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Neal SJ, Rajasekaran A, Jusić N, Taylor L, Read M, Alfandari D, Pignoni F, Moody SA. Using Xenopus to discover new candidate genes involved in BOR and other congenital hearing loss syndromes. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:212-240. [PMID: 37830236 PMCID: PMC11014897 DOI: 10.1002/jez.b.23222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/15/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Hearing in infants is essential for brain development, acquisition of verbal language skills, and development of social interactions. Therefore, it is important to diagnose hearing loss soon after birth so that interventions can be provided as early as possible. Most newborns in the United States are screened for hearing deficits and commercially available next-generation sequencing hearing loss panels often can identify the causative gene, which may also identify congenital defects in other organs. One of the most prevalent autosomal dominant congenital hearing loss syndromes is branchio-oto-renal syndrome (BOR), which also presents with defects in craniofacial structures and the kidney. Currently, mutations in three genes, SIX1, SIX5, and EYA1, are known to be causative in about half of the BOR patients that have been tested. To uncover new candidate genes that could be added to congenital hearing loss genetic screens, we have combined the power of Drosophila mutants and protein biochemical assays with the embryological advantages of Xenopus, a key aquatic animal model with a high level of genomic similarity to human, to identify potential Six1 transcriptional targets and interacting proteins that play a role during otic development. We review our transcriptomic, yeast 2-hybrid, and proteomic approaches that have revealed a large number of new candidates. We also discuss how we have begun to identify how Six1 and co-factors interact to direct developmental events necessary for normal otic development.
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Affiliation(s)
- Scott J. Neal
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Anindita Rajasekaran
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Nisveta Jusić
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Louis Taylor
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Mai Read
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Francesca Pignoni
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
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Uno Y, Matsubara K. Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:230-241. [PMID: 38155517 DOI: 10.1002/jez.2776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
Sex determination systems have greatly diversified between amphibians and reptiles, with such as the different sex chromosome compositions within a single species and transition between temperature-dependent sex determination (TSD) and genetic sex determination (GSD). In most sex chromosome studies on amphibians and reptiles, the whole-genome sequence of Xenopous tropicalis and chicken have been used as references to compare the chromosome homology of sex chromosomes among each of these taxonomic groups, respectively. In the present study, we reviewed existing reports on sex chromosomes, including karyotypes, in amphibians and reptiles. Furthermore, we compared the identified genetic linkages of sex chromosomes in amphibians and reptiles with the chicken genome as a reference, which is believed to resemble the ancestral tetrapod karyotype. Our findings revealed that sex chromosomes in amphibians are derived from genetic linkages homologous to various chicken chromosomes, even among several frogs within single families, such as Ranidae and Pipidae. In contrast, sex chromosomes in reptiles exhibit conserved genetic linkages with chicken chromosomes, not only across most species within a single family, but also within closely related families. The diversity of sex chromosomes in amphibians and reptiles may be attributed to the flexibility of their sex determination systems, including the ease of sex reversal in these animals.
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Affiliation(s)
- Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazumi Matsubara
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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Thakkar N, Giesecke A, Bazalova O, Martinek J, Smykal V, Stanewsky R, Dolezel D. Evolution of casein kinase 1 and functional analysis of new doubletime mutants in Drosophila. Front Physiol 2022; 13:1062632. [PMID: 36589447 PMCID: PMC9794997 DOI: 10.3389/fphys.2022.1062632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Circadian clocks are timing devices that rhythmically adjust organism's behavior, physiology, and metabolism to the 24-h day-night cycle. Eukaryotic circadian clocks rely on several interlocked transcription-translation feedback loops, where protein stability is the key part of the delay between transcription and the appearance of the mature proteins within the feedback loops. In bilaterian animals, including mammals and insects, the circadian clock depends on a homologous set of proteins. Despite mostly conserved clock components among the fruit fly Drosophila and mammals, several lineage-specific differences exist. Here we have systematically explored the evolution and sequence variability of insect DBT proteins and their vertebrate homologs casein kinase 1 delta (CKIδ) and epsilon (CKIε), dated the origin and separation of CKIδ from CKIε, and identified at least three additional independent duplications of the CKIδ/ε gene in Petromyzon, Danio, and Xenopus. We determined conserved regions in DBT specific to Diptera, and functionally tested a subset of those in D. melanogaster. Replacement of Lysine K224 with acidic residues strongly impacts the free-running period even in heterozygous flies, whereas homozygous mutants are not viable. K224D mutants have a temperature compensation defect with longer free-running periods at higher temperatures, which is exactly the opposite trend of what was reported for corresponding mammalian mutants. All DBTs of dipteran insects contain the NKRQK motif at positions 220-224. The occurrence of this motif perfectly correlates with the presence of BRIDE OF DOUBLETIME, BDBT, in Diptera. BDBT is a non-canonical FK506-binding protein that physically interacts with Drosophila DBT. The phylogeny of FK506-binding proteins suggests that BDBT is either absent or highly modified in non-dipteran insects. In addition to in silico analysis of DBT/CKIδ/ε evolution and diversity, we have identified four novel casein kinase 1 genes specific to the Drosophila genus.
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Affiliation(s)
- Nirav Thakkar
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Astrid Giesecke
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Olga Bazalova
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Jan Martinek
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Vlastimil Smykal
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany,*Correspondence: Ralf Stanewsky, ; David Dolezel,
| | - David Dolezel
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia,*Correspondence: Ralf Stanewsky, ; David Dolezel,
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5
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Torres-Aguila NP, Salonna M, Hoppler S, Ferrier DEK. Evolutionary diversification of the canonical Wnt signaling effector TCF/LEF in chordates. Dev Growth Differ 2022; 64:120-137. [PMID: 35048372 PMCID: PMC9303524 DOI: 10.1111/dgd.12771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/29/2022]
Abstract
Wnt signaling is essential during animal development and regeneration, but also plays an important role in diseases such as cancer and diabetes. The canonical Wnt signaling pathway is one of the most conserved signaling cascades in the animal kingdom, with the T‐cell factor/lymphoid enhancer factor (TCF/LEF) proteins being the major mediators of Wnt/β‐catenin‐regulated gene expression. In comparison with invertebrates, vertebrates possess a high diversity of TCF/LEF family genes, implicating this as a possible key change to Wnt signaling at the evolutionary origin of vertebrates. However, the precise nature of this diversification is only poorly understood. The aim of this study is to clarify orthology, paralogy, and isoform relationships within the TCF/LEF gene family within chordates via in silico comparative study of TCF/LEF gene structure, molecular phylogeny, and gene synteny. Our results support the notion that the four TCF/LEF paralog subfamilies in jawed vertebrates (gnathostomes) evolved via the two rounds of whole‐genome duplications that occurred during early vertebrate evolution. Importantly, gene structure comparisons and synteny analysis of jawless vertebrate (cyclostome) TCFs suggest that a TCF7L2‐like form of gene structure is a close proxy for the ancestral vertebrate structure. In conclusion, we propose a detailed evolutionary path based on a new pre‐whole‐genome duplication vertebrate TCF gene model. This ancestor gene model highlights the chordate and vertebrate innovations of TCF/LEF gene structure, providing the foundation for understanding the role of Wnt/β‐catenin signaling in vertebrate evolution.
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Affiliation(s)
- Nuria P Torres-Aguila
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, UK
| | - Marika Salonna
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Stefan Hoppler
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - David E K Ferrier
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, UK
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Xu Y, Li L, Zheng J, Wang M, Jiang B, Zhai Y, Lu L, Zhang C, Kuang Z, Yang X, Jin LN, Lin G, Zhang C. Pharmacological modulation of the cAMP signaling of two isoforms of melanocortin-3 receptor by melanocortin receptor accessory proteins in the tetrapod Xenopus laevis. Endocr Connect 2021; 10:1477-1488. [PMID: 34678757 PMCID: PMC8630767 DOI: 10.1530/ec-21-0179] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
As a member of the seven-transmembrane rhodopsin-like G protein-coupled receptor superfamily, the melanocortin-3 receptor (MC3R) is vital for the regulation of energy homeostasis and rhythms synchronizing in mammals, and its pharmacological effect could be directly influenced by the presence of melanocortin receptor accessory proteins (MRAPs), MRAP1 and MRAP2. The tetrapod amphibian Xenopus laevis (xl) retains higher duplicated genome than extant teleosts and serves as an ideal model system for embryonic development and physiological studies. However, the melanocortin system of the Xenopus laevis has not yet been thoroughly evaluated. In this work, we performed sequence alignment, phylogenetic tree, and synteny analysis of two xlMC3Rs. Co-immunoprecipitation and immunofluorescence assay further confirmed the co-localization and in vitro interaction of xlMC3Rs with xlMRAPs on the plasma membrane. Our results demonstrated that xlMRAP2.L/S could improve α-MSH-stimulated xlMC3Rs signaling and suppress their surface expression. Moreover, xlMC3R.L showed a similar profile on the ligands and surface expression in the presence of xlMRAP1.L. Overall, the distinct pharmacological modulation of xlMC3R.L and xlMC3R.S by dual MRAP2 proteins elucidated the functional consistency of melanocortin system during genomic duplication of tetrapod vertebrates.
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Affiliation(s)
- Ying Xu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lei Li
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jihong Zheng
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Meng Wang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Bopei Jiang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yue Zhai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Liumei Lu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cong Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhe Kuang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaomei Yang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Correspondence should be addressed to X Yang or L-N Jin or G Lin or C Zhang: or or or
| | - Li-Na Jin
- Department of Hematology, Changzheng Hospital, Naval Medical University, Shanghai, China
- Correspondence should be addressed to X Yang or L-N Jin or G Lin or C Zhang: or or or
| | - Gufa Lin
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Correspondence should be addressed to X Yang or L-N Jin or G Lin or C Zhang: or or or
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Correspondence should be addressed to X Yang or L-N Jin or G Lin or C Zhang: or or or
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Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.
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Roco ÁS, Liehr T, Ruiz-García A, Guzmán K, Bullejos M. Comparative Distribution of Repetitive Sequences in the Karyotypes of Xenopus tropicalis and Xenopus laevis (Anura, Pipidae). Genes (Basel) 2021; 12:617. [PMID: 33919402 PMCID: PMC8143290 DOI: 10.3390/genes12050617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/29/2022] Open
Abstract
Xenopus laevis and its diploid relative, Xenopus tropicalis, are the most used amphibian models. Their genomes have been sequenced, and they are emerging as model organisms for research into disease mechanisms. Despite the growing knowledge on their genomes based on data obtained from massive genome sequencing, basic research on repetitive sequences in these species is lacking. This study conducted a comparative analysis of repetitive sequences in X. laevis and X. tropicalis. Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) with Cot DNA of both species revealed a conserved enrichment of repetitive sequences at the ends of the chromosomes in these Xenopus species. The repeated sequences located on the short arm of chromosome 3 from X. tropicalis were not related to the sequences on the short arm of chromosomes 3L and 3S from X. laevis, although these chromosomes were homoeologous, indicating that these regions evolved independently in these species. Furthermore, all the other repetitive sequences in X. tropicalis and X. laevis may be species-specific, as they were not revealed in cross-species hybridizations. Painting experiments in X. laevis with chromosome 7 from X. tropicalis revealed shared sequences with the short arm of chromosome 3L. These regions could be related by the presence of the nucleolus organizer region (NOR) in both chromosomes, although the region revealed by chromosome painting in the short arm of chromosome 3L in X. laevis did not correspond to 18S + 28S rDNA sequences, as they did not colocalize. The identification of these repeated sequences is of interest as they provide an explanation to some problems already described in the genome assemblies of these species. Furthermore, the distribution of repetitive DNA in the genomes of X. laevis and X. tropicalis might be a valuable marker to assist us in understanding the genome evolution in a group characterized by numerous polyploidization events coupled with hybridizations.
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Affiliation(s)
- Álvaro S. Roco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany;
| | - Adrián Ruiz-García
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Kateryna Guzmán
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
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Boudinot P, Bird S, Du Pasquier L, Collet B. The repertoire of vertebrate STAT transcription factors: Origin and variations in fish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103929. [PMID: 33271121 DOI: 10.1016/j.dci.2020.103929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/15/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
The stat gene family diversified during early vertebrate evolution thanks to two rounds of whole genome duplication (WGD) to produce a typical repertoire composed of 6 STAT factors (named 1-6). In contrast, only one or two stat genes have been reported in C. elegans and in D. melanogaster. The main types of STAT found from bony fish to mammals are present in Agnathan genomes, but a typical STAT1-6 repertoire is only observed in jawed vertebrates. Comparative syntenies showed that STAT6 was the closest to the ancestor of the family. An extensive survey of stat genes across fish including polyploid species showed that whole genome duplications did not lead to a uniform expansion of stat genes. While 2 to 5 stat1 are present in salmonids, whose genome duplicated about 35My ago, only one copy of stat2 and stat6 is retained. In contrast, common carp, with a recent whole genome duplication (5-10My), possesses a doubled stat repertoire indicating that the elimination of stat2 and stat6 additional copies is not immediate. Altogether our data shed light on the multiplicity of evolutionary pathways followed by key components of the canonical cytokine receptor signalling pathway, and point to differential selective constraints exerted on these factors.
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Affiliation(s)
- Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
| | - Steve Bird
- Biomedical Unit, School of Science, University of Waikato, Hamilton, 3240, New Zealand
| | - Louis Du Pasquier
- Zoology and Evolutionary Biology, University of Basel, 4051, Basel, Switzerland
| | - Bertrand Collet
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
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10
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Heterogeneity of synonymous substitution rates in the Xenopus frog genome. PLoS One 2020; 15:e0236515. [PMID: 32764757 PMCID: PMC7413554 DOI: 10.1371/journal.pone.0236515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
With the increasing availability of high quality genomic data, there is opportunity to deeply explore the genealogical relationships of different gene loci between closely related species. In this study, we utilized genomes of Xenopus laevis (XLA, a tetraploid species with (L) and (S) sub-genomes) and X. tropicalis (XTR, a diploid species) to investigate whether synonymous substitution rates among orthologous or homoeologous genes displayed any heterogeneity. From over 1500 orthologous/homoeologous genes collected, we calculated proportion of synonymous substitutions between genomes/sub-genomes (k) and found variation within and between chromosomes. Within most chromosomes, we identified higher k with distance from the centromere, likely attributed to higher substitution rates and recombination in these regions. Using maximum likelihood methods, we identified further evidence supporting rate heterogeneity, and estimated species divergence times and ancestral population sizes. Estimated species divergence times (XLA.L-XLA.S: ~25.5 mya; XLA-XTR: ~33.0 mya) were slightly younger compared to a past study, attributed to consideration of population size in our study. Meanwhile, we found very large estimated population size in the ancestral populations of the two species (NA = 2.55 x 106). Local hybridization and population structure, which have not yet been well elucidated in frogs, may be a contributing factor to these possible large population sizes.
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11
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Wang M, Wu H, Liu Y, Chen LM. Activation of mouse NBCe1-B by Xenopus laevis and mouse IRBITs: Role of the variable Nt appendage of IRBITs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183240. [PMID: 32119862 DOI: 10.1016/j.bbamem.2020.183240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/24/2022]
Abstract
The IP3 receptor binding protein released with inositol 1,4,5-trisphosphate (IRBIT) plays important roles in the regulation of intracellular Ca2+ signaling and intracellular pH. The mammals express two IRBIT paralogs, i.e., IRBIT1 (encoded by AHCYL1) and IRBIT2 (encoded by AHCYL2). The clawed frog Xenopus laevis oocyte is widely used for biophysical studies on ion channels and transporters. It remains unknown whether endogenous IRBIT is expressed in Xenopus oocytes. Here, we cloned from frog oocyte irbit2.L and irbit2.S, orthologs of mammalian IRBIT2. When over-expressed, the frog IRBITs powerfully stimulate the electrogenic Na+/HCO3- cotransporter NBCe1-B as mouse IRBIT2-V2 does. Expression of an isolated Nt fragment of NBCe1-B containing the IRBIT-binding domain greatly decreases NBCe1-B activity in oocytes, suggesting that the basal activity of NBCe1-B contains a large component derived from the stimulation by endogenous frog IRBIT. The frog IRBITs are highly homologous to the mammalian ones in the carboxyl-terminal region, but varies greatly in the amino-terminal (Nt) appendage. Interestingly, truncation study showed that the Nt appendage of IRBIT1 and the long Nt appendage of IRBIT2-V2 modestly enhance, whereas the short Nt appendage of IRBIT2-V4 greatly inhibits the functional interaction between IRBIT and NBCe1-B. Finally, Ala-substitution of Ser68, a key phosphorylation site in the PEST domain of IRBIT, causes distinct functional consequences depending on the structural context of the Nt appendage in different IRBIT isoforms. We conclude that the Nt appendage of IRBITs is not necessary for, but plays an important regulatory role in the functional interaction between IRBIT and NBCe1-B.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei 430074, China
| | - Han Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei 430074, China
| | - Ying Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei 430074, China.
| | - Li-Ming Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei 430074, China.
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12
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Ohta Y, Kasahara M, O'Connor TD, Flajnik MF. Inferring the "Primordial Immune Complex": Origins of MHC Class I and Antigen Receptors Revealed by Comparative Genomics. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:1882-1896. [PMID: 31492741 PMCID: PMC6761025 DOI: 10.4049/jimmunol.1900597] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
Comparative analyses suggest that the MHC was derived from a prevertebrate "primordial immune complex" (PIC). PIC duplicated twice in the well-studied two rounds of genome-wide duplications (2R) early in vertebrate evolution, generating four MHC paralogous regions (predominantly on human chromosomes [chr] 1, 6, 9, 19). Examining chiefly the amphibian Xenopus laevis, but also other vertebrates, we identified their MHC paralogues and mapped MHC class I, AgR, and "framework" genes. Most class I genes mapped to MHC paralogues, but a cluster of Xenopus MHC class Ib genes (xnc), which previously was mapped outside of the MHC paralogues, was surrounded by genes syntenic to mammalian CD1 genes, a region previously proposed as an MHC paralogue on human chr 1. Thus, this gene block is instead the result of a translocation that we call the translocated part of the MHC paralogous region (MHCtrans) Analyses of Xenopus class I genes, as well as MHCtrans, suggest that class I arose at 1R on the chr 6/19 ancestor. Of great interest are nonrearranging AgR-like genes mapping to three MHC paralogues; thus, PIC clearly contained several AgR precursor loci, predating MHC class I/II. However, all rearranging AgR genes were found on paralogues derived from the chr 19 precursor, suggesting that invasion of a variable (V) exon by the RAG transposon occurred after 2R. We propose models for the evolutionary history of MHC/TCR/Ig and speculate on the dichotomy between the jawless (lamprey and hagfish) and jawed vertebrate adaptive immune systems, as we found genes related to variable lymphocyte receptors also map to MHC paralogues.
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Affiliation(s)
- Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201; and
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201;
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13
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Mitros T, Lyons JB, Session AM, Jenkins J, Shu S, Kwon T, Lane M, Ng C, Grammer TC, Khokha MK, Grimwood J, Schmutz J, Harland RM, Rokhsar DS. A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis. Dev Biol 2019; 452:8-20. [PMID: 30980799 DOI: 10.1016/j.ydbio.2019.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/12/2019] [Accepted: 03/22/2019] [Indexed: 12/19/2022]
Abstract
The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.
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Affiliation(s)
- Therese Mitros
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Jessica B Lyons
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Adam M Session
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA.
| | - Jerry Jenkins
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
| | - Shengquiang Shu
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA.
| | - Taejoon Kwon
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
| | - Maura Lane
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, FMP 410, 333 Cedar St./LCI 305, New Haven, CT 06520, USA.
| | - Connie Ng
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Timothy C Grammer
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, FMP 410, 333 Cedar St./LCI 305, New Haven, CT 06520, USA.
| | - Jane Grimwood
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
| | - Jeremy Schmutz
- Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.
| | - Richard M Harland
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA.
| | - Daniel S Rokhsar
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 9040495, Japan.
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14
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Jalvy S, Veschambre P, Fédou S, Rezvani HR, Thézé N, Thiébaud P. Leukemia inhibitory factor signaling in Xenopus embryo: Insights from gain of function analysis and dominant negative mutant of the receptor. Dev Biol 2019; 447:200-213. [DOI: 10.1016/j.ydbio.2018.12.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 01/19/2023]
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15
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Knytl M, Tlapakova T, Vankova T, Krylov V. Silurana Chromosomal Evolution: A New Piece to the Puzzle. Cytogenet Genome Res 2018; 156:223-228. [PMID: 30537723 DOI: 10.1159/000494708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2018] [Indexed: 12/22/2022] Open
Abstract
The African clawed frogs of the subgenus Silurana comprise both diploid and tetraploid species. The root of the polyploidization event leading to the extant Xenopus calcaratus, X. mellotropicalis, and X. epitropicalis is not fully understood so far. In X. mellotropicalis, we previously proposed 2 evolutionary scenarios encompassing complete (scenario A) or incomplete (scenario B) translocation of a heterochromatic block from chromosome 9 to 2 in a diploid ancestor. To resolve this puzzle, we performed FISH coupled with tyramide signal amplification (FISH-TSA) using 5 X. tropicalis and X. mellotropicalis single copy gene probes (gyg2, cept1, fn1, ndufs1, and sf3b1) reflecting borders of the heterochromatic blocks in X. tropicalis chromosome 9 (XTR 9) and X. mellotropicalis chromosome 9b (XME 9b) and XME 2a. cDNA sequencing recognized both homoeologous genes in X. mellotropicalis. Comparison of gene physical mapping between X. tropicalis and X. mellotropicalis clearly confirmed complete rather than incomplete translocation t(9;2) of the heterochromatic block in the diploid predecessor and thus favored scenario A regarding the formation of an ancestral allotetraploid karyotype.
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16
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Tandon P, Conlon F, Furlow JD, Horb ME. Expanding the genetic toolkit in Xenopus: Approaches and opportunities for human disease modeling. Dev Biol 2017; 426:325-335. [PMID: 27109192 PMCID: PMC5074924 DOI: 10.1016/j.ydbio.2016.04.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/23/2016] [Accepted: 04/12/2016] [Indexed: 11/29/2022]
Abstract
The amphibian model Xenopus, has been used extensively over the past century to study multiple aspects of cell and developmental biology. Xenopus offers advantages of a non-mammalian system, including high fecundity, external development, and simple housing requirements, with additional advantages of large embryos, highly conserved developmental processes, and close evolutionary relationship to higher vertebrates. There are two main species of Xenopus used in biomedical research, Xenopus laevis and Xenopus tropicalis; the common perception is that both species are excellent models for embryological and cell biological studies, but only Xenopus tropicalis is useful as a genetic model. The recent completion of the Xenopus laevis genome sequence combined with implementation of genome editing tools, such as TALENs (transcription activator-like effector nucleases) and CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated nucleases), greatly facilitates the use of both Xenopus laevis and Xenopus tropicalis for understanding gene function in development and disease. In this paper, we review recent advances made in Xenopus laevis and Xenopus tropicalis with TALENs and CRISPR-Cas and discuss the various approaches that have been used to generate knockout and knock-in animals in both species. These advances show that both Xenopus species are useful for genetic approaches and in particular counters the notion that Xenopus laevis is not amenable to genetic manipulations.
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Affiliation(s)
- Panna Tandon
- University of North Carolina McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, United States.
| | - Frank Conlon
- University of North Carolina McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, United States
| | - J David Furlow
- Deparment of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95616, United States
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, United States.
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17
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Suzuki A, Uno Y, Takahashi S, Grimwood J, Schmutz J, Mawaribuchi S, Yoshida H, Takebayashi-Suzuki K, Ito M, Matsuda Y, Rokhsar D, Taira M. Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Dev Biol 2017; 426:236-244. [PMID: 27720224 DOI: 10.1016/j.ydbio.2016.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 01/21/2023]
Abstract
Extracellular factors belonging to the TGF-β family play pivotal roles in the formation and patterning of germ layers during early Xenopus embryogenesis. Here, we show that the vg1 and nodal3 genes of Xenopus laevis are present in gene clusters on chromosomes XLA1L and XLA3L, respectively, and that both gene clusters have been completely lost from the syntenic S chromosome regions. The presence of gene clusters and chromosome-specific gene loss were confirmed by cDNA FISH analyses. Sequence and expression analyses revealed that paralogous genes in the vg1 and nodal3 clusters on the L chromosomes were also altered compared to their Xenopus tropicalis orthologs. X. laevis vg1 and nodal3 paralogs have potentially become pseudogenes or sub-functionalized genes and are expressed at different levels. As X. tropicalis has a single vg1 gene on chromosome XTR1, the ancestral vg1 gene in X. laevis appears to have been expanded on XLA1L. Of note, two reported vg1 genes, vg1(S20) and vg1(P20), reside in the cluster on XLA1L. The nodal3 gene cluster is also present on X. tropicalis chromosome XTR3, but phylogenetic analysis indicates that nodal3 genes in X. laevis and X. tropicalis were independently expanded and/or evolved in concert within each cluster by gene conversion. These findings provide insights into the function and molecular evolution of TGF-β family genes in response to allotetraploidization.
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Affiliation(s)
- Atsushi Suzuki
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Yoshinobu Uno
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Shuji Takahashi
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Shuuji Mawaribuchi
- School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku, Sagamihara 252-0373, Japan
| | - Hitoshi Yoshida
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Kimiko Takebayashi-Suzuki
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Michihiko Ito
- School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku, Sagamihara 252-0373, Japan
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Daniel Rokhsar
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, CA 94720-3200, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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18
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Waples RK, Seeb JE, Seeb LW. Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta). Mol Ecol 2017; 26:4131-4144. [PMID: 28452089 DOI: 10.1111/mec.14163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/01/2017] [Accepted: 04/10/2017] [Indexed: 12/19/2022]
Abstract
Whole-genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently, paralogs are often excluded from studies. The effects of an ancient whole-genome duplication (approximately 88 MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing on 10 collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and rediploidized regions of the genome. We use a pedigree and high-density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run-timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid-derived species.
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Affiliation(s)
- R K Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - J E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - L W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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19
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Mawaribuchi S, Takahashi S, Wada M, Uno Y, Matsuda Y, Kondo M, Fukui A, Takamatsu N, Taira M, Ito M. Sex chromosome differentiation and the W- and Z-specific loci in Xenopus laevis. Dev Biol 2017; 426:393-400. [DOI: 10.1016/j.ydbio.2016.06.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/09/2016] [Accepted: 06/09/2016] [Indexed: 12/22/2022]
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20
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Knytl M, Smolík O, Kubíčková S, Tlapáková T, Evans BJ, Krylov V. Chromosome divergence during evolution of the tetraploid clawed frogs, Xenopus mellotropicalis and Xenopus epitropicalis as revealed by Zoo-FISH. PLoS One 2017; 12:e0177087. [PMID: 28545147 PMCID: PMC5436656 DOI: 10.1371/journal.pone.0177087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 04/21/2017] [Indexed: 02/04/2023] Open
Abstract
Whole genome duplication (WGD) generates new species and genomic redundancy. In African clawed frogs of the genus Xenopus, this phenomenon has been especially important in that (i) all but one extant species are polyploid and (ii) whole genome sequences of some species provide an evidence for genomic rearrangements prior to or after WGD. Within Xenopus in the subgenus Silurana, at least one allotetraploidization event gave rise to three extant tetraploid (2n = 4x = 40) species–Xenopus mellotropicalis, X. epitropicalis, and X. calcaratus–but it is not yet clear the degree to which these tetraploid genomes experienced rearrangements prior to or after allotetraploidization. To explore genome evolution during diversification of these species, we performed cytogenetic analyses of X. mellotropicalis, including assessment of the localization of nucleolar organizer region, chromosome banding, and determination of the p/q arm ratios for each chromosome pair. We compared these data to a previously characterized karyotype of X. epitropicalis. Morphometric, C-banding and Zoo-FISH data support a previously hypothesized common allotetraploid predecessor of these species. Zoo-FISH with whole chromosome painting (WCP) probes derived from the closely related diploid species X. tropicalis confirmed the existence of ten chromosomal quartets in X. mellotropicalis somatic cells, as expected by its ploidy level and tetraploid ancestry. The p/q arm ratio of chromosome 2a was found to be substantially different between X. mellotropicalis (0.81) and X. epitropicalis (0.67), but no substantial difference between these two species was detected in this ratio for the homoeologous chromosome pair 2b, or for other chromosome pairs. Additionally, we identified variation between these two species in the locations of a heterochromatic block on chromosome pair 2a. These results are consistent with a dynamic history of genomic rearrangements before and/or after genome duplication, a surprising finding given the otherwise relatively conserved genomic structure of most frogs.
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Affiliation(s)
- Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
| | - Ondřej Smolík
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Svatava Kubíčková
- Department of Genetics and Reproduction, CEITEC -Veterinary Research Institute, Brno, Czech Republic
| | - Tereza Tlapáková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ben J. Evans
- Department of Biology, Life Sciences Building Room 328, Mc Master University, Hamilton, Ontario, Canada
| | - Vladimír Krylov
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
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21
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Ochi H, Kawaguchi A, Tanouchi M, Suzuki N, Kumada T, Iwata Y, Ogino H. Co-accumulation of cis-regulatory and coding mutations during the pseudogenization of the Xenopus laevis homoeologs six6.L and six6.S. Dev Biol 2017; 427:84-92. [PMID: 28501477 DOI: 10.1016/j.ydbio.2017.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/29/2017] [Accepted: 05/08/2017] [Indexed: 01/01/2023]
Abstract
Common models for the evolution of duplicated genes after genome duplication are subfunctionalization, neofunctionalization, and pseudogenization. Although the crucial roles of cis-regulatory mutations in subfunctionalization are well-documented, their involvement in pseudogenization and/or neofunctionalization remains unclear. We addressed this issue by investigating the evolution of duplicated homeobox genes, six6.L and six6.S, in the allotetraploid frog Xenopus laevis. Based on a comparative expression analysis, we observed similar eye-specific expression patterns for the two loci and their single ortholog in the ancestral-type diploid species Xenopus tropicalis. However, we detected lower levels of six6.S expression than six6.L expression. The six6.S enhancer sequence was more highly diverged from the orthologous enhancer of X. tropicalis than the six6.L enhancer, and showed weaker activity in a transgenic reporter assay. Based on a phylogenetic analysis of the protein sequences, we observed greater divergence between X. tropicalis Six6 and Six6.S than between X. tropicalis Six6 and Six6.L, and the observed mutations were reminiscent of a microphthalmia mutation in human SIX6. Misexpression experiments showed that six6.S has weaker eye-enlarging activity than six6.L, and targeted disruption of six6.L reduced the eye size more significantly than that of six6.S. These results suggest that enhancer attenuation stimulates the accumulation of hypomorphic coding mutations, or vice versa, in one duplicated gene copy and facilitates pseudogenization. We also underscore the value of the allotetraploid genome of X. laevis as a resource for studying latent pathogenic mutations.
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Affiliation(s)
- Haruki Ochi
- Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata, Yamagata Prefecture 990-9585, Japan
| | - Akane Kawaguchi
- Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Mikio Tanouchi
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagami-yama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Nanoka Suzuki
- Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata, Yamagata Prefecture 990-9585, Japan
| | - Tatsuki Kumada
- Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata, Yamagata Prefecture 990-9585, Japan
| | - Yui Iwata
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagami-yama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hajime Ogino
- Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan; Amphibian Research Center, Hiroshima University, 1-3-1 Kagami-yama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
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22
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Asymmetrically reduced expression of hand1 homeologs involving a single nucleotide substitution in a cis -regulatory element. Dev Biol 2017; 425:152-160. [DOI: 10.1016/j.ydbio.2017.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 01/28/2023]
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23
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Toombs JA, Sytnikova YA, Chirn GW, Ang I, Lau NC, Blower MD. Xenopus Piwi proteins interact with a broad proportion of the oocyte transcriptome. RNA (NEW YORK, N.Y.) 2017; 23:504-520. [PMID: 28031481 PMCID: PMC5340914 DOI: 10.1261/rna.058859.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
Piwi proteins utilize small RNAs (piRNAs) to recognize target transcripts such as transposable elements (TE). However, extensive piRNA sequence diversity also suggests that Piwi/piRNA complexes interact with many transcripts beyond TEs. To determine Piwi target RNAs, we used ribonucleoprotein-immunoprecipitation (RIP) and cross-linking and immunoprecipitation (CLIP) to identify thousands of transcripts associated with the Piwi proteins XIWI and XILI (Piwi-protein-associated transcripts, PATs) from early stage oocytes of X. laevis and X. tropicalis Most PATs associate with both XIWI and XILI and include transcripts of developmentally important proteins in oogenesis and embryogenesis. Only a minor fraction of PATs in both frog species displayed near perfect matches to piRNAs. Since predicting imperfect pairing between all piRNAs and target RNAs remains intractable, we instead determined that PAT read counts correlate well with the lengths and expression levels of transcripts, features that have also been observed for oocyte mRNAs associated with Drosophila Piwi proteins. We used an in vitro assay with exogenous RNA to confirm that XIWI associates with RNAs in a length- and concentration-dependent manner. In this assay, noncoding transcripts with many perfectly matched antisense piRNAs were unstable, whereas coding transcripts with matching piRNAs were stable, consistent with emerging evidence that Piwi proteins both promote the turnover of TEs and other RNAs, and may also regulate mRNA localization and translation. Our study suggests that Piwi proteins play multiple roles in germ cells and establishes a tractable vertebrate system to study the role of Piwi proteins in transcript regulation.
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Affiliation(s)
- James A Toombs
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yuliya A Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Gung-Wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Ignatius Ang
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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24
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Sequential Turnovers of Sex Chromosomes in African Clawed Frogs ( Xenopus) Suggest Some Genomic Regions Are Good at Sex Determination. G3-GENES GENOMES GENETICS 2016; 6:3625-3633. [PMID: 27605520 PMCID: PMC5100861 DOI: 10.1534/g3.116.033423] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of African clawed frogs (genus Xenopus). Here, we extend these discoveries by demonstrating that yet another sex determination system exists in Xenopus, specifically in the species Xenopus borealis. This system evolved recently in an ancestor of X. borealis that had the same sex determination system as X. laevis, a system which itself is newly evolved. Strikingly, the genomic region carrying the sex determination factor in X. borealis is homologous to that of therian mammals, including humans. Our results offer insights into how the genetic underpinnings of conserved phenotypes evolve, and suggest an important role for cooption of genetic building blocks with conserved developmental roles.
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25
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Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJC, Fujiyama A, Harland RM, Taira M, Rokhsar DS. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 2016; 538:336-343. [PMID: 27762356 PMCID: PMC5313049 DOI: 10.1038/nature19840] [Citation(s) in RCA: 648] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 09/09/2016] [Indexed: 02/07/2023]
Abstract
To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We demonstrate the allotetraploid origin of X. laevis by partitioning its genome into two homeologous subgenomes, marked by distinct families of “fossil” transposable elements. Based on the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged ~34 million years ago (Mya) and combined to form an allotetraploid ~17–18 Mya. 56% of all genes are retained in two homeologous copies. Protein function, gene expression, and the amount of flanking conserved sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
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Affiliation(s)
- Adam M Session
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Yoshinobu Uno
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Taejoon Kwon
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Jarrod A Chapman
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Atsushi Toyoda
- Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Shuji Takahashi
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Akimasa Fukui
- Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Hikosaka
- Division of Human Sciences, Graduate School of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Atsushi Suzuki
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mariko Kondo
- Misaki Marine Biological Station (MMBS), Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Simon J van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Ian Quigley
- Salk Institute, Molecular Neurobiology Laboratory, La Jolla, San Diego, California 92037, USA
| | - Sven Heinz
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, San Diego, California 92037, USA
| | - Hajime Ogino
- Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan
| | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jessica B Lyons
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | | | | | - Yoko Kuroki
- Department of Genome Medicine, National Research Institute for Child Health and Development, NCCHD, 2-10-1, Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Toshiaki Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Minoru Watanabe
- Institute of Institution of Liberal Arts and Fundamental Education, Tokushima University, 1-1 Minamijosanjima-cho, Tokushima 770-8502, Japan
| | - Ozren Bogdanovic
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Georgios Georgiou
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Sarita S Paranjpe
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Ila van Kruijsbergen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Shengquiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Joseph Carlson
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Tsutomu Kinoshita
- Department of Life Science, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, 655 W Baltimore St, Baltimore, Maryland 21201, USA
| | - Shuuji Mawaribuchi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, Tokyo 108-8641, Japan
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Therese Mitros
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Sahar V Mozaffari
- Department of Human Genetics, University of Chicago, 920 E. 58th St, CLSC 431F, Chicago, Illinois 60637, USA
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568, Japan
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Takamasa S Yamamoto
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Chiyo Takagi
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Rebecca Heald
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley California 94720-3200, USA
| | - Kelly Miller
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley California 94720-3200, USA
| | | | - Jacob Kitzman
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle Washington 98195-5065, USA
| | - Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Yumi Izutsu
- Department of Biology, Faculty of Science, Niigata University, 8050, Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Jacques Robert
- Department of Microbiology &Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Joshua Fortriede
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Kevin Burns
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Darwin S Dichmann
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, 655 W Baltimore St, Baltimore, Maryland 21201, USA
| | - Douglas W Houston
- The University of Iowa, Department of Biology, 257 Biology Building, Iowa City, Iowa 52242-1324, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle Washington 98195-5065, USA
| | - Louis DuPasquier
- Department of Zoology and Evolutionary Biology, University of Basel, Basel CH-4051, Switzerland
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Michihiko Ito
- Department of Biological Sciences, School of Science, Kitasato University, 1-15-1 Minamiku, Sagamihara, Kanagawa 252-0373, Japan
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Makoto Asashima
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Naoto Ueno
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Gert Jan C Veenstra
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Asao Fujiyama
- Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Principles of Informatics, National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan.,Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizoka 411-8540, Japan
| | - Richard M Harland
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daniel S Rokhsar
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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26
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Schmitz JF, Zimmer F, Bornberg-Bauer E. Mechanisms of transcription factor evolution in Metazoa. Nucleic Acids Res 2016; 44:6287-97. [PMID: 27288445 PMCID: PMC5291267 DOI: 10.1093/nar/gkw492] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/18/2016] [Accepted: 05/22/2016] [Indexed: 11/12/2022] Open
Abstract
Transcriptions factors (TFs) are pivotal for the regulation of virtually all cellular processes, including growth and development. Expansions of TF families are causally linked to increases in organismal complexity. Here we study the evolutionary dynamics, genetic causes and functional implications of the five largest metazoan TF families. We find that family expansions dominate across the whole metazoan tree; however, some branches experience exceptional family-specific accelerated expansions. Additionally, we find that such expansions are often predated by modular domain rearrangements, which spur the expansion of a new sub-family by separating it from the rest of the TF family in terms of protein-protein interactions. This separation allows for radical shifts in the functional spectrum of a duplicated TF. We also find functional differentiation inside TF sub-families as changes in expression specificity. Furthermore, accelerated family expansions are facilitated by repeats of sequence motifs such as C2H2 zinc fingers. We quantify whole genome duplications and single gene duplications as sources of TF family expansions, implying that some, but not all, TF duplicates are preferentially retained. We conclude that trans-regulatory changes (domain rearrangements) are instrumental for fundamental functional innovations, that cis-regulatory changes (affecting expression) accomplish wide-spread fine tuning and both jointly contribute to the functional diversification of TFs.
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Affiliation(s)
- Jonathan F Schmitz
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany
| | - Fabian Zimmer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany
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27
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Sang Y, Liu Q, Lee J, Ma W, McVey DS, Blecha F. Expansion of amphibian intronless interferons revises the paradigm for interferon evolution and functional diversity. Sci Rep 2016; 6:29072. [PMID: 27356970 PMCID: PMC4928184 DOI: 10.1038/srep29072] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/14/2016] [Indexed: 01/12/2023] Open
Abstract
Interferons (IFNs) are key cytokines identified in vertebrates and evolutionary dominance of intronless IFN genes in amniotes is a signature event in IFN evolution. For the first time, we show that the emergence and expansion of intronless IFN genes is evident in amphibians, shown by 24–37 intronless IFN genes in each frog species. Amphibian IFNs represent a molecular complex more complicated than those in other vertebrate species, which revises the established model of IFN evolution to facilitate re-inspection of IFN molecular and functional diversity. We identified these intronless amphibian IFNs and their intron-containing progenitors, and functionally characterized constitutive and inductive expression and antimicrobial roles in infections caused by zoonotic pathogens, such as influenza viruses and Listeria monocytogenes. Amphibians, therefore, may serve as overlooked vectors/hosts for zoonotic pathogens, and the amphibian IFN system provides a model to study IFN evolution in molecular and functional diversity in coping with dramatic environmental changes during terrestrial adaption.
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Affiliation(s)
- Yongming Sang
- Departments of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA
| | - Qinfang Liu
- Departments of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA
| | - Jinhwa Lee
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA
| | - Wenjun Ma
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA.,Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS, USA
| | - D Scott McVey
- Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA.,Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS, USA
| | - Frank Blecha
- Departments of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, USA
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28
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Keinath MC, Voss SR, Tsonis PA, Smith JJ. A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution. Dev Biol 2016; 426:211-218. [PMID: 27265323 DOI: 10.1016/j.ydbio.2016.05.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Genetic linkage maps are fundamental resources that enable diverse genetic and genomic approaches, including quantitative trait locus (QTL) analyses and comparative studies of genome evolution. It is straightforward to build linkage maps for species that are amenable to laboratory culture and genetic crossing designs, and that have relatively small genomes and few chromosomes. It is more difficult to generate linkage maps for species that do not meet these criteria. Here, we introduce a method to rapidly build linkage maps for salamanders, which are known for their enormous genome sizes. As proof of principle, we developed a linkage map with thousands of molecular markers (N=2349) for the Eastern newt (Notophthalmus viridescens). The map contains 12 linkage groups (152.3-934.7cM), only one more than the number of chromosome pairs. Importantly, this map was generated using RNA isolated from a single wild caught female and her 28 offspring. We used the map to reveal chromosome-scale conservation of synteny among N. viridescens, A. mexicanum (Urodela), and chicken (Amniota), and to identify large conserved segments between N. viridescens and Xenopus tropicalis (Anura). We also show that met1, a major effect QTL that regulates the expression of alternate metamorphic and paedomorphic modes of development in Ambystoma, associates with a chromosomal fusion that is not found in the N. viridescens map. Our results shed new light on the ancestral amphibian karyotype and reveal specific fusion and translocation events that shaped the genomes of three amphibian model taxa. The ability to rapidly build linkage maps for large salamander genomes will enable genetic and genomic analyses within this important vertebrate group, and more generally, empower comparative studies of vertebrate biology and evolution.
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Affiliation(s)
- Melissa C Keinath
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - S Randal Voss
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; Spinal Cord and Brain and Injury Research Center, University of Kentucky, Lexington, KY 40506, USA
| | | | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
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Abe G, Lee SH, Li IJ, Chang CJ, Tamura K, Ota KG. Open and closed evolutionary paths for drastic morphological changes, involving serial gene duplication, sub-functionalization, and selection. Sci Rep 2016; 6:26838. [PMID: 27220684 PMCID: PMC4879570 DOI: 10.1038/srep26838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022] Open
Abstract
Twin-tail goldfish strains are examples of drastic morphological alterations that emerged through domestication. Although this mutation is known to be caused by deficiency of one of two duplicated chordin genes, it is unknown why equivalent mutations have not been observed in other domesticated fish species. Here, we compared the chordin gene morphant phenotypes of single-tail goldfish and common carp (close relatives, both of which underwent chordin gene duplication and domestication). Morpholino-induced knockdown depleted chordin gene expression in both species; however, while knockdown reproduced twin-tail morphology in single-tail goldfish, it had no effect on common carp morphology. This difference can be explained by the observation that expression patterns of the duplicated chordin genes overlap completely in common carp, but are sub-functionalized in goldfish. Our finding implies that goldfish drastic morphological changes might be enhanced by the subsequent occurrence of three different types of evolutionary event (duplication, sub-functionalization, and selection) in a certain order.
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Affiliation(s)
- Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
- Laboratory of Organ Morphogenesis, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai 980-8578, Japan
| | - Shu-Hua Lee
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Chun-Ju Chang
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Koji Tamura
- Laboratory of Organ Morphogenesis, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai 980-8578, Japan
| | - Kinya G. Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
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Ota KG, Abe G. Goldfish morphology as a model for evolutionary developmental biology. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2016; 5:272-95. [PMID: 26952007 PMCID: PMC6680352 DOI: 10.1002/wdev.224] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 12/06/2015] [Accepted: 12/07/2015] [Indexed: 12/11/2022]
Abstract
Morphological variation of the goldfish is known to have been established by artificial selection for ornamental purposes during the domestication process. Chinese texts that date to the Song dynasty contain descriptions of goldfish breeding for ornamental purposes, indicating that the practice originated over one thousand years ago. Such a well-documented goldfish breeding process, combined with the phylogenetic and embryological proximities of this species with zebrafish, would appear to make the morphologically diverse goldfish strains suitable models for evolutionary developmental (evodevo) studies. However, few modern evodevo studies of goldfish have been conducted. In this review, we provide an overview of the historical background of goldfish breeding, and the differences between this teleost and zebrafish from an evolutionary perspective. We also summarize recent progress in the field of molecular developmental genetics, with a particular focus on the twin-tail goldfish morphology. Furthermore, we discuss unanswered questions relating to the evolution of the genome, developmental robustness, and morphologies in the goldfish lineage, with the goal of blazing a path toward an evodevo study paradigm using this teleost species as a new model species. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
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Riadi G, Ossandón F, Larraín J, Melo F. Towards the bridging of molecular genetics data across Xenopus species. BMC Genomics 2016; 17:161. [PMID: 26925848 PMCID: PMC4772642 DOI: 10.1186/s12864-016-2440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/05/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The clawed African frog Xenopus laevis has been one of the main vertebrate models for studies in developmental biology. However, for genetic studies, Xenopus tropicalis has been the experimental model of choice because it shorter life cycle and due to a more tractable genome that does not result from genome duplication as in the case of X. laevis. Today, although still organized in a large number of scaffolds, nearly 85% of X. tropicalis and 89% of X. laevis genomes have been sequenced. There is expectation for a comparative physical map that can be used as a Rosetta Stone between X. laevis genetic studies and X. tropicalis genomic research. RESULTS In this work, we have mapped using coarse-grained alignment the 18 chromosomes of X. laevis, release 9.1, on the 10 reference scaffolds representing the haploid genome of X. tropicalis, release 9.0. After validating the mapping with theoretical data, and estimating reference averages of genome sequence identity, 37 to 44% between the two species, we have carried out a synteny analysis for 2,112 orthologous genes. We found that 99.6% of genes are in the same organization. CONCLUSIONS Taken together, our results make possible to establish the correspondence between 62 and 65.5% of both genomes, percentage of identity, synteny and automatic annotation of transcripts of both species, providing a new and more comprehensive tool for comparative analysis of these two species, by allowing to bridge molecular genetics data among them.
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Affiliation(s)
- Gonzalo Riadi
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile.
| | | | - Juan Larraín
- Center for Aging and Regeneration and Millennium Nucleus in Regenerative Biology, Santiago, Chile.
| | - Francisco Melo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Michalak K, Maciak S, Kim YB, Santopietro G, Oh JH, Kang L, Garner HR, Michalak P. Nucleolar dominance and maternal control of 45S rDNA expression. Proc Biol Sci 2015; 282:20152201. [PMID: 26645200 PMCID: PMC4685780 DOI: 10.1098/rspb.2015.2201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/10/2015] [Indexed: 12/17/2022] Open
Abstract
Using a system of interspecies hybrids, trihybrids, and recombinants with varying proportions of genomes from three distinct Xenopus species, we provide evidence for de novo epigenetic silencing of paternal 45 S ribosomal ribonucleic acid (rRNA) genes and their species-dependent expression dominance that escapes transcriptional inactivation after homologous recombination. The same pattern of imprinting is maintained in the offspring from mothers being genetic males (ZZ) sex-reversed to females, indicating that maternal control of ribosomal deoxyribonucleic acid (rDNA) expression is not sex-chromosome linked. Nucleolar dominance (nucleolus underdevelopment) in Xenopus hybrids appears to be associated with a major non-Mendelian reduction in the number of 45 S rDNA gene copies rather than a specific pattern of their expression. The loss of rRNA gene copies in F1 hybrids was non-random with respect to the parental species, with the transcriptionally dominant variant preferentially removed from hybrid zygotes. This dramatic disruption in the structure and function of 45 S rDNA impacts transcriptome patterns of small nucleolar RNAs and messenger RNAs, with genes from the ribosome and oxidative stress pathways being among the most affected. Unorthodoxies of rDNA inheritance and expression may be interpreted as hallmarks of genetic conflicts between parental genomes, as well as defensive epigenetic mechanisms employed to restore genome integrity.
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Affiliation(s)
- Katarzyna Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sebastian Maciak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA Institute of Biology, University of Bialystok, PL-15-245, Poland
| | - Young Bun Kim
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Jung Hun Oh
- Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Lin Kang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Harold R Garner
- The Edward Via College of Osteopathic Medicine, Blacksburg, VA 24060, USA
| | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
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Zhang C, Ye L, Chen Y, Xiao J, Wu Y, Tao M, Xiao Y, Liu S. The chromosomal constitution of fish hybrid lineage revealed by 5S rDNA FISH. BMC Genet 2015; 16:140. [PMID: 26635010 PMCID: PMC4669654 DOI: 10.1186/s12863-015-0295-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/16/2015] [Indexed: 11/17/2022] Open
Abstract
Background The establishment of the bisexual fertile fish hybrid lineage including the allodiploid and allotetraploid hybrids, from interspecific hybridization of red crucian carp (Carassius auratus red var. 2n = 100, 2n = AA) (♀) × common carp (Cyprinus carpio L. 2n = 100, 2n = BB) (♂), provided a good platform to investigate genetic relationship between the parents and their hybrid progenies. Results The chromosomal inheritance of diploid and allotetraploid hybrid progenies in successive generations, was studied by applying 5S rDNA fluorescence in situ hybridization. Signals of 5S rDNA distinguished the chromosomal constitution of common carp (B-genome) from red crucian carp (A-genome), in which two strong signals were observed on the first submetacentric chromosome, while no major signal was found in common carp. After fish hybridization, one strong signal of 5S rDNA was detected in the same locus on the chromosome of diploid hybrids. As expected, two strong signals were observed in 4nF3 tetraploid hybrids offspring and it is worth mentioning that two strong signals were detected in a separating bivalent of a primary spermatocyte in 4nF3. Furthermore, the mitosis of heterozygous chromosomes was shown normal and stable with blastular tissue histological studies. Conclusions We revealed that 5S rDNA signal can be applied to discern A-genome from B-genome, and that 5S rDNA bearing chromosomes can be stably passed down in successive generations. Our work provided a significant method in fish breeding and this is important for studies in fish evolutionary biology.
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Affiliation(s)
- Chun Zhang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Lihai Ye
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Yiyi Chen
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Jun Xiao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Yanhong Wu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Min Tao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Yamei Xiao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of the Ministry of Education of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 2015; 408:345-57. [PMID: 26391338 PMCID: PMC4684507 DOI: 10.1016/j.ydbio.2015.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 08/18/2015] [Accepted: 09/09/2015] [Indexed: 12/18/2022]
Abstract
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
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Affiliation(s)
- Ian M Grant
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yun Shen
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prasad Trivedi
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John B Karpinka
- Xenbase, Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Limin Liu
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Aaron M Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - P Todd Stukenberg
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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Saritas-Yildirim B, Pliner HA, Ochoa A, Silva EM. Genome-Wide Identification and Expression of Xenopus F-Box Family of Proteins. PLoS One 2015; 10:e0136929. [PMID: 26327321 PMCID: PMC4556705 DOI: 10.1371/journal.pone.0136929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/11/2015] [Indexed: 02/05/2023] Open
Abstract
Protein degradation via the multistep ubiquitin/26S proteasome pathway is a rapid way to alter the protein profile and drive cell processes and developmental changes. Many key regulators of embryonic development are targeted for degradation by E3 ubiquitin ligases. The most studied family of E3 ubiquitin ligases is the SCF ubiquitin ligases, which use F-box adaptor proteins to recognize and recruit target proteins. Here, we used a bioinformatics screen and phylogenetic analysis to identify and annotate the family of F-box proteins in the Xenopus tropicalis genome. To shed light on the function of the F-box proteins, we analyzed expression of F-box genes during early stages of Xenopus development. Many F-box genes are broadly expressed with expression domains localized to diverse tissues including brain, spinal cord, eye, neural crest derivatives, somites, kidneys, and heart. All together, our genome-wide identification and expression profiling of the Xenopus F-box family of proteins provide a foundation for future research aimed to identify the precise role of F-box dependent E3 ubiquitin ligases and their targets in the regulatory circuits of development.
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Affiliation(s)
- Banu Saritas-Yildirim
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Hannah A. Pliner
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Angelica Ochoa
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Elena M. Silva
- Department of Biology, Georgetown University, Washington, DC, United States of America
- * E-mail:
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Karyological analyses of Pseudhymenochirus merlini and Hymenochirus boettgeri provide new insights into the chromosome evolution in the anuran family Pipidae. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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37
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Smith JJ, Keinath MC. The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications. Genome Res 2015; 25:1081-90. [PMID: 26048246 PMCID: PMC4509993 DOI: 10.1101/gr.184135.114] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 06/03/2015] [Indexed: 01/17/2023]
Abstract
It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ∼ 99), spanning a total of 5570.25 cM. Comparative mapping data yield strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionarily independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations of vertebrate evolution.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Melissa C Keinath
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
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Igawa T, Watanabe A, Suzuki A, Kashiwagi A, Kashiwagi K, Noble A, Guille M, Simpson DE, Horb ME, Fujii T, Sumida M. Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis. PLoS One 2015. [PMID: 26222540 PMCID: PMC4519292 DOI: 10.1371/journal.pone.0133963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.
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Affiliation(s)
- Takeshi Igawa
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
| | - Ai Watanabe
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Atsushi Suzuki
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akihiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Keiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Anna Noble
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - Matt Guille
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - David E. Simpson
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Marko E. Horb
- Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Tamotsu Fujii
- Department of Health Sciences, Faculty of Human Culture & Science, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Masayuki Sumida
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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Schmid M, Steinlein C. Chromosome Banding in Amphibia. XXXII. The Genus Xenopus (Anura, Pipidae). Cytogenet Genome Res 2015; 145:201-17. [PMID: 26112092 DOI: 10.1159/000433481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mitotic chromosomes of 16 species of the frog genus Xenopus were prepared from kidney and lung cell cultures. In the chromosomes of 7 species, high-resolution replication banding patterns could be induced by treating the cultures with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT) in succession, and in 6 of these species the BrdU/dT-banded chromosomes could be arranged into karyotypes. In the 3 species of the clade with 2n = 20 and 4n = 40 chromosomes (X. tropicalis, X. epitropicalis, X. new tetraploid 1), as well as in the 3 species with 4n = 36 chromosomes (X. laevis, X. borealis, X. muelleri), the BrdU/dT-banded karyotypes show a high degree of homoeology, though differences were detected between these groups. Translocations, inversions, insertions or sex-specific replication bands were not observed. Minor replication asynchronies found between chromosomes probably involve heterochromatic regions. BrdU/dT replication banding of Xenopus chromosomes provides the landmarks necessary for the exact physical mapping of genes and repetitive sequences. FISH with an X. laevis 5S rDNA probe detected multiple hybridization sites at or near the long-arm telomeric regions in most chromosomes of X. laevis and X. borealis, whereas in X. muelleri, the 5S rDNA sequences are located exclusively at the long-arm telomeres of a single chromosome pair. Staining with the AT base pair-specific fluorochrome quinacrine mustard revealed brightly fluorescing heterochromatic regions in the majority of X. borealis chromosomes which are absent in other Xenopus species.
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Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Abstract
This review summarizes the current status of the known extant genuine polyploid anuran and urodelan species, as well as spontaneously originated and/or experimentally produced amphibian polyploids. The mechanisms by which polyploids can originate, the meiotic pairing configurations, the diploidization processes operating in polyploid genomes, the phenomenon of hybridogenesis, and the relationship between polyploidization and sex chromosome evolution are discussed. The polyploid systems in some important amphibian taxa are described in more detail.
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Kwon T. Benchmarking Transcriptome Quantification Methods for Duplicated Genes in Xenopus laevis. Cytogenet Genome Res 2015; 145:253-64. [DOI: 10.1159/000431386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Xenopus is an important model organism for the study of genome duplication in vertebrates. With the full genome sequence of diploid Xenopus tropicalis available, and that of allotetraploid X. laevis close to being finished, we will be able to expand our understanding of how duplicated genes have evolved. One of the key features in the study of the functional consequence of gene duplication is how their expression patterns vary across different conditions, and RNA-seq seems to have enough resolution to discriminate the expression of highly similar duplicated genes. However, most of the current RNA-seq analysis methods were not designed to study samples with duplicate genes such as in X. laevis. Here, various computational methods to quantify gene expression in RNA-seq data were evaluated, using 2 independent X. laevis egg RNA-seq datasets and 2 reference databases for duplicated genes. The fact that RNA-seq can measure expression levels of similar duplicated genes was confirmed, but long paired-end reads are more informative than short single-end reads to discriminate duplicated genes. Also, it was found that bowtie, one of the most popular mappers in RNA-seq analysis, reports significantly smaller numbers of unique hits according to a mapping quality score compared to other mappers tested (BWA, GSNAP, STAR). Calculated from unique hits based on a mapping quality score, both expression levels and the expression ratio of duplicated genes can be estimated consistently among biological replicates, demonstrating that this method can successfully discriminate the expression of each copy of a duplicated gene pair. This comprehensive evaluation will be a useful guideline for studying gene expression of organisms with genome duplication using RNA-seq in the future.
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Krylov V, Tlapakova T. Xenopus Cytogenetics and Chromosomal Evolution. Cytogenet Genome Res 2015; 145:192-200. [PMID: 26022679 DOI: 10.1159/000406550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genus Xenopus represents important model organisms in the field of developmental biology and chromosomal evolution. Developmental processes are tightly coupled with the analysis of gene function via genetic linkage and mapping. Cytogenetic techniques such as chromosome banding or FISH are essential tools for the determination of gene position and subsequently for the construction of linkage and physical maps. Here, we present a summary of key achievements in X. tropicalis and X. laevis cytogenetics with emphasis on the gene localization to chromosomes. The second part of this review is focused on the chromosomal evolution regarding both above-mentioned species. With respect to methodology, hybridization techniques such as FISH and chromosome-specific painting FISH are highlighted.
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Affiliation(s)
- Vladimir Krylov
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Nakade S, Sakuma T, Sakane Y, Hara Y, Kurabayashi A, Kashiwagi K, Kashiwagi A, Yamamoto T, Obara M. Homeolog-specific targeted mutagenesis in Xenopus laevis using TALENs. In Vitro Cell Dev Biol Anim 2015; 51:879-84. [PMID: 25920501 DOI: 10.1007/s11626-015-9912-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/03/2015] [Indexed: 12/21/2022]
Abstract
Transcription activator-like effector nucleases (TALENs) have previously been used for targeted genome editing in various organisms including Xenopus laevis. However, because of genomic polyploidization, X. laevis usually possess homeologous genes (homeologs) with quite similar sequences that make the analysis of gene function difficult. In the present study, we show methodological examples of targeted gene modification of X. laevis homeologs. The X. laevis cytoglobin gene (cygb) consists of two homeologs (xlcygba and xlcygbb), and molecular phylogenetic analysis suggested that they have potentially different functions. Thus, there is a need to establish a method of homeolog-specific gene disruption to clarify gene functions in detail. Here, we show successful examples of homeolog-specific and simultaneous gene disruption for xlcygba and xlcygbb. We found that selective digestion can be performed with at least three mismatches in TALEN target sites in both homeologs. This report paves the way for the functional analyses of X. laevis homeologs, even those containing nearly identical sequences.
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Affiliation(s)
- Shota Nakade
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Yuto Sakane
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Yoshihiro Hara
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan
| | - Atsushi Kurabayashi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Keiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Akihiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
| | - Masanobu Obara
- Department of Biological Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M. A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis. Cytogenet Genome Res 2015; 145:187-91. [PMID: 25871511 DOI: 10.1159/000381292] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Xenopus laevis (XLA) is an allotetraploid species which appears to have undergone whole-genome duplication after the interspecific hybridization of 2 diploid species closely related to Silurana/Xenopus tropicalis (XTR). Previous cDNA fluorescence in situ hybridization (FISH) experiments have identified 9 sets of homoeologous chromosomes in X. laevis, in which 8 sets correspond to chromosomes 1-8 of X. tropicalis (XTR1-XTR8), and the last set corresponds to a fusion of XTR9 and XTR10. In addition, recent X. laevis genome sequencing and BAC-FISH experiments support this physiological relationship and show no gross chromosome translocation in the X. laevis karyotype. Therefore, for the benefit of both comparative cytogenetics and genome research, we here propose a new chromosome nomenclature for X. laevis based on the phylogenetic relationship and chromosome length, i.e. XLA1L, XLA1S, XLA2L, XLA2S, and so on, in which the numbering of XLA chromosomes corresponds to that in X. tropicalis and the postfixes 'L' and 'S' stand for 'long' and 'short' chromosomes in the homoeologous pairs, which can be distinguished cytologically by their relative size. The last chromosome set is named XLA9L and XLA9S, in which XLA9 corresponds to both XTR9 and XTR10, and hence, to emphasize the phylogenetic relationship to X. tropicalis, XLA9_10L and XLA9_10S are also used as synonyms.
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Affiliation(s)
- Yoichi Matsuda
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Abstract
Diseases affecting endodermal organs like the pancreas, lung and gastrointestinal (GI) tract have a substantial impact on human welfare. Since many of these are congenital defects that arise as a result of defects during development broad efforts are focused on understanding the development of these organs so as to better identify risk factors, disease mechanisms and therapeutic targets. Studies implementing model systems, like the amphibian Xenopus, have contributed immensely to our understanding of signaling (e.g. Wnt, FGF, BMP, RA) pathways and gene regulation (e.g. hhex, ptf1a, ngn3) that underlie normal development as well as disease progression. Recent advances in genome engineering further enhance the capabilities of the Xenopus model system for pursuing biomedical research, and will undoubtedly result in a boom of new information underlying disease mechanisms ultimately leading to advancements in diagnosis and therapy.
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Figuet E, Ballenghien M, Romiguier J, Galtier N. Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates. Genome Biol Evol 2014; 7:240-50. [PMID: 25527834 PMCID: PMC4316630 DOI: 10.1093/gbe/evu277] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.
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Affiliation(s)
- Emeric Figuet
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Marion Ballenghien
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Jonathan Romiguier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland
| | - Nicolas Galtier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
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Kirmizitas A, Gillis WQ, Zhu H, Thomsen GH. Gtpbp2 is required for BMP signaling and mesoderm patterning in Xenopus embryos. Dev Biol 2014; 392:358-67. [PMID: 24858484 DOI: 10.1016/j.ydbio.2014.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/27/2014] [Accepted: 05/07/2014] [Indexed: 12/26/2022]
Abstract
Smad proteins convey canonical intracellular signals for activated receptors in the TGFβ superfamily, but the activity of Smads and their impact on target genes are further regulated by a wide variety of cofactors and partner proteins. We have identified a new Smad1 partner, a GTPase named Gtpbp2 that is a distant relative of the translation factor eEf1a. Gtpbp2 affects canonical signaling in the BMP branch of the TGFβ superfamily, as morpholino knockdown of Gtpbp2 decreases, and overexpression of Gtpbp2 enhances, animal cap responses to BMP4. During Xenopus development, gtpbp2 transcripts are maternally expressed and localized to the egg animal pole, and partitioned into the nascent ectodermal and mesodermal cells during cleavage and early gastrulation stages. Subsequently, gtpbp2 is expressed in the neural folds, and in early tadpoles undergoing organogenesis gtpbp2 is expressed prominently in the brain, eyes, somites, ventral blood island and branchial arches. Consistent with its expression, morpholino knockdown of Gtpbp2 causes defects in ventral-posterior germ layer patterning, gastrulation and tadpole morphology. Overexpressed Gtpbp2 can induce ventral-posterior marker genes and localize to cell nuclei in Xenopus animal caps, highlighting its role in regulating BMP signaling in the early embryo. Here, we introduce this large GTPase as a novel factor in BMP signaling and ventral-posterior patterning.
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Affiliation(s)
- Arif Kirmizitas
- Department of Biochemistry and Cell Biology, Graduate Program in Molecular and Cellular Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - William Q Gillis
- Department of Biochemistry and Cell Biology, Graduate Program in Molecular and Cellular Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Haitao Zhu
- Department of Biochemistry and Cell Biology, Graduate Program in Molecular and Cellular Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Gerald H Thomsen
- Department of Biochemistry and Cell Biology, Graduate Program in Molecular and Cellular Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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Schmitt SM, Gull M, Brändli AW. Engineering Xenopus embryos for phenotypic drug discovery screening. Adv Drug Deliv Rev 2014; 69-70:225-46. [PMID: 24576445 DOI: 10.1016/j.addr.2014.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 02/08/2023]
Abstract
Many rare human inherited diseases remain untreatable despite the fact that the disease causing genes are known and adequate mouse disease models have been developed. In vivo phenotypic drug screening relies on isolating drug candidates by their ability to produce a desired therapeutic phenotype in whole organisms. Embryos of zebrafish and Xenopus frogs are abundant, small and free-living. They can be easily arrayed in multi-well dishes and treated with small organic molecules. With the development of novel genome modification tools, such a zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas, it is now possible to efficiently engineer non-mammalian models of inherited human diseases. Here, we will review the rapid progress made in adapting these novel genome editing tools to Xenopus. The advantages of Xenopus embryos as in vivo models to study human inherited diseases will be presented and their utility for drug discovery screening will be discussed. Being a tetrapod, Xenopus complements zebrafish as an indispensable non-mammalian animal model for the study of human disease pathologies and the discovery of novel therapeutics for inherited diseases.
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Sakane Y, Sakuma T, Kashiwagi K, Kashiwagi A, Yamamoto T, Suzuki KIT. Targeted mutagenesis of multiple and paralogous genes in Xenopus laevis using two pairs of transcription activator-like effector nucleases. Dev Growth Differ 2013; 56:108-14. [PMID: 24329851 DOI: 10.1111/dgd.12105] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 10/20/2013] [Accepted: 10/20/2013] [Indexed: 11/28/2022]
Abstract
Transcription activator-like effector nucleases (TALENs) have been extensively used in genome editing in various organisms. In some cases, however, it is difficult to efficiently disrupt both paralogous genes using a single pair of TALENs in Xenopus laevis because of its polyploidy. Here, we report targeted mutagenesis of multiple and paralogous genes using two pairs of TALENs in X. laevis. First, we show simultaneous targeted mutagenesis of three genes, tyrosinase paralogues (tyra and tyrb) and enhanced green fluorescent protein (egfp) by injection of two TALENs pairs in transgenic embryos carrying egfp. Consistent with the high frequency of both severe phenotypic traits, albinism and loss of GFP fluorescence, frameshift mutation rates of tyr paralogues and egfp reached 40-80%. Next, we show early introduction of TALEN-mediated mutagenesis of these target loci during embryogenesis. Finally, we also demonstrate that two different pairs of TALENs can simultaneously introduce mutations to both paralogues encoding histone chaperone with high efficiency. Our results suggest that targeted mutagenesis of multiple genes using TALENs can be applied to analyze the functions of paralogous genes with redundancy in X. laevis.
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Affiliation(s)
- Yuto Sakane
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
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50
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Cytogenetic analysis of Phyllomedusa distincta Lutz, 1950 (2n = 2x = 26), P. tetraploidea Pombal and Haddad, 1992 (2n = 4x = 52), and their natural triploid hybrids (2n = 3x = 39) (Anura, Hylidae, Phyllomedusinae). BMC Genet 2013; 14:75. [PMID: 24001221 PMCID: PMC3766241 DOI: 10.1186/1471-2156-14-75] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/27/2013] [Indexed: 01/28/2023] Open
Abstract
Background Natural polyploidy has played an important role during the speciation and evolution of vertebrates, including anurans, with more than 55 described cases. The species of the Phyllomedusa burmeisteri group are mostly characterized by having 26 chromosomes, but a karyotype with 52 chromosomes was described in P. tetraploidea. This species was found in sintopy with P. distincta in two localities of São Paulo State (Brazil), where triploid animals also occur, as consequence of natural hybridisation. We analyse the chromosomes of P. distincta, P. tetraploidea, and their triploid hybrids, to enlighten the origin of polyploidy and to obtain some evidence on diploidisation of tetraploid karyotype. Results Phyllomedusa distincta was 2n = 2x = 26, whereas P. tetraploidea was 2n = 4x = 52, and the hybrid individuals was 2n = 3x = 39. In meiotic phases, bivalents were observed in the diploid males, whereas both bivalents and tetravalents were observed in the tetraploid males. Univalents, bivalents or trivalents; metaphase II cells carrying variable number of chromosomes; and spermatids were detected in the testis preparations of the triploid males, indicating that the triploids were not completely sterile. In natural and experimental conditions, the triploids cross with the parental species, producing abnormal egg clutches and tadpoles with malformations. The embryos and tadpoles exhibited intraindividual karyotype variability and all of the metaphases contained abnormal constitutions. Multiple NORs, detected by Ag-impregnation and FISH with an rDNA probe, were observed on chromosome 1 in the three karyotypic forms; and, additionally, on chromosome 9 in the diploids, mostly on chromosome 8 in the tetraploids, and on both chromosome 8 and 9 in the triploids. Nevertheless, NOR-bearing chromosome 9 was detected in the tetraploids, and chromosome 9 carried active or inactive NORs in the triploids. C-banding, base-specific fluorochrome stainings with CMA3 and DAPI, FISH with a telomeric probe, and BrdU incorporation in DNA showed nearly equivalent patterns in the karyotypes of P. distincta, P. tetraploidea, and the triploid hybrids. Conclusions All the used cytogenetic techniques have provided strong evidence that the process of diploidisation, an essential step for stabilising the selective advantages produced by polyploidisation, is under way in distinct quartets of the tetraploid karyotype.
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