School of Ecology, Sun Yat-sen University, 135 Xingang West Road, Binjiang Road, Haizhu District, Guangdong Province, China
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA
| | - Molly Schumer
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Howard Hughes Medical Institute, 327 Campus Drive, Stanford, CA 94305, USA.
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8
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A fish is not a mouse: understanding differences in background genetics is critical for reproducibility. Lab Anim (NY) 2020; 50:19-25. [PMID: 33268901 DOI: 10.1038/s41684-020-00683-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023]
Abstract
Poorly controlled background genetics in animal models contributes to the lack of reproducibility that is increasingly recognized in biomedical research. The laboratory zebrafish, Danio rerio, has been an important model organism for decades in many research areas, yet inbred strains and traditionally managed outbred stocks are not available for this species. Sometimes incorrectly referred to as 'inbred strains' or 'strains', zebrafish wild-type lines possess background genetics that are often not well characterized, and breeding practices for these lines have not been consistent over time or among institutions. In this Perspective, we trace key milestones in the history of one of the most widely used genetic backgrounds, the AB line, to illustrate the dynamic complexity within an example background that is largely invisible when reading the scientific literature. Failure to adequately control for genetic background compromises the validity of experimental outcomes. We therefore propose that authors provide as much specific detail about the origin and genetic makeup of zebrafish lines as is reasonable and possible, and that the terms used to describe background genetics be applied in a way that is consistent with other fish and mammalian model organisms. We strongly encourage the adoption of genetic monitoring for the characterization of existing zebrafish lines, to help detect genetic contamination in breeding colonies and to verify the level of genetic heterogeneity in breeding colonies over time. Careful attention to background genetics will improve transparency and reproducibility, therefore improving the utility of the zebrafish as a model organism.
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9
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Lu Y, Boswell M, Boswell W, Salinas RY, Savage M, Reyes J, Walter S, Marks R, Gonzalez T, Medrano G, Warren WC, Schartl M, Walter RB. Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns. BMC Genomics 2020; 21:787. [PMID: 33176680 PMCID: PMC7659085 DOI: 10.1186/s12864-020-07202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 10/28/2020] [Indexed: 11/25/2022] Open
Abstract
Background Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period. Results Our results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs. Conclusions These observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Raquel Ybanez Salinas
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,The University of Texas MD Anderson Cancer Center, Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Jose Reyes
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Sean Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Rebecca Marks
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Trevor Gonzalez
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Geraldo Medrano
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
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10
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Lu Y, Olivas TJ, Boswell M, Boswell W, Warren WC, Schartl M, Walter RB. Intra-Strain Genetic Variation of Platyfish ( Xiphophorus maculatus) Strains Determines Tumorigenic Trajectory. Front Genet 2020; 11:562594. [PMID: 33133148 PMCID: PMC7573281 DOI: 10.3389/fgene.2020.562594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022] Open
Abstract
Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.
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Affiliation(s)
- Yuan Lu
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - Taryn J Olivas
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, United States
| | - Mikki Boswell
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - William Boswell
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - Wes C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States.,Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Ronald B Walter
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
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11
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van Kruistum H, Guernsey MW, Baker JC, Kloet SL, Groenen MAM, Pollux BJA, Megens HJ. The Genomes of the Livebearing Fish Species Poeciliopsis retropinna and Poeciliopsis turrubarensis Reflect Their Different Reproductive Strategies. Mol Biol Evol 2020; 37:1376-1386. [PMID: 31960923 PMCID: PMC7182214 DOI: 10.1093/molbev/msaa011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The evolution of a placenta is predicted to be accompanied by rapid evolution of genes involved in processes that regulate mother-offspring interactions during pregnancy, such as placenta formation, embryonic development, and nutrient transfer to offspring. However, these predictions have only been tested in mammalian species, where only a single instance of placenta evolution has occurred. In this light, the genus Poeciliopsis is a particularly interesting model for placenta evolution, because in this genus a placenta has evolved independently from the mammalian placenta. Here, we present and compare genome assemblies of two species of the livebearing fish genus Poeciliopsis (family Poeciliidae) that differ in their reproductive strategy: Poeciliopsis retropinna which has a well-developed complex placenta and P. turrubarensis which lacks a placenta. We applied different assembly strategies for each species: PacBio sequencing for P. retropinna (622-Mb assembly, scaffold N50 of 21.6 Mb) and 10× Genomics Chromium technology for P. turrubarensis (597-Mb assembly, scaffold N50 of 4.2 Mb). Using the high contiguity of these genome assemblies and near-completeness of gene annotations to our advantage, we searched for gene duplications and performed a genome-wide scan for genes evolving under positive selection. We find rapid evolution in major parts of several molecular pathways involved in parent-offspring interaction in P. retropinna, both in the form of gene duplications as well as positive selection. We conclude that the evolution of the placenta in the genus Poeciliopsis is accompanied by rapid evolution of genes involved in similar genomic pathways as found in mammals.
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Affiliation(s)
- Henri van Kruistum
- Animal Breeding and Genomics Group, Wageningen University, Wageningen, The Netherlands
- Experimental Zoology Group, Wageningen University, Wageningen, The Netherlands
| | - Michael W Guernsey
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Susan L Kloet
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics Group, Wageningen University, Wageningen, The Netherlands
| | - Bart J A Pollux
- Experimental Zoology Group, Wageningen University, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Group, Wageningen University, Wageningen, The Netherlands
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12
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Liu Y, Blackburn H, Taylor SS, Tiersch TR. Development of germplasm repositories to assist conservation of endangered fishes: Examples from small-bodied livebearing fishes. Theriogenology 2019; 135:138-151. [PMID: 31220687 PMCID: PMC6612591 DOI: 10.1016/j.theriogenology.2019.05.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 12/29/2022]
Abstract
Germplasm repositories are a necessary tool for comprehensive conservation programs to fully preserve valuable genetic resources of imperiled animals. Cryopreserved germplasm can be used in the future to produce live young for integration into other conservation projects, such as habitat restoration, captive breeding, and translocations; thus compensating for genetic losses or negative changes that would otherwise be permanent. Although hundreds of cryopreservation protocols for various aquatic species have been published, there are great difficulties in moving such research forward into applied conservation projects. Successful freezing of sperm in laboratories for research does not guarantee successful management and incorporation of genetic resources into conservation programs in reality. The goal of the present review is to provide insights and practical strategies to apply germplasm repositories as a real-world tool to assist conservation of imperiled aquatic species. Live-bearing (viviparous) fishes are used as models herein to help explain concepts because they are good examples for aquatic species in general, especially small-bodied fishes. Small live-bearing fishes are among the most at-risk fish groups in the world, and need urgent conservation attention. However, development of germplasm repositories for small live-bearing fishes is challenged by their unusual reproductive characteristics, such as formation of sperm bundles, initiation of spermatozoa motility in an isotonic environment, internal fertilization and gestation, and the bearing of live young. The development of germplasm repositories for goodeids and Xiphophorus species can provide examples for addressing these challenges. Germplasm repositories must contain multiple basic components, including frozen samples, genetic assessment and information systems. Standardization and process generalization are important strategies to help develop reliable and efficient repositories. An ideal conservation or recovery program for imperiled species should include a comprehensive approach, that combines major concerns such as habitat (by restoration projects), population propagation and maintenance (by captive breeding or translocation projects), and preservation of genetic diversity (by repository projects). In this context, strong collaboration among different sectors and people with different expertise is a key to the success of such comprehensive programs.
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Affiliation(s)
- Yue Liu
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, USA; Department of Biological and Agricultural Engineering, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Harvey Blackburn
- National Animal Germplasm Program, United States Department of Agriculture, Agricultural Research Service, Fort Collins, CO, USA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Terrence R Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, USA.
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13
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Hagedorn M, Varga Z, Walter RB, Tiersch TR. Workshop report: Cryopreservation of aquatic biomedical models. Cryobiology 2019; 86:120-129. [PMID: 30389588 PMCID: PMC9903301 DOI: 10.1016/j.cryobiol.2018.10.264] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023]
Abstract
The genetic resources of aquatic biomedical model organisms are the products of millions of years of evolution, decades of scientific development, and hundreds of millions of dollars of research funding investment. Genetic resources (e.g., specific alleles, transgenes, or combinations) of each model organism can be considered a form of scientific wealth that can be accumulated and exchanged, typically in the form of live animals or germplasm. Large-scale maintenance of live aquatic organisms that carry these genetic resources is inefficient, costly, and risky. In situ maintenance may be substantially enhanced and backed up by combining cryopreserved germplasm repositories and genetic information systems with live animal culture. Unfortunately, cryopreservation has not advanced much beyond the status of an exploratory research for most aquatic species, lacks widespread application, and methods for successful cryopreservation remain poorly defined. For most aquatic species biological materials other than sperm or somatic cells are not comprehensively banked to represent and preserve a broad range of genetic diversity for each species. Therefore, new approaches and standardization are needed for repository-level application to ensure reproducible recovery of cryopreserved materials. Additionally, development of new technologies is needed to address preservation of novel biological materials, such as eggs and embryos of aquatic species. To address these goals, the Office of Research Infrastructure Programs (ORIP) of the National Institutes of Health (NIH) hosted the Cryopreservation of Aquatic Biomedical Models Workshop on January 7 to 8, 2017, in conjunction with the 8th Aquatic Animal Models of Human Disease Conference in Birmingham, Alabama. The goals of the workshop were to assess the status of germplasm cryopreservation in various biomedical aquatic models and allow representatives of the scientific community to develop and prioritize a consensus of specific actionable recommendations that will move the field of cryopreservation of aquatic resources forward. This workshop included sessions devoted to new approaches for cryopreservation of aquatic species, discussion of current efforts and approaches in preservation of aquatic model germplasm, consideration of needs for standardization of methods to support reproducibility, and enhancement of repository development by establishment of scalable high-throughput technologies. The following three broad recommendations were forwarded from workshop attendees: 1: Establish a comprehensive, centralized unit ("hub") to programmatically develop training for and documentation of cryopreservation methods for aquatic model systems. This would include development of species-specific protocols and approaches, outreach programs, community development and standardization, freezing services and training of the next generation of experts in aquatic cryopreservation. 2: Provide mechanisms to support innovative technical advancements that will increase the reliability, reproducibility, simplicity, throughput, and efficiency of the cryopreservation process, including vitrification and pipelines for sperm, oocytes, eggs, embryos, larvae, stem cells, and somatic cells of all aquatic species. This recommendation encompasses basic cryopreservation knowledge and engineering technology, such as microfluidics and automated processing technologies. 3: Implement mechanisms that allow the various aquatic model stock centers to increase their planning, personnel, ability to secure genetic resources and to promote interaction within an integrated, comprehensive repository network for aquatic model species repositories.
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Affiliation(s)
- Mary Hagedorn
- Smithsonian Conservation Biology Institute (SCBI) and Hawaii Institute of Marine Biology (HIMB), Kaneohe, HI, USA.
| | - Zoltan Varga
- Zebrafish International Research Center, University of Oregon, Eugene, OR, USA
| | - Ronald B Walter
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Terrence R Tiersch
- Aquatic Germplasm and Genetic Resources Center, Louisiana State University Agricultural Center (LSUAC), Baton Rouge, LA, USA
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14
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Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model. PLoS Genet 2018; 14:e1007875. [PMID: 30586357 PMCID: PMC6324826 DOI: 10.1371/journal.pgen.1007875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 01/06/2023] Open
Abstract
Understanding the genetic mechanisms underlying segregation of phenotypic variation through successive generations is important for understanding physiological changes and disease risk. Tracing the etiology of variation in gene expression enables identification of genetic interactions, and may uncover molecular mechanisms leading to the phenotypic expression of a trait, especially when utilizing model organisms that have well-defined genetic lineages. There are a plethora of studies that describe relationships between gene expression and genotype, however, the idea that global variations in gene expression are also controlled by genotype remains novel. Despite the identification of loci that control gene expression variation, the global understanding of how genome constitution affects trait variability is unknown. To study this question, we utilized Xiphophorus fish of different, but tractable genetic backgrounds (inbred, F1 interspecies hybrids, and backcross hybrid progeny), and measured each individual’s gene expression concurrent with the degrees of inter-individual expression variation. We found, (a) F1 interspecies hybrids exhibited less variability than inbred animals, indicting gene expression variation is not affected by the fraction of heterozygous loci within an individual genome, and (b), that mixing genotypes in backcross populations led to higher levels of gene expression variability, supporting the idea that expression variability is caused by heterogeneity of genotypes of cis or trans loci. In conclusion, heterogeneity of genotype, introduced by inheritance of different alleles, accounts for the largest effects on global phenotypical variability. Phenotypical variability is a multi-factorial phenomenon. Although it has been shown that inheriting certain gene is associated with lower phenotypical variability, how genome complexity affect phenotypical variability is still unclear. To study this question, we used inbred Xiphophorus fish, backcross interspecies hybrids, and F1 interspecies hybrids between select Xiphophorus species to model genetic composition with minimum, medium, and maximum heterozygosity respectively, and measured their global gene expression variability. We found gene expression variation is not affected by the percentage of heterozygous loci in individual genome, but instead related to heterogeneity of genotype at local or remote loci.
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15
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Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M. Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nat Commun 2018; 9:5136. [PMID: 30510159 PMCID: PMC6277394 DOI: 10.1038/s41467-018-07648-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome. Fish have a high diversity of sex-determining systems, but the mechanisms responsible for this are not well understood. Here, Franchini et al. show how hybridization and backcrossing have led to the evolution of a new sex chromosome in swordtail fish during 30 years of experimental evolution.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75123, Sweden
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | | | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, 78666-4616, TX, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany. .,Radcliffe Institute for Advanced Study, Harvard University, 9 Garden Street, Cambridge, MA, 02139, USA.
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany. .,Comprehensive Cancer Centre, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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16
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Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Comparison of Xiphophorus and human melanoma transcriptomes reveals conserved pathway interactions. Pigment Cell Melanoma Res 2018; 31:496-508. [PMID: 29316274 PMCID: PMC6013346 DOI: 10.1111/pcmr.12686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/23/2017] [Indexed: 12/14/2022]
Abstract
Comparative analysis of human and animal model melanomas can uncover conserved pathways and genetic changes that are relevant for the biology of cancer cells. Spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny may be informative in identifying genes and functional pathways that are similarly related to melanoma development in all vertebrates, including humans. To assess functional pathways involved in the Xiphophorus melanoma, we performed gene expression profiling of the melanomas produced in interspecies BC1 and successive backcross generations (i.e., BC5 ) of the cross: X. hellerii × [X. maculatus Jp 163 A × X. hellerii]. Using RNA-Seq, we identified genes that are transcriptionally co-expressed with the driver oncogene, xmrk. We determined functional pathways in the fish melanoma that are also present in human melanoma cohorts that may be related to dedifferentiation based on the expression levels of pigmentation genes. Shared pathways between human and Xiphophorus melanomas are related to inflammation, cell migration, cell proliferation, pigmentation, cancer development, and metastasis. Our results suggest xmrk co-expressed genes are associated with dedifferentiation and highlight these signaling pathways as playing important roles in melanomagenesis.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Michael Hausmann
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Janine Regneri
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
- Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, USA
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
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17
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Lu Y, Reyes J, Walter S, Gonzalez T, Medrano G, Boswell M, Boswell W, Savage M, Walter R. Characterization of basal gene expression trends over a diurnal cycle in Xiphophorus maculatus skin, brain and liver. Comp Biochem Physiol C Toxicol Pharmacol 2018; 208:2-11. [PMID: 29203320 PMCID: PMC5936649 DOI: 10.1016/j.cbpc.2017.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/10/2017] [Accepted: 11/28/2017] [Indexed: 12/20/2022]
Abstract
Evolutionarily conserved diurnal circadian mechanisms maintain oscillating patterns of gene expression based on the day-night cycle. Xiphophorus fish have been used to evaluate transcriptional responses after exposure to various light sources and it was determined that each source incites distinct genetic responses in skin tissue. However, basal expression levels of genes that show oscillating expression patterns in day-night cycle, may affect the outcomes of such experiments, since basal gene expression levels at each point in the circadian path may influence the profile of identified light responsive genes. Lack of knowledge regarding diurnal fluctuations in basal gene expression patterns may confound the understanding of genetic responses to external stimuli (e.g., light) since the dynamic nature of gene expression implies animals subjected to stimuli at different times may be at very different stages within the continuum of genetic homeostasis. We assessed basal gene expression changes over a 24-hour period in 200 select Xiphophorus gene targets known to transcriptionally respond to various types of light exposure. We identified 22 genes in skin, 36 genes in brain and 28 genes in liver that exhibit basal oscillation of expression patterns. These genes, including known circadian regulators, produced the expected expression patterns over a 24-hour cycle when compared to circadian regulatory genes identified in other species, especially human and other vertebrate animal models. Our results suggest the regulatory network governing diurnal oscillating gene expression is similar between Xiphophorus and other vertebrates for the three Xiphophorus organs tested. In addition, we were able to categorize light responsive gene sets in Xiphophorus that do, and do not, exhibit circadian based oscillating expression patterns.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Jose Reyes
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Sean Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Trevor Gonzalez
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Geraldo Medrano
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA.
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18
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Hoffberg SL, Troendle NJ, Glenn TC, Mahmud O, Louha S, Chalopin D, Bennetzen JL, Mauricio R. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library. G3 (BETHESDA, MD.) 2018; 8:1855-1861. [PMID: 29703783 PMCID: PMC5982815 DOI: 10.1534/g3.118.200101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022]
Abstract
The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species.
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Affiliation(s)
| | | | - Travis C Glenn
- Department of Genetics
- Department of Environmental Health Science
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
| | - Ousman Mahmud
- Department of Genetics
- Department of Computational Biology
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
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Warren WC, García-Pérez R, Xu S, Lampert KP, Chalopin D, Stöck M, Loewe L, Lu Y, Kuderna L, Minx P, Montague MJ, Tomlinson C, Hillier LW, Murphy DN, Wang J, Wang Z, Garcia CM, Thomas GWC, Volff JN, Farias F, Aken B, Walter RB, Pruitt KD, Marques-Bonet T, Hahn MW, Kneitz S, Lynch M, Schartl M. Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly. Nat Ecol Evol 2018; 2:669-679. [PMID: 29434351 PMCID: PMC5866774 DOI: 10.1038/s41559-018-0473-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022]
Abstract
The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.
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Affiliation(s)
- Wesley C. Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | | | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Kathrin P. Lampert
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon I, Lyon, France
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Laurence Loewe
- Laboratory of Genetics and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Yuan Lu
- Texas State University, Department of Chemistry and Biochemistry, San Marcos, TX 78666, USA
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Michael J. Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - LaDeana W. Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Daniel N. Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - John Wang
- Biodiversity Research Center, Academica Sinica Taipei, Taiwan
| | - Zhongwei Wang
- Department of Physiological Chemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany; present address: Institute of Hydrobiology, Chinese Academy of Sciences, China
| | - Constantino Macias Garcia
- Instituto de Ecología, Universidad Nacional Autónoma de México, CP 04510, Ciudad Universitaria, México DF
| | | | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon I, Lyon, France
| | - Fabiana Farias
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ronald B. Walter
- Texas State University, Department of Chemistry and Biochemistry, San Marcos, TX 78666, USA
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Center for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, and Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Matthew W. Hahn
- Indiana University, Department of Biology, Bloomington, IN 47405, USA
| | - Susanne Kneitz
- Department of Physiological Chemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Michael Lynch
- Indiana University, Department of Biology, Bloomington, IN 47405, USA
| | - Manfred Schartl
- Department of Physiological Chemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX 77843, USA, and Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany
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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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Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids. Mol Carcinog 2017; 56:1935-1944. [PMID: 28345808 DOI: 10.1002/mc.22651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 01/10/2023]
Abstract
Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1 ) hybrids and 13 fifth generation (BC5 ) hybrids. Allele-specific expression was determined for all genes and assigned to parental allele inheritance for each backcross hybrid individual. Results showed that genes residing in a 5.81 Mbp region on LG5 were exclusively expressed from the X. hellerii alleles in tumor-bearing BC1 hybrids. This observation indicates this region is consistently homozygous for X. hellerii alleles in tumor bearing animals, and therefore defines this region to be the R(Diff) locus. The R(Diff) locus harbors 164 gene models and includes the previously characterized R(Diff) candidate, cdkn2x. Twenty-one genes in the R(Diff) region show differential expression in the tumor samples compared to normal skin tissue. These results further characterize the R(Diff) locus and suggest tumor suppression may require a multigenic region rather than a single gene variant. Differences in gene expression between tumor and normal skin tissue in this region may indicate interactions among several genes are required for backcross hybrid melanoma development.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Michael Hausmann
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Janine Regneri
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, Texas
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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