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Yuan Z, Song Y, Zhang S, Chen Y, Xu M, Fan G, Liu X. The Chromosome-Scale Genome of Chitala ornata Illuminates the Evolution of Early Teleosts. BIOLOGY 2024; 13:478. [PMID: 39056673 PMCID: PMC11274187 DOI: 10.3390/biology13070478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
Teleosts are the most prolific vertebrates, occupying the vast majority of aquatic environments, and their pectoral fins have undergone remarkable physiological transformations throughout their evolution. Studying early teleost fishes, such as those belonging to the Osteoglossiformes order, could offer crucial insights into the adaptive evolution of pectoral fins within this group. In this study, we have assembled a chromosomal-level genome for the Clown featherback (Chitala ornata), achieving the highest quality genome assembly for Osteoglossiformes to date, with a contig N50 of 32.78 Mb and a scaffold N50 of 40.73 Mb. By combining phylogenetic analysis, we determined that the Clown featherback diverged approximately 202 to 203 million years ago (Ma), aligning with continental separation events. Our analysis revealed the intriguing discovery that a unique deletion of regulatory elements is adjacent to the Gli3 gene, specifically in teleosts. This deletion might be tied to the specialized adaptation of their pectoral fins. Furthermore, our findings indicate that specific contractions and expansions of transposable elements (TEs) in teleosts, including the Clown featherback, could be connected to their adaptive evolution. In essence, this study not only provides a high-quality genomic resource for Osteoglossiformes but also sheds light on the evolutionary trajectory of early teleosts.
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Affiliation(s)
- Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Z.Y.)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Z.Y.)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yadong Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
| | - Mengyang Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
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2
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Benard EL, Küçükaylak I, Hatzold J, Berendes KU, Carney TJ, Beleggia F, Hammerschmidt M. wnt10a is required for zebrafish median fin fold maintenance and adult unpaired fin metamorphosis. Dev Dyn 2024; 253:566-592. [PMID: 37870737 PMCID: PMC11035493 DOI: 10.1002/dvdy.672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/03/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Mutations of human WNT10A are associated with odonto-ectodermal dysplasia syndromes. Here, we present analyses of wnt10a loss-of-function mutants in the zebrafish. RESULTS wnt10a mutant zebrafish embryos display impaired tooth development and a collapsing median fin fold (MFF). Rescue experiments show that wnt10a is essential for MFF maintenance both during embryogenesis and later metamorphosis. The MFF collapse could not be attributed to increased cell death or altered proliferation rates of MFF cell types. Rather, wnt10a mutants show reduced expression levels of dlx2a in distal-most MFF cells, followed by compromised expression of col1a1a and other extracellular matrix proteins encoding genes. Transmission electron microscopy analysis shows that although dermal MFF compartments of wnt10a mutants initially are of normal morphology, with regular collagenous actinotrichia, positioning of actinotrichia within the cleft of distal MFF cells becomes compromised, coinciding with actinotrichia shrinkage and MFF collapse. CONCLUSIONS MFF collapse of wnt10a mutant zebrafish is likely caused by the loss of distal properties in the developing MFF, strikingly similar to the proposed molecular pathomechanisms underlying the teeth defects caused by the loss of Wnt10 in fish and mammals. In addition, it points to thus fur unknown mechanisms controlling the linear growth and stability of actinotrichia and their collagen fibrils.
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Affiliation(s)
- Erica L. Benard
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Ismail Küçükaylak
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Julia Hatzold
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Kilian U.W. Berendes
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Thomas J. Carney
- Discovery Research Division, Institute of Molecular and
Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research),
Singapore, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological
University, Singapore, Republic of Singapore
| | - Filippo Beleggia
- Department I of Internal Medicine, Faculty of Medicine and
University Hospital Cologne, University of Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine
and University Hospital Cologne, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne
Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital Cologne,
University of Cologne, Cologne, Germany
| | - Matthias Hammerschmidt
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of
Cologne, Cologne, Germany
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3
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Bayramov AV, Yastrebov SA, Mednikov DN, Araslanova KR, Ermakova GV, Zaraisky AG. Paired fins in vertebrate evolution and ontogeny. Evol Dev 2024; 26:e12478. [PMID: 38650470 DOI: 10.1111/ede.12478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The origin of paired appendages became one of the most important adaptations of vertebrates, allowing them to lead active lifestyles and explore a wide range of ecological niches. The basic form of paired appendages in evolution is the fins of fishes. The problem of paired appendages has attracted the attention of researchers for more than 150 years. During this time, a number of theories have been proposed, mainly based on morphological data, two of which, the Balfour-Thacher-Mivart lateral fold theory and Gegenbaur's gill arch theory, have not lost their relevance. So far, however, none of the proposed ideas has been supported by decisive evidence. The study of the evolutionary history of the appearance and development of paired appendages lies at the intersection of several disciplines and involves the synthesis of paleontological, morphological, embryological, and genetic data. In this review, we attempt to summarize and discuss the results accumulated in these fields and to analyze the theories put forward regarding the prerequisites and mechanisms that gave rise to paired fins and limbs in vertebrates.
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Affiliation(s)
- Andrey V Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Yastrebov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry N Mednikov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Galina V Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Regenerative Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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4
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Kudoh H, Yonei-Tamura S, Abe G, Iwakiri J, Uesaka M, Makino T, Tamura K. Genomic screening of fish-specific genes in gnathostomes and their functions in fin development. Dev Growth Differ 2024; 66:235-247. [PMID: 38439516 DOI: 10.1111/dgd.12918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/06/2024]
Abstract
In this study, we comprehensively searched for fish-specific genes in gnathostomes that contribute to development of the fin, a fish-specific trait. Many previous reports suggested that animal group-specific genes are often important for group-specific traits. Clarifying the roles of fish-specific genes in fin development of gnathostomes, for example, can help elucidate the mechanisms underlying the formation of this trait. We first identified 91 fish-specific genes in gnathostomes by comparing the gene repertoire in 16 fish and 35 tetrapod species. RNA-seq analysis narrowed down the 91 candidates to 33 genes that were expressed in the developing pectoral fin. We analyzed the functions of approximately half of the candidate genes by loss-of-function analysis in zebrafish. We found that some of the fish-specific and fin development-related genes, including fgf24 and and1/and2, play roles in fin development. In particular, the newly identified fish-specific gene qkia is expressed in the developing fin muscle and contributes to muscle morphogenesis in the pectoral fin as well as body trunk. These results indicate that the strategy of identifying animal group-specific genes is functional and useful. The methods applied here could be used in future studies to identify trait-associated genes in other animal groups.
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Affiliation(s)
- Hidehiro Kudoh
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sayuri Yonei-Tamura
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Gembu Abe
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Division of Developmental Biology, Department of Functional Morphology, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Junichi Iwakiri
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masahiro Uesaka
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takashi Makino
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Koji Tamura
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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5
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Cadiz L, Reed M, Monis S, Akimenko MA, Jonz MG. Identification of signalling pathways involved in gill regeneration in zebrafish. J Exp Biol 2024; 227:jeb246290. [PMID: 38099598 PMCID: PMC10906665 DOI: 10.1242/jeb.246290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/04/2023] [Indexed: 01/31/2024]
Abstract
The occurrence of regeneration of the organs involved in respiratory gas exchange amongst vertebrates is heterogeneous. In some species of amphibians and fishes, the gills regenerate completely following resection or amputation, whereas in mammals, only partial, facultative regeneration of lung tissue occurs following injury. Given the homology between gills and lungs, the capacity of gill regeneration in aquatic species is of major interest in determining the underlying molecular or signalling pathways involved in respiratory organ regeneration. In the present study, we used adult zebrafish (Danio rerio) to characterize signalling pathways involved in the early stages of gill regeneration. Regeneration of the gills was induced by resection of gill filaments and observed over a period of up to 10 days. We screened for the effects on regeneration of the drugs SU5402, dorsomorphin and LY411575, which inhibit FGF, BMP or Notch signalling pathways, respectively. Exposure to each drug for 5 days significantly reduced regrowth of filament tips in regenerating tissue, compared with unresected controls. In separate experiments under normal conditions of regeneration, we used reverse transcription quantitative PCR and observed an increased expression of genes encoding for the bone morphogenetic factor, Bmp2b, fibroblast growth factor, Fgf8a, a transcriptional regulator (Her6) involved in Notch signalling, and Sonic Hedgehog (Shha), in regenerating gills at 10 day post-resection, compared with unresected controls. In situ hybridization confirmed that all four genes were expressed in regenerating gill tissue. This study implicates BMP, FGF, Notch and Shh signalling in gill regeneration in zebrafish.
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Affiliation(s)
- Laura Cadiz
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
| | - Maddison Reed
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
| | - Simon Monis
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
| | | | - Michael G. Jonz
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
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6
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Rajan AM, Rosin NL, Labit E, Biernaskie J, Liao S, Huang P. Single-cell analysis reveals distinct fibroblast plasticity during tenocyte regeneration in zebrafish. SCIENCE ADVANCES 2023; 9:eadi5771. [PMID: 37967180 PMCID: PMC10651129 DOI: 10.1126/sciadv.adi5771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Despite their importance in tissue maintenance and repair, fibroblast diversity and plasticity remain poorly understood. Using single-cell RNA sequencing, we uncover distinct sclerotome-derived fibroblast populations in zebrafish, including progenitor-like perivascular/interstitial fibroblasts, and specialized fibroblasts such as tenocytes. To determine fibroblast plasticity in vivo, we develop a laser-induced tendon ablation and regeneration model. Lineage tracing reveals that laser-ablated tenocytes are quickly regenerated by preexisting fibroblasts. By combining single-cell clonal analysis and live imaging, we demonstrate that perivascular/interstitial fibroblasts actively migrate to the injury site, where they proliferate and give rise to new tenocytes. By contrast, perivascular fibroblast-derived pericytes or specialized fibroblasts, including tenocytes, exhibit no regenerative plasticity. Active Hedgehog (Hh) signaling is required for the proliferation of activated fibroblasts to ensure efficient tenocyte regeneration. Together, our work highlights the functional diversity of fibroblasts and establishes perivascular/interstitial fibroblasts as tenocyte progenitors that promote tendon regeneration in a Hh signaling-dependent manner.
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Affiliation(s)
- Arsheen M. Rajan
- Department of Biochemistry and Molecular Biology, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nicole L. Rosin
- Faculty of Veterinary Medicine, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Elodie Labit
- Faculty of Veterinary Medicine, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Shan Liao
- Inflammation Research Network, Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Peng Huang
- Department of Biochemistry and Molecular Biology, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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7
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Herbert AL, Allard CAH, McCoy MJ, Wucherpfennig JI, Krueger SP, Chen HI, Gourlay AN, Jackson KD, Abbo LA, Bennett SH, Sears JD, Rhyne AL, Bellono NW, Kingsley DM. The genetic basis of novel trait gain in walking fish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.562356. [PMID: 37873105 PMCID: PMC10592820 DOI: 10.1101/2023.10.14.562356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A major goal in biology is to understand how organisms evolve novel traits. Multiple studies have identified genes contributing to regressive evolution, the loss of structures that existed in a recent ancestor. However, fewer examples exist for genes underlying constructive evolution, the gain of novel structures and capabilities in lineages that previously lacked them. Sea robins are fish that have evolved enlarged pectoral fins, six mobile locomotory fin rays (legs) and six novel macroscopic lobes in the central nervous system (CNS) that innervate the corresponding legs. Here, we establish successful husbandry and use a combination of transcriptomics, CRISPR-Cas9 editing, and behavioral assays to identify key transcription factors that are required for leg formation and function in sea robins. We also generate hybrids between two sea robin species with distinct leg morphologies and use allele-specific expression analysis and gene editing to explore the genetic basis of species-specific trait diversity, including a novel sensory gain of function. Collectively, our study establishes sea robins as a new model for studying the genetic basis of novel organ formation, and demonstrates a crucial role for the conserved limb gene tbx3a in the evolution of chemosensory legs in walking fish.
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Affiliation(s)
- Amy L Herbert
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Corey AH Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Matthew J McCoy
- Department of Pathology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Stephanie P Krueger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | | | - Kohle D Jackson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Lisa A Abbo
- Marine Biological Laboratory, Woods Hole, MA, 02543 USA
| | | | | | | | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - David M Kingsley
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford CA 94305 USA
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8
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Lyubetsky VA, Rubanov LI, Tereshina MB, Ivanova AS, Araslanova KR, Uroshlev LA, Goremykina GI, Yang JR, Kanovei VG, Zverkov OA, Shitikov AD, Korotkova DD, Zaraisky AG. Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations. Biol Direct 2023; 18:45. [PMID: 37568147 PMCID: PMC10416458 DOI: 10.1186/s13062-023-00405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND It is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid contents of proteins. Recently, evidence has accumulated that significant evolutionary transformations could also be associated with the loss/emergence of whole genes. The targeted identification of such genes is a challenging problem for both bioinformatics and evo-devo research. RESULTS To solve this problem we propose the WINEGRET method, named after the first letters of the title. Its main idea is to search for genes that satisfy two requirements: first, the desired genes were lost/emerged at the same evolutionary stage at which the phenotypic trait of interest was lost/emerged, and second, the expression of these genes changes significantly during the development of the trait of interest in the model organism. To verify the first requirement, we do not use existing databases of orthologs, but rely purely on gene homology and local synteny by using some novel quickly computable conditions. Genes satisfying the second requirement are found by deep RNA sequencing. As a proof of principle, we used our method to find genes absent in extant amniotes (reptiles, birds, mammals) but present in anamniotes (fish and amphibians), in which these genes are involved in the regeneration of large body appendages. As a result, 57 genes were identified. For three of them, c-c motif chemokine 4, eotaxin-like, and a previously unknown gene called here sod4, essential roles for tail regeneration were demonstrated. Noteworthy, we established that the latter gene belongs to a novel family of Cu/Zn-superoxide dismutases lost by amniotes, SOD4. CONCLUSIONS We present a method for targeted identification of genes whose loss/emergence in evolution could be associated with the loss/emergence of a phenotypic trait of interest. In a proof-of-principle study, we identified genes absent in amniotes that participate in body appendage regeneration in anamniotes. Our method provides a wide range of opportunities for studying the relationship between the loss/emergence of phenotypic traits and the loss/emergence of specific genes in evolution.
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Affiliation(s)
- Vassily A Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
- Department of Mechanics and Mathematics, Lomonosov Moscow State University, Kolmogorova Str., 1, Moscow, Russia, 119234
| | - Lev I Rubanov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Maria B Tereshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasiya S Ivanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, USA
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
| | - Leonid A Uroshlev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32, Vavilova Str., Moscow, Russia, 119991
| | - Galina I Goremykina
- Plekhanov Russian University of Economics, Stremyanny Lane 36, Moscow, Russia
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Vladimir G Kanovei
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Oleg A Zverkov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Alexander D Shitikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
| | - Daria D Korotkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997.
- Pirogov Russian National Research Medical University, Moscow, Russia.
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9
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Zhang Y, Mei Y, Cao A, Li S, He C, Song L, Gao J, Zhu Y, Cao X. Transcriptome analyses of betta fish (Betta splendens) provide novel insights into fin regeneration and color-related genes. Gene 2023:147508. [PMID: 37230203 DOI: 10.1016/j.gene.2023.147508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 05/27/2023]
Abstract
The betta fish (Betta splendens), an important ornamental fish, haswell-developed and colorful fins.After fin amputation, betta fish can easily regenerate finssimilar to the originalsin terms of structureand color. The powerful fin regeneration ability and a variety of colors in the betta fish are fascinating. However, the underlying molecular mechanisms are still not fully understood. In this study, tail fin amputation and regeneration experiments were performed on two kinds of betta fish: red and white color betta fish. Then, transcriptome analyseswere conducted to screen out fin regeneration and color-relatedgenes in betta fish. Through enrichment analyses of differentially expressed genes (DEGs), we founda series of enrichment pathways and genes related to finregeneration, including cell cycle (i.e. plcg2), TGF-beta signaling pathway (i.e. bmp6), PI3K-Akt signaling pathway (i.e. loxl2aand loxl2b), Wnt signaling pathway(i.e. lef1), gap junctions (i.e. cx43), angiogenesis (i.e. foxp1), and interferon regulatory factor (i.e. irf8). Meanwhile, some fin color-related pathways and genes were identified in betta fish, especially melanogenesis (i.e. tyr, tyrp1a, tyrp1b, and mc1r) and carotenoid color genes (i.e. pax3, pax7, sox10, and ednrba). In conclusion, this studycan not only enrich the research onfish tissue regeneration, but also has a potential significance for the aquaculture and breeding of the betta fish.
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Affiliation(s)
- Yunbang Zhang
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China
| | - Yihui Mei
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Aiying Cao
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Sen Li
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Chuan He
- Beijing Aquaculture Technology Extention Station, Beijing 100176, China
| | - Liyuan Song
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Gao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China
| | - Yurong Zhu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China.
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10
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Charest F, Mondéjar Fernández J, Grünbaum T, Cloutier R. Evolution of median fin patterning and modularity in living and fossil osteichthyans. PLoS One 2023; 18:e0272246. [PMID: 36921006 PMCID: PMC10016723 DOI: 10.1371/journal.pone.0272246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Morphological and developmental similarities, and interactions among developing structures are interpreted as evidences of modularity. Such similarities exist between the dorsal and anal fins of living actinopterygians, on the anteroposterior axis: (1) both fins differentiate in the same direction [dorsal and anal fin patterning module (DAFPM)], and (2) radials and lepidotrichia differentiate in the same direction [endoskeleton and exoskeleton module (EEM)]. To infer the evolution of these common developmental patternings among osteichthyans, we address (1) the complete description and quantification of the DAFPM and EEM in a living actinopterygian (the rainbow trout Oncorhynchus mykiss) and (2) the presence of these modules in fossil osteichthyans (coelacanths, lungfishes, porolepiforms and 'osteolepiforms'). In Oncorhynchus, sequences of skeletal elements are determined based on (1) apparition (radials and lepidotrichia), (2) chondrification (radials), (3) ossification (radials and lepidotrichia), and (4) segmentation plus bifurcation (lepidotrichia). Correlations are then explored between sequences. In fossil osteichthyans, sequences are determined based on (1) ossification (radials and lepidotrichia), (2) segmentation, and (3) bifurcation of lepidotrichia. Segmentation and bifurcation patterns were found crucial for comparisons between extant and extinct osteichthyan taxa. Our data suggest that the EEM is plesiomorphic at least for actinopterygians, and the DAFPM is plesiomorphic for osteichthyans, with homoplastic dissociation. Finally, recurrent patterns suggest the presence of a Lepidotrichia Patterning Module (LPM).
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Affiliation(s)
- France Charest
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
- Parc National de Miguasha, Nouvelle, Québec, Canada
| | - Jorge Mondéjar Fernández
- Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany
- Centre de Recherche en Paléontologie–Paris, Département Origines & Évolution, Muséum National d’Histoire Naturelle, UMR 7207 (MNHN–Sorbonne Université–CNRS), Paris, France
| | - Thomas Grünbaum
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Richard Cloutier
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
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11
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Rees L, König D, Jaźwińska A. Regeneration of the dermal skeleton and wound epidermis formation depend on BMP signaling in the caudal fin of platyfish. Front Cell Dev Biol 2023; 11:1134451. [PMID: 36846592 PMCID: PMC9946992 DOI: 10.3389/fcell.2023.1134451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Fin regeneration has been extensively studied in zebrafish, a genetic model organism. Little is known about regulators of this process in distant fish taxa, such as the Poeciliidae family, represented by the platyfish. Here, we used this species to investigate the plasticity of ray branching morphogenesis following either straight amputation or excision of ray triplets. This approach revealed that ray branching can be conditionally shifted to a more distal position, suggesting non-autonomous regulation of bone patterning. To gain molecular insights into regeneration of fin-specific dermal skeleton elements, actinotrichia and lepidotrichia, we localized expression of the actinodin genes and bmp2 in the regenerative outgrowth. Blocking of the BMP type-I receptor suppressed phospho-Smad1/5 immunoreactivity, and impaired fin regeneration after blastema formation. The resulting phenotype was characterized by the absence of bone and actinotrichia restoration. In addition, the wound epidermis displayed extensive thickening. This malformation was associated with expanded Tp63 expression from the basal epithelium towards more superficial layers, suggesting abnormal tissue differentiation. Our data add to the increasing evidence for the integrative role of BMP signaling in epidermal and skeletal tissue formation during fin regeneration. This expands our understanding of common mechanisms guiding appendage restoration in diverse clades of teleosts.
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Affiliation(s)
- Lana Rees
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Désirée König
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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12
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Nakagawa H, Aramaki T, Kondo S, Kuroda J. Collagen9a1c localizes to collagen fibers called actinotrichia in zebrafish fins. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000747. [PMID: 37090155 PMCID: PMC10119692 DOI: 10.17912/micropub.biology.000747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/20/2023] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
Teleost fish fins are supported by spear-shaped collagen crystals called actinotrichia. Actinotrichia are distributed radially at the distal end of the fins and thought to be necessary for proper formation of the fin and fin-bones. We previously reported that collagen9a1c ( col9a1c ) gene product is essential for the regular arrangement of actinotrichia using col9a1c -knockout zebrafish. Here, we examined the localization pattern of the EGFP-tagged Col9a1c protein in the fins to understand its role in the arrangement of actinotrichia. We found that EGFP-Col9a1c specifically localizes to actinotrichia.
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Affiliation(s)
- Hibiki Nakagawa
- Graduate school of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshihiro Aramaki
- Graduate school of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeru Kondo
- Graduate school of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Junpei Kuroda
- Graduate school of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Correspondence to: Junpei Kuroda (
)
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13
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Gene expression changes during the evolution of the tetrapod limb. Biol Futur 2022; 73:411-426. [PMID: 36355308 DOI: 10.1007/s42977-022-00136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.
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14
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Elf3 deficiency during zebrafish development alters extracellular matrix organization and disrupts tissue morphogenesis. PLoS One 2022; 17:e0276255. [DOI: 10.1371/journal.pone.0276255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
E26 transformation specific (ETS) family transcription factors are expressed during embryogenesis and are involved in various cellular processes such as proliferation, migration, differentiation, angiogenesis, apoptosis, and survival of cellular lineages to ensure appropriate development. Dysregulated expression of many of the ETS family members is detected in different cancers. The human ELF3, a member of the ETS family of transcription factors, plays a role in the induction and progression of human cancers is well studied. However, little is known about the role of ELF3 in early development. Here, the zebrafish elf3 was cloned, and its expression was analyzed during zebrafish development. Zebrafish elf3 is maternally deposited. At different developmental stages, elf3 expression was detected in different tissue, mainly neural tissues, endoderm-derived tissues, cartilage, heart, pronephric duct, blood vessels, and notochord. The expression levels were high at the tissue boundaries. Elf3 loss-of-function consequences were examined by using translation blocking antisense morpholino oligonucleotides, and effects were validated using CRISPR/Cas9 knockdown. Elf3-knockdown produced short and bent larvae with notochord, craniofacial cartilage, and fin defects. The extracellular matrix (ECM) in the fin and notochord was disorganized. Neural defects were also observed. Optic nerve fasciculation (bundling) and arborization in the optic tectum were defective in Elf3-morphants, and fragmentation of spinal motor neurons were evident. Dysregulation of genes encoding ECM proteins and matrix metalloprotease (MMP) and disorganization of ECM may play a role in the observed defects in Elf3 morphants. We conclude that zebrafish Elf3 is required for epidermal, mesenchymal, and neural tissue development.
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15
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Paulissen SM, Castranova DM, Krispin SM, Burns MC, Menéndez J, Torres-Vázquez J, Weinstein BM. Anatomy and development of the pectoral fin vascular network in the zebrafish. Development 2022; 149:dev199676. [PMID: 35132436 PMCID: PMC8959142 DOI: 10.1242/dev.199676] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022]
Abstract
The pectoral fins of teleost fish are analogous structures to human forelimbs, and the developmental mechanisms directing their initial growth and patterning are conserved between fish and tetrapods. The forelimb vasculature is crucial for limb function, and it appears to play important roles during development by promoting development of other limb structures, but the steps leading to its formation are poorly understood. In this study, we use high-resolution imaging to document the stepwise assembly of the zebrafish pectoral fin vasculature. We show that fin vascular network formation is a stereotyped, choreographed process that begins with the growth of an initial vascular loop around the pectoral fin. This loop connects to the dorsal aorta to initiate pectoral vascular circulation. Pectoral fin vascular development continues with concurrent formation of three elaborate vascular plexuses, one in the distal fin that develops into the fin-ray vasculature and two near the base of the fin in association with the developing fin musculature. Our findings detail a complex, yet highly choreographed, series of steps involved in the development of a complete, functional, organ-specific vascular network.
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Affiliation(s)
- Scott M. Paulissen
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Daniel M. Castranova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Shlomo M. Krispin
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Margaret C. Burns
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Javier Menéndez
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center, NY 10016, USA
| | - Jesús Torres-Vázquez
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center, NY 10016, USA
| | - Brant M. Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
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16
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Shih YH, Portman D, Idrizi F, Grosse A, Lawson ND. Integrated molecular analysis identifies a conserved pericyte gene signature in zebrafish. Development 2021; 148:273393. [PMID: 34751773 DOI: 10.1242/dev.200189] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Pericytes reside in capillary beds where they share a basement membrane with endothelial cells and regulate their function. However, little is known about embryonic pericyte development, in part, due to lack of specific molecular markers and genetic tools. Here, we applied single cell RNA-sequencing (scRNA-seq) of platelet derived growth factor beta (pdgfrb)-positive cells to molecularly characterize pericytes in zebrafish larvae. scRNA-seq revealed zebrafish cells expressing mouse pericyte gene orthologs, and comparison with bulk RNA-seq from wild-type and pdgfrb mutant larvae further refined a pericyte gene set. Subsequent integration with mouse pericyte scRNA-seq profiles revealed a core set of conserved pericyte genes. Using transgenic reporter lines, we validated pericyte expression of two genes identified in our analysis: NDUFA4 mitochondrial complex associated like 2a (ndufa4l2a), and potassium voltage-gated channel, Isk-related family, member 4 (kcne4). Both reporter lines exhibited pericyte expression in multiple anatomical locations, and kcne4 was also detected in a subset of vascular smooth muscle cells. Thus, our integrated molecular analysis revealed a molecular profile for zebrafish pericytes and allowed us to develop new tools to observe these cells in vivo.
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Affiliation(s)
- Yu-Huan Shih
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daneal Portman
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Feston Idrizi
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ann Grosse
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan D Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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17
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Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity. Nat Commun 2021; 12:5557. [PMID: 34548488 PMCID: PMC8455560 DOI: 10.1038/s41467-021-25810-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Precise cis-regulatory control of gene expression is essential for normal embryogenesis and tissue development. The BMP antagonist Gremlin1 (Grem1) is a key node in the signalling system that coordinately controls limb bud development. Here, we use mouse reverse genetics to identify the enhancers in the Grem1 genomic landscape and the underlying cis-regulatory logics that orchestrate the spatio-temporal Grem1 expression dynamics during limb bud development. We establish that transcript levels are controlled in an additive manner while spatial regulation requires synergistic interactions among multiple enhancers. Disrupting these interactions shows that altered spatial regulation rather than reduced Grem1 transcript levels prefigures digit fusions and loss. Two of the enhancers are evolutionary ancient and highly conserved from basal fishes to mammals. Analysing these enhancers from different species reveal the substantial spatial plasticity in Grem1 regulation in tetrapods and basal fishes, which provides insights into the fin-to-limb transition and evolutionary diversification of pentadactyl limbs. The BMP antagonist Gremlin1 balances BMP and SHH signalling, endowing limb bud development with robustness. Here, the authors identify enhancers controlling Grem1 levels in an additive, and spatial regulation in a synergistic manner, providing digit patterning with cis-regulatory robustness and evolutionary plasticity.
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18
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Nakagawa H, Kuroda J, Aramaki T, Kondo S. Mechanical role of actinotrichia in shaping the caudal fin of zebrafish. Dev Biol 2021; 481:52-63. [PMID: 34537221 DOI: 10.1016/j.ydbio.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/18/2021] [Accepted: 09/10/2021] [Indexed: 11/25/2022]
Abstract
Spear-like collagen complexes, known as actinotrichia, underlie the epidermal cell layer in the tip of teleost fins and are known to contribute toward fin formation; however, their specific role remains largely unclear. In this study, we investigated of actinotrichia in the role of caudal fin formation by generating collagen9a1c (col9a1c)-knockout zebrafish. Although actinotrichia were initially produced normally and aligned correctly in the knockout fish, the number of actinotrichia decreased as the fish grew and their alignment became disordered. Simultaneously, the fin tip gradually shortened in the dorsal-ventral direction and the entire fin became oval-shaped, while the fin-rays rarely bifurcated and instead underwent fusion, suggesting that actinotrichia are essential for spreading fins dorsoventrally. Furthermore, the epithelial cells that are usually thinly spread in normal fish became spherical in the knockout fish, reducing the area covered by each cell and thus the area of the fin tip. Together, these findings suggest that the tight alignment of actinotrichia provides physical support in the dorsal-ventral direction that allows caudal fins to expand in a triangular-shape.
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Affiliation(s)
- Hibiki Nakagawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Junpei Kuroda
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshihiro Aramaki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeru Kondo
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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19
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Catania F, Ujvari B, Roche B, Capp JP, Thomas F. Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution. Front Oncol 2021; 11:732081. [PMID: 34568068 PMCID: PMC8462274 DOI: 10.3389/fonc.2021.732081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Although neo-Darwinian (and less often Lamarckian) dynamics are regularly invoked to interpret cancer's multifarious molecular profiles, they shine little light on how tumorigenesis unfolds and often fail to fully capture the frequency and breadth of resistance mechanisms. This uncertainty frames one of the most problematic gaps between science and practice in modern times. Here, we offer a theory of adaptive cancer evolution, which builds on a molecular mechanism that lies outside neo-Darwinian and Lamarckian schemes. This mechanism coherently integrates non-genetic and genetic changes, ecological and evolutionary time scales, and shifts the spotlight away from positive selection towards purifying selection, genetic drift, and the creative-disruptive power of environmental change. The surprisingly simple use-it or lose-it rationale of the proposed theory can help predict molecular dynamics during tumorigenesis. It also provides simple rules of thumb that should help improve therapeutic approaches in cancer.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Deakin, VIC, Australia
| | - Benjamin Roche
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
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20
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Thompson AW, Hawkins MB, Parey E, Wcisel DJ, Ota T, Kawasaki K, Funk E, Losilla M, Fitch OE, Pan Q, Feron R, Louis A, Montfort J, Milhes M, Racicot BL, Childs KL, Fontenot Q, Ferrara A, David SR, McCune AR, Dornburg A, Yoder JA, Guiguen Y, Roest Crollius H, Berthelot C, Harris MP, Braasch I. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat Genet 2021; 53:1373-1384. [PMID: 34462605 PMCID: PMC8423624 DOI: 10.1038/s41588-021-00914-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Elise Parey
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (the Graduate University for Advanced Studies), Hayama, Japan
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Emily Funk
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Animal Science Department, University of California Davis, Davis, CA, USA
| | - Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Olivia E Fitch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Qiaowei Pan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra Louis
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | | | - Marine Milhes
- GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
| | - Brett L Racicot
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Solomon R David
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA
- Center for Human Health and the Environment, NC State University, Raleigh, NC, USA
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA.
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21
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Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs. DIVERSITY 2021. [DOI: 10.3390/d13080384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.
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22
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Mansuit R, Herrel A. The Evolution of Appendicular Muscles During the Fin-to-Limb Transition: Possible Insights Through Studies of Soft Tissues, a Perspective. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.702576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The evolution of the appendages during the fin-to-limb transition has been extensively studied, yet the majority of studies focused on the skeleton and the fossil record. Whereas the evolution of the anatomy of the appendicular musculature has been studied, the changes in the muscular architecture during the fin-to-limb transition remain largely unstudied, yet may provide important new insights. The fin-to-limb transition is associated with the appearance of a new mode of locomotion and the associated shift from pectoral to pelvic dominance. Here, we propose ways to investigate this question and review data on muscle mass and muscle architecture of the pectoral and pelvic muscles in extant vertebrates. We explore whether changes in appendage type are associated with changes in the muscular architecture and the relative investment in different muscle groups. These preliminary data show a general increase in the muscle mass of the appendages relative to the body mass during the fin-to-limb transition. The locomotor shift suggested to occur during the fin-to-limb transition appears supported by our preliminary data since in “fish” the pectoral fins are heavier than the pelvic fins, whereas in tetrapods, the forelimb muscles are less developed than the hind limb muscles. Finally, a shift in the investment in different muscle groups with an increase of the contribution of the superficial groups in tetrapods compared to “fish” appears to take place. Our study highlights the potential of investigating quantitative features of the locomotor muscles, yet also demonstrates the lack of quantitative data allowing to test these ideas.
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23
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Aman AJ, Kim M, Saunders LM, Parichy DM. Thyroid hormone regulates abrupt skin morphogenesis during zebrafish postembryonic development. Dev Biol 2021; 477:205-218. [PMID: 34089732 PMCID: PMC10069294 DOI: 10.1016/j.ydbio.2021.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 10/21/2022]
Abstract
Thyroid hormone is a key regulator of post-embryonic vertebrate development. Skin is a biomedically important thyroid hormone target organ, but the cellular and molecular mechanisms underlying skin pathologies associated with thyroid dysfunction remain obscure. The transparent skin of zebrafish is an accessible model system for studying vertebrate skin development. During post-embryonic development of the zebrafish, scales emerge in the skin from a hexagonally patterned array of dermal papillae, like other vertebrate skin appendages such as feathers and hair follicles. We show here that thyroid hormone regulates the rate of post-embryonic dermal development through interaction with nuclear hormone receptors. This couples skin development with body growth to generate a well ordered array of correctly proportioned scales. This work extends our knowledge of thyroid hormone actions on skin by providing in-vivo evidence that thyroid hormone regulates multiple aspects of dermal development.
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Affiliation(s)
- Andrew J Aman
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Margaret Kim
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, 22903, USA.
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24
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Castro J, Beviano V, Paço A, Leitão-Castro J, Cadete F, Francisco M, Freitas R. Hoxd13/Bmp2-mediated mechanism involved in zebrafish finfold design. Sci Rep 2021; 11:7165. [PMID: 33785799 PMCID: PMC8009906 DOI: 10.1038/s41598-021-86621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The overexpression of hoxd13a during zebrafish fin development causes distal endochondral expansion and simultaneous reduction of the finfold, mimicking the major events thought to have happened during the fin-to-limb transition in Vertebrates. We investigated the effect of hoxd13a overexpression on putative downstream targets and found it to cause downregulation of proximal fin identity markers (meis1 and emx2) and upregulation of genes involved in skeletogenesis/patterning (fbn1, dacha) and AER/Finfold maintenance (bmps). We then show that bmp2b overexpression leads to finfold reduction, recapitulating the phenotype observed in hoxd13a-overexpressing fins. In addition, we show that during the development of the long finfold in leot1/lofdt1 mutants, hoxd13a and bmp2b are downregulated. Our results suggest that modulation of the transcription factor Hoxd13 during evolution may have been involved in finfold reduction through regulation of the Bmp signalling that then activated apoptotic mechanisms impairing finfold elongation.
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Affiliation(s)
- João Castro
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Vanessa Beviano
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Ana Paço
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Joana Leitão-Castro
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Francisco Cadete
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Miguel Francisco
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Renata Freitas
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal ,Cell Growth and Differentiation Group, IBMC/I3S, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
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25
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Leurs N, Martinand-Mari C, Ventéo S, Haitina T, Debiais-Thibaud M. Evolution of Matrix Gla and Bone Gla Protein Genes in Jawed Vertebrates. Front Genet 2021; 12:620659. [PMID: 33790944 PMCID: PMC8006282 DOI: 10.3389/fgene.2021.620659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/08/2021] [Indexed: 01/05/2023] Open
Abstract
Matrix Gla protein (Mgp) and bone Gla protein (Bgp) are vitamin-K dependent proteins that bind calcium in their γ-carboxylated versions in mammals. They are recognized as positive (Bgp) or negative (Mgp and Bgp) regulators of biomineralization in a number of tissues, including skeletal tissues of bony vertebrates. The Mgp/Bgp gene family is poorly known in cartilaginous fishes, which precludes the understanding of the evolution of the biomineralization toolkit at the emergence of jawed vertebrates. Here we took advantage of recently released genomic and transcriptomic data in cartilaginous fishes and described the genomic loci and gene expression patterns of the Mgp/Bgp gene family. We identified three genes, Mgp1, Mgp2, and Bgp, in cartilaginous fishes instead of the single previously reported Mgp gene. We describe their genomic loci, resulting in a dynamic evolutionary scenario for this gene family including several events of local (tandem) duplications, but also of translocation events, along jawed vertebrate evolution. We describe the expression patterns of Mgp1, Mgp2, and Bgp in embryonic stages covering organogenesis in the small-spotted catshark Scyliorhinus canicula and present a comparative analysis with Mgp/Bgp family members previously described in bony vertebrates, highlighting ancestral features such as early embryonic, soft tissues, and neuronal expressions, but also derived features of cartilaginous fishes such as expression in fin supporting fibers. Our results support an ancestral function of Mgp in skeletal mineralization and a later derived function of Bgp in skeletal development that may be related to the divergence of bony vertebrates.
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Affiliation(s)
- Nicolas Leurs
- ISEM, CNRS, IRD, EPHE, Univ. Montpellier, Montpellier, France
| | | | - Stéphanie Ventéo
- Institute for Neurosciences of Montpellier, Saint Eloi Hospital, Inserm UMR 1051, Univ. Montpellier, Montpellier, France
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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26
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Onimaru K, Tatsumi K, Tanegashima C, Kadota M, Nishimura O, Kuraku S. Developmental hourglass and heterochronic shifts in fin and limb development. eLife 2021; 10:62865. [PMID: 33560225 PMCID: PMC7932699 DOI: 10.7554/elife.62865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here, we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open-chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls. Animals come in all shapes and sizes. This diversity arose through genetic mutations during evolution, but it is unclear exactly how these variations led to the formation of new shapes. There is increasing evidence to suggest that not all shapes are possible and that variability between animals is limited by a phenomenon known as “developmental constraint”. These limitations direct parts of the body towards a specific shape as they develop in the embryo. Therefore, understanding the mechanisms underlying these developmental constraints could help explain how different body shapes evolved. The limbs of humans and other mammals evolved from the fins of fish, and this transition is often used to study the role developmental constraints play in evolution. This is an ideal model as there is already a detailed fossil record mapping this evolutionary event, and data pinpointing some of the genes involved in the development of limbs and fins. But this data is incomplete, and a full comparison between the genes activated in the fin and the limb during embryonic development had not been achieved. This is because most fish used for research have undergone recent genetic changes, making it hard to spot which genetic differences are linked to the evolution of the limb. To overcome this barrier, Onimaru et al. compared genetic data from the developing limbs of mice to the developing fins of the brown-banded bamboo shark, which evolves much slower than other fish. This revealed that although many genes commonly played a role in the development of the fin and the limb in the embryo, the activity of these shared genes was not the same. For example, genes that switched on in the late stages of limb development, switched off in the late stages of fin development. But in the middle of development, those differences were relatively small and both species activated very similar sets of genes. Many of these genes were pleiotropic, which means they have important roles in other tissues and therefore mutate less often. This suggests that the mid-stage of limb development is under the strongest level of constraint. Darwin’s theory of natural selection explains that mutations drive evolution. But the theory cannot predict what kinds of new body shapes new mutations will produce. Understanding how the activity levels of different genes affect development could help to fill this knowledge gap. This has potential medical applications, for example, understanding why some genetic changes cause more serious problems than others. This work suggests that mutations in genes that are active during the mid-stage of limb development may have the most serious impact.
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Affiliation(s)
- Koh Onimaru
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,Laboratory for Bioinformatics Research, RIKEN BDR, Wako City, Japan.,Molecular Oncology Laboratory, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
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27
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Wang K, Wang J, Zhu C, Yang L, Ren Y, Ruan J, Fan G, Hu J, Xu W, Bi X, Zhu Y, Song Y, Chen H, Ma T, Zhao R, Jiang H, Zhang B, Feng C, Yuan Y, Gan X, Li Y, Zeng H, Liu Q, Zhang Y, Shao F, Hao S, Zhang H, Xu X, Liu X, Wang D, Zhu M, Zhang G, Zhao W, Qiu Q, He S, Wang W. African lungfish genome sheds light on the vertebrate water-to-land transition. Cell 2021; 184:1362-1376.e18. [PMID: 33545087 DOI: 10.1016/j.cell.2021.01.047] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/09/2020] [Accepted: 01/27/2021] [Indexed: 12/26/2022]
Abstract
Lungfishes are the closest extant relatives of tetrapods and preserve ancestral traits linked with the water-to-land transition. However, their huge genome sizes have hindered understanding of this key transition in evolution. Here, we report a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 Mb and 2.81 Gb, respectively. The large size of the lungfish genome is due mainly to retrotransposons. Genes with ultra-long length show similar expression levels to other genes, indicating that lungfishes have evolved high transcription efficacy to keep gene expression balanced. Together with transcriptome and experimental data, we identified potential genes and regulatory elements related to such terrestrial adaptation traits as pulmonary surfactant, anxiolytic ability, pentadactyl limbs, and pharyngeal remodeling. Our results provide insights and key resources for understanding the evolutionary pathway leading from fishes to humans.
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Affiliation(s)
- Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jun Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jue Ruan
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Guangyi Fan
- BGI-Qingdao, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiang Hu
- Grandomics Biosciences, Beijing 102200, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- BGI-Shenzhen, Shenzhen 518083, China
| | - Youan Zhu
- Institute of Vertebrate Paleontology and Paleoanthropology, China Academy of Sciences, Beijing 100044, China
| | - Yue Song
- BGI-Qingdao, Qingdao 266555, China
| | - Huatao Chen
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Tiantian Ma
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Haifeng Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Bin Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qun Liu
- BGI-Qingdao, Qingdao 266555, China
| | | | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | | | - He Zhang
- BGI-Qingdao, Qingdao 266555, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Liu
- BGI-Qingdao, Qingdao 266555, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102200, China
| | - Min Zhu
- Institute of Vertebrate Paleontology and Paleoanthropology, China Academy of Sciences, Beijing 100044, China
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wenming Zhao
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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28
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Lebedeva L, Zhumabayeva B, Gebauer T, Kisselev I, Aitasheva Z. Zebrafish ( Danio rerio) as a Model for Understanding the Process of Caudal Fin Regeneration. Zebrafish 2020; 17:359-372. [PMID: 33259770 DOI: 10.1089/zeb.2020.1926] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
After its introduction for scientific investigation in the 1950s, the cypriniform zebrafish, Danio rerio, has become a valuable model for the study of regenerative processes and mechanisms. Zebrafish exhibit epimorphic regeneration, in which a nondifferentiated cell mass formed after amputation is able to fully regenerate lost tissue such as limbs, heart muscle, brain, retina, and spinal cord. The process of limb regeneration in zebrafish comprises several stages characterized by the activation of specific signaling pathways and gene expression. We review current research on key factors in limb regeneration using zebrafish as a model.
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Affiliation(s)
- Lina Lebedeva
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, The Republic of Kazakhstan
| | - Beibitgul Zhumabayeva
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, The Republic of Kazakhstan
| | - Tatyana Gebauer
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Ilya Kisselev
- Institute of General Genetics and Cytology, Almaty, The Republic of Kazakhstan
| | - Zaure Aitasheva
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, The Republic of Kazakhstan
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29
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Kuroda J, Itabashi T, Iwane AH, Aramaki T, Kondo S. The Physical Role of Mesenchymal Cells Driven by the Actin Cytoskeleton Is Essential for the Orientation of Collagen Fibrils in Zebrafish Fins. Front Cell Dev Biol 2020; 8:580520. [PMID: 33154970 PMCID: PMC7591588 DOI: 10.3389/fcell.2020.580520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Fibrous collagen imparts physical strength and flexibility to tissues by forming huge complexes. The density and orientation of collagen fibers must be correctly specified for the optimal physical property of the collagen complex. However, little is known about its underlying cellular mechanisms. Actinotrichia are collagen fibers aligned at the fin-tip of bony fish and are easily visible under the microscope due to their thick, linear structure. We used the actinotrichia as a model system to investigate how cells manipulate collagen fibers. The 3D image obtained by focused ion beam scanning electron microscopy (FIB-SEM) showed that the pseudopodia of mesenchymal cells encircle the multiple actinotrichia. We then co-incubated the mesenchymal cells and actinotrichia in vitro, and time-lapse analysis revealed how cells use pseudopods to align collagen fiber orientation. This in vitro behavior is dependent on actin polymerization in mesenchymal cells. Inhibition of actin polymerization in mesenchymal cells results in mis-orientation of actinotrichia in the fin. These results reveal how mesenchymal cells are involved in fin formation and have important implications for the physical interaction between cells and collagen fibers.
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Affiliation(s)
- Junpei Kuroda
- Graduate School of Frontier Bioscience, Osaka University, Suita, Japan
- RIKEN Center for Biosystems Dynamics Research, Higashi-Hiroshima, Japan
| | - Takeshi Itabashi
- RIKEN Center for Biosystems Dynamics Research, Higashi-Hiroshima, Japan
| | - Atsuko H. Iwane
- RIKEN Center for Biosystems Dynamics Research, Higashi-Hiroshima, Japan
| | - Toshihiro Aramaki
- Graduate School of Frontier Bioscience, Osaka University, Suita, Japan
| | - Shigeru Kondo
- Graduate School of Frontier Bioscience, Osaka University, Suita, Japan
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30
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Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes. eLife 2020; 9:55792. [PMID: 32831172 PMCID: PMC7486121 DOI: 10.7554/elife.55792] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023] Open
Abstract
The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.
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Affiliation(s)
- Nathan D Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Masahiro Shin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Ann Grosse
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
| | - Onur Yukselen
- Bioinformatics Core, University of Massachusetts Medical School, Worcester, United States
| | - Oliver A Stone
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Lihua Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
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31
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Differences in postembryonic dorsal fin development resulted in phenotypic divergence in two goldfish strains, Red Cap Oranda and Ranchu. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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32
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Woltering JM, Irisarri I, Ericsson R, Joss JMP, Sordino P, Meyer A. Sarcopterygian fin ontogeny elucidates the origin of hands with digits. SCIENCE ADVANCES 2020; 6:eabc3510. [PMID: 32875118 PMCID: PMC7438105 DOI: 10.1126/sciadv.abc3510] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/09/2020] [Indexed: 05/03/2023]
Abstract
How the hand and digits originated from fish fins during the Devonian fin-to-limb transition remains unsolved. Controversy in this conundrum stems from the scarcity of ontogenetic data from extant lobe-finned fishes. We report the patterning of an autopod-like domain by hoxa13 during fin development of the Australian lungfish, the most closely related extant fish relative of tetrapods. Differences from tetrapod limbs include the absence of digit-specific expansion of hoxd13 and hand2 and distal limitation of alx4 and pax9, which potentially evolved through an enhanced response to shh signaling in limbs. These developmental patterns indicate that the digit program originated in postaxial fin radials and later expanded anteriorly inside of a preexisting autopod-like domain during the evolution of limbs. Our findings provide a genetic framework for the transition of fins into limbs that supports the significance of classical models proposing a bending of the tetrapod metapterygial axis.
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Affiliation(s)
- Joost M. Woltering
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| | - Iker Irisarri
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| | | | | | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
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Yoshida K, Kawakami K, Abe G, Tamura K. Zebrafish can regenerate endoskeleton in larval pectoral fin but the regenerative ability declines. Dev Biol 2020; 463:110-123. [PMID: 32422142 DOI: 10.1016/j.ydbio.2020.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 01/12/2023]
Abstract
We show for the first time endoskeletal regeneration in the developing pectoral fin of zebrafish. The developing pectoral fin contains an aggregation plate of differentiated chondrocytes (endochondral disc; primordium for endoskeletal components, proximal radials). The endochondral disc can be regenerated after amputation in the middle of the disc. The regenerated disc sufficiently forms endoskeletal patterns. Early in the process of regenerating the endochondral disc, epithelium with apical ectodermal ridge (AER) marker expression rapidly covers the amputation plane, and mesenchymal cells start to actively proliferate. Taken together with re-expression of a blastema marker gene, msxb, and other developmental genes, it is likely that regeneration of the endochondral disc recaptures fin development as epimorphic limb regeneration does. The ability of endoskeletal regeneration declines during larval growth, and adult zebrafish eventually lose the ability to regenerate endoskeletal components such that amputated endoskeletons become enlarged. Endoskeletal regeneration in the zebrafish pectoral fin will serve as a new model system for successful appendage regeneration in mammals.
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Affiliation(s)
- Keigo Yoshida
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan; Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Gembu Abe
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Koji Tamura
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan.
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Enny A, Flaherty K, Mori S, Turner N, Nakamura T. Developmental constraints on fin diversity. Dev Growth Differ 2020; 62:311-325. [PMID: 32396685 PMCID: PMC7383993 DOI: 10.1111/dgd.12670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 12/31/2022]
Abstract
The fish fin is a breathtaking repository full of evolutionary diversity, novelty, and convergence. Over 500 million years, the adaptation to novel habitats has provided landscapes of fin diversity. Although comparative anatomy of evolutionarily divergent patterns over centuries has highlighted the fundamental architectures and evolutionary trends of fins, including convergent evolution, the developmental constraints on fin evolution, which bias the evolutionary trajectories of fin morphology, largely remain elusive. Here, we review the evolutionary history, developmental mechanisms, and evolutionary underpinnings of paired fins, illuminating possible developmental constraints on fin evolution. Our compilation of anatomical and genetic knowledge of fin development sheds light on the canalized and the unpredictable aspects of fin shape in evolution. Leveraged by an arsenal of genomic and genetic tools within the working arena of spectacular fin diversity, evolutionary developmental biology embarks on the establishment of conceptual framework for developmental constraints, previously enigmatic properties of evolution.
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Affiliation(s)
- Alyssa Enny
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
| | - Kathleen Flaherty
- Rutgers Animal CareRutgers the State University of New JerseyPiscatawayNJUSA
| | - Shunsuke Mori
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
| | - Natalie Turner
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
| | - Tetsuya Nakamura
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
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35
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Recent advancements in understanding fin regeneration in zebrafish. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 9:e367. [DOI: 10.1002/wdev.367] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 11/07/2022]
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Li L, Zhang J, Akimenko MA. Inhibition of mmp13a during zebrafish fin regeneration disrupts fin growth, osteoblasts differentiation, and Laminin organization. Dev Dyn 2019; 249:187-198. [PMID: 31487071 DOI: 10.1002/dvdy.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/29/2019] [Accepted: 08/31/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Matrix metalloproteinases 13 (MMP13) is a potent endopeptidase that regulate cell growth, migration, and extracellular matrix remodeling. However, its role in fin regeneration remains unclear. RESULTS mmp13a expression is strongly upregulated during blastema formation and persists in the distal blastema. mmp13a knockdown via morpholino electroporation impairs regenerative outgrowth by decreasing cell proliferation, which correlates with a downregulation of fgf10a and sall4 expression in the blastema. Laminin distribution in the basement membrane is also affected in mmp13a MO-injected rays. Another impact of mmp13a knockdown is observed in the skeletal elements of the fin rays. Expression of two main components of actinotrichia, Collagen II and Actinodin 1 is highly reduced in mmp13a MO-injected rays leading to highly disorganized actinotrichia pattern. Inhibition of mmp13a strongly affects bone formation as shown by a reduction of Zns5 and sp7 expression and of bone matrix mineralization in rays. These defects are accompanied by a significant increase in apoptosis in mmp13a MO-injected fin regenerates. CONCLUSION Defects of expression of this multifunctional proteinase drastically affects osteoblast differentiation, bone and actinotrichia formation as well as Laminin distribution in the basement membrane of the fin regenerate, suggesting the important role of Mmp13 during the regenerative process.
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Affiliation(s)
- Li Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, China.,CAREG, University of Ottawa, Ottawa, Ontario, Canada.,Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jing Zhang
- CAREG, University of Ottawa, Ottawa, Ontario, Canada.,Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marie-Andrée Akimenko
- CAREG, University of Ottawa, Ottawa, Ontario, Canada.,Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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ECM alterations in Fndc3a (Fibronectin Domain Containing Protein 3A) deficient zebrafish cause temporal fin development and regeneration defects. Sci Rep 2019; 9:13383. [PMID: 31527654 PMCID: PMC6746793 DOI: 10.1038/s41598-019-50055-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/05/2019] [Indexed: 11/08/2022] Open
Abstract
Fin development and regeneration are complex biological processes that are highly relevant in teleost fish. They share genetic factors, signaling pathways and cellular properties to coordinate formation of regularly shaped extremities. Especially correct tissue structure defined by extracellular matrix (ECM) formation is essential. Gene expression and protein localization studies demonstrated expression of fndc3a (fibronectin domain containing protein 3a) in both developing and regenerating caudal fins of zebrafish (Danio rerio). We established a hypomorphic fndc3a mutant line (fndc3awue1/wue1) via CRISPR/Cas9, exhibiting phenotypic malformations and changed gene expression patterns during early stages of median fin fold development. These developmental effects are mostly temporary, but result in a fraction of adults with permanent tail fin deformations. In addition, caudal fin regeneration in adult fndc3awue1/wue1 mutants is hampered by interference with actinotrichia formation and epidermal cell organization. Investigation of the ECM implies that loss of epidermal tissue structure is a common cause for both of the observed defects. Our results thereby provide a molecular link between these developmental processes and foreshadow Fndc3a as a novel temporal regulator of epidermal cell properties during extremity development and regeneration in zebrafish.
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38
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Guerrero-Castilla A, Olivero-Verbel J, Sandoval IT, Jones DA. Toxic effects of a methanolic coal dust extract on fish early life stage. CHEMOSPHERE 2019; 227:100-108. [PMID: 30986591 DOI: 10.1016/j.chemosphere.2019.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Coal dust is a contaminant that impacts the terrestrial and aquatic environment with a complex mixture of chemicals, including PAHs and metals. This study aims to evaluate the toxic effect of a methanolic coal dust extract on a fish early life stage by analyzing phenotypic alterations, transcriptome changes, and mortality in zebrafish (ZF) embryos. ZF embryos were exposed to methanolic coal dust extract at 1-5000 mg·L-1 and monitored using bright field microscopy 24 and 48 hpf to determine malformations and mortality. In situ hybridization, RNA sequencing, and qRT-PCR were employed to identify transcriptome changes in malformed embryos. Three malformed phenotypes were generated in a dose-dependent manner. In situ hybridization analysis revealed brain, somite, dorsal cord, and heart tube development biomarker alterations. Gene expression profile analysis identified changes in genes related to structural constituent of muscle, calcium ion binding, actin binding, melanin metabolic process, muscle contraction, sarcomere organization, cardiac myofibril assembly, oxidation-reduction process, pore complex, supramolecular fiber, striated muscle thin filament, Z disc, and intermediate filament. This study shows, for the first time, the malformations generated by a mixture of pollutants from a methanolic coal dust extract on a fish early life stage, constituting a potential risk for normal embryonic development of other aquatic vertebrate organisms. Furthermore, we establish that phenotypes and changes in gene expression induced by the extract constitute a target for future studies about mechanical toxicity and their utility as sensitive tools in environmental risk assessments for biota and humans exposed to coal mining activities.
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Affiliation(s)
- Angélica Guerrero-Castilla
- Facultad de Ciencias de la Salud, Química y Farmacia, Universidad Arturo Prat, Casilla 121, Iquique, 1100000, Chile; Faculty of Pharmaceutical Sciences, Environmental and Computational Chemistry Group, University of Cartagena, Cartagena, 130015, Colombia.
| | - Jesús Olivero-Verbel
- Faculty of Pharmaceutical Sciences, Environmental and Computational Chemistry Group, University of Cartagena, Cartagena, 130015, Colombia
| | - Imelda T Sandoval
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - David A Jones
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
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39
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Li L, Xiao Q, Wang L, Chang Z. Expression analysis of And4 during fin regeneration in Misgurnus anguillicaudatus provides insights into its function. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:935-942. [PMID: 30612337 DOI: 10.1007/s10695-018-0602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Identifying proteins that regulate fin injury is critical to our understanding of regeneration as it relates to both acute wound injury and tissue formation. We have cloned the full-length cDNA of the actinodin4 (and4) gene of Misgurnus anguillicaudatus (MaAnd4) by the RACE method (GenBank Accession No. MG385835). Quantitative RT-PCR analysis during fin regeneration indicated a sudden increase in MaAnd4 expression, with a peak at 3 days post amputation (dpa). In situ analysis showed that MaAnd4 is located in the distal blastema and cells lining the regions of actinotrichia formation at 3 dpa. The highest levels of MaAnd4 expression were observed in the adult testis as well as in the gastrulae during embryonic development. Southern blotting confirmed the existence of and4 in teleosts but not in tetrapods examined. The results show the expression of this gene in actinotrichia formation and its association with fin/limb regeneration ability in teleosts.
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Affiliation(s)
- Li Li
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, 453007, Henan, China.
| | - Qian Xiao
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, 453007, Henan, China
| | - Linlin Wang
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, 453007, Henan, China
| | - Zhongjie Chang
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, 453007, Henan, China
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40
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Phan HE, Northorp M, Lalonde RL, Ngo D, Akimenko MA. Differential actinodin1 regulation in embryonic development and adult fin regeneration in Danio rerio. PLoS One 2019; 14:e0216370. [PMID: 31048899 PMCID: PMC6497306 DOI: 10.1371/journal.pone.0216370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
Actinotrichia are the first exoskeletal elements formed during zebrafish fin development. These rigid fibrils serve as skeletal support for the fin fold and as substrates for mesenchymal cell migration. In the adult intact fins, actinotrichia are restricted to the distal domain of the fin. Following fin amputation, actinotrichia also reform during regeneration. The actinodin gene family codes for structural proteins of actinotrichia. We have previously identified cis-acting regulatory elements in a 2kb genomic region upstream of the first exon of actinodin1, termed 2P, required for tissue-specific expression in the fin fold ectoderm and mesenchyme during embryonic development. Indeed, 2P contains an ectodermal enhancer in a 150bp region named epi. Deletion of epi from 2P results in loss of ectodermal-specific activity. In the present study, we sought to further characterize the activity of these regulatory sequences throughout fin development and during adult fin regeneration. Using a reporter transgenic approach, we show that a site within the epi region, termed epi3, contains an early mesenchymal-specific repressor. We also show that the larval fin fold ectodermal enhancer within epi3 remains functional in the basal epithelial layer during fin regeneration. We show that the first non-coding exon and first intron of actinodin1 contains a transcriptional enhancer and an alternative promoter that are necessary for the persistence of reporter expression reminiscent of actinodin1 expression during adulthood. Altogether, we have identified cis-acting regulatory elements that are required for tissue-specific expression as well as full recapitulation of actinodin1 expression during adulthood. Furthermore, the characterization of these elements provides us with useful molecular tools for the enhancement of transgene expression in adulthood.
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Affiliation(s)
- Hue-Eileen Phan
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marissa Northorp
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert L. Lalonde
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Dung Ngo
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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41
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Mier P, Andrade-Navarro MA. Traitpedia: a collaborative effort to gather species traits. Bioinformatics 2019; 35:1079-1081. [PMID: 30165582 PMCID: PMC6419907 DOI: 10.1093/bioinformatics/bty743] [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: 06/05/2018] [Revised: 08/17/2018] [Accepted: 08/23/2018] [Indexed: 11/25/2022] Open
Abstract
Summary Traitpedia is a collaborative database aimed to collect binary traits in a tabular form for a growing number of species. Availability and implementation Traitpedia can be accessed from http://cbdm-01.zdv.uni-mainz.de/~munoz/traitpedia. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pablo Mier
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
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42
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Schmidt JR, Geurtzen K, von Bergen M, Schubert K, Knopf F. Glucocorticoid Treatment Leads to Aberrant Ion and Macromolecular Transport in Regenerating Zebrafish Fins. Front Endocrinol (Lausanne) 2019; 10:674. [PMID: 31636606 PMCID: PMC6787175 DOI: 10.3389/fendo.2019.00674] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
Abstract
Long-term glucocorticoid administration in patients undergoing immunosuppressive and anti-inflammatory treatment is accompanied by impaired bone formation and increased fracture risk. Furthermore, glucocorticoid treatment can lead to impaired wound healing and altered cell metabolism. Recently, we showed that exposure of zebrafish to the glucocorticoid prednisolone during fin regeneration impacts negatively on the length, bone formation, and osteoblast function of the regenerate. The underlying cellular and molecular mechanisms of impairment, however, remain incompletely understood. In order to further elucidate the anti-regenerative effects of continued glucocorticoid exposure on fin tissues, we performed proteome profiling of fin regenerates undergoing prednisolone treatment, in addition to profiling of homeostatic fin tissue and fins undergoing undisturbed regeneration. By using LC-MS (liquid chromatography-mass spectrometry) we identified more than 6,000 proteins across all tissue samples. In agreement with previous reports, fin amputation induces changes in chromatin structure and extracellular matrix (ECM) composition within the tissue. Notably, prednisolone treatment leads to impaired expression of selected ECM components in the fin regenerate. Moreover, the function of ion transporting ATPases and other proteins involved in macromolecule and vesicular transport mechanisms of the cell appears to be altered by prednisolone treatment. In particular, acidification of membrane-enclosed organelles such as lysosomes is inhibited. Taken together, our data indicate that continued synthetic glucocorticoid exposure in zebrafish deteriorates cellular trafficking processes in the regenerating fin, which interferes with appropriate tissue restoration upon injury.
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Affiliation(s)
- Johannes R. Schmidt
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Karina Geurtzen
- CRTD—Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- *Correspondence: Kristin Schubert
| | - Franziska Knopf
- CRTD—Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Healthy Aging, Technische Universität (TU) Dresden, Dresden, Germany
- Franziska Knopf
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43
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Siomava N, Shkil F, Voronezhskaya E, Diogo R. Development of zebrafish paired and median fin musculature: basis for comparative, developmental, and macroevolutionary studies. Sci Rep 2018; 8:14187. [PMID: 30242203 PMCID: PMC6155031 DOI: 10.1038/s41598-018-32567-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/11/2018] [Indexed: 12/18/2022] Open
Abstract
The model organism Dario rerio (zebrafish) is widely used in evo-devo and comparative studies. Nevertheless, little is known about the development and differentiation of the appendicular musculature in this fish. In this study, we examined the development of the muscles of all five zebrafish fin types (pectoral, pelvic, anal, dorsal and caudal). We describe the development of the muscles of these fins, including some muscles that were never mentioned in the literature, such as the interhypurales of the caudal fin. Interestingly, these caudal muscles are present in early stages but absent in adult zebrafishes. We also compare various stages of zebrafish fin muscle development with the configuration found in other extant fishes, including non-teleostean actinopterygians as well as cartilaginous fishes. The present work thus provides a basis for future developmental, comparative, evolutionary and evo-devo studies and emphasizes the importance of developmental works on muscles for a more comprehensive understanding of the origin, development and evolution of the appendicular appendages of vertebrate animals.
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Affiliation(s)
- Natalia Siomava
- Department of Anatomy, Howard University College of Medicine, 520 W Street NW, 20059, Washington, DC, USA
| | - Fedor Shkil
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, ul. Vavilova 26, 119334, Moskva, Russia.,Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, pr. Leninskii 33, Moscow, 119071, Russia
| | - Elena Voronezhskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, ul. Vavilova 26, 119334, Moskva, Russia
| | - Rui Diogo
- Department of Anatomy, Howard University College of Medicine, 520 W Street NW, 20059, Washington, DC, USA.
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44
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Kuroda J, Iwane AH, Kondo S. Roles of basal keratinocytes in actinotrichia formation. Mech Dev 2018; 153:54-63. [PMID: 30194970 DOI: 10.1016/j.mod.2018.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/31/2022]
Abstract
The embryonic fins and the tip of adult fins of teleost fish are supported by rows of straight, unmineralized fibrils called actinotrichia. The proximal ends of the actinotrichia are bundled and the mineralized bones called lepidotrichia are made along them. Since malformation in actinotrichia causes wavy fin bones, the correct configuration of actinotrichia is essential for the correct construction of the fin shape. Past studies suggested that two types of cells, basal keratinocytes, and mesenchymal cells involve in the formation of actinotrichia. However, the mechanism how these cells contribute is unknown. In this study, we elucidated the role of basal keratinocytes in actinotrichia formation. First, we developed the imaging tool that specifically visualizes the basal keratinocytes and actinotrichia. Then, we established the in vitro culture method of the basal keratinocytes and found that the keratinocytes developed fine needle-like structures in it. The TEM image of them showed the specific shadow pattern of actinotrichia, indicating that the fine needle-like structures are the newly made actinotrichia. Finally, we cultured the basal keratinocytes with mature actinotrichia and observed that the basal keratinocytes actively holded actinotrichia with their membrane, and often generated a linear array of cells holding a single actinotrichium. This behavior suggested a mechanism with which long actinotrichia are made by relatively small cells. Our results clarified the role of basal keratinocyte and provided a novel insight into understanding the mechanism of actinotrichia formation.
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Affiliation(s)
- Junpei Kuroda
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 1-3, Suita, Osaka 565-0871, Japan
| | - Atsuko H Iwane
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 1-3, Suita, Osaka 565-0871, Japan; Biosystems Dynamics Center, Riken, Kagamiyama 3-10-23, Higashi Hiroshima, Hiroshima 739-0046, Japan
| | - Shigeru Kondo
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 1-3, Suita, Osaka 565-0871, Japan.
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45
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Wood TWP, Nakamura T. Problems in Fish-to-Tetrapod Transition: Genetic Expeditions Into Old Specimens. Front Cell Dev Biol 2018; 6:70. [PMID: 30062096 PMCID: PMC6054942 DOI: 10.3389/fcell.2018.00070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/15/2018] [Indexed: 12/30/2022] Open
Abstract
The fish-to-tetrapod transition is one of the fundamental problems in evolutionary biology. A significant amount of paleontological data has revealed the morphological trajectories of skeletons, such as those of the skull, vertebrae, and appendages in vertebrate history. Shifts in bone differentiation, from dermal to endochondral bones, are key to explaining skeletal transformations during the transition from water to land. However, the genetic underpinnings underlying the evolution of dermal and endochondral bones are largely missing. Recent genetic approaches utilizing model organisms—zebrafish, frogs, chickens, and mice—reveal the molecular mechanisms underlying vertebrate skeletal development and provide new insights for how the skeletal system has evolved. Currently, our experimental horizons to test evolutionary hypotheses are being expanded to non-model organisms with state-of-the-art techniques in molecular biology and imaging. An integration of functional genomics, developmental genetics, and high-resolution CT scanning into evolutionary inquiries allows us to reevaluate our understanding of old specimens. Here, we summarize the current perspectives in genetic programs underlying the development and evolution of the dermal skull roof, shoulder girdle, and appendages. The ratio shifts of dermal and endochondral bones, and its underlying mechanisms, during the fish-to-tetrapod transition are particularly emphasized. Recent studies have suggested the novel cell origins of dermal bones, and the interchangeability between dermal and endochondral bones, obscuring the ontogenetic distinction of these two types of bones. Assimilation of ontogenetic knowledge of dermal and endochondral bones from different structures demands revisions of the prevalent consensus in the evolutionary mechanisms of vertebrate skeletal shifts.
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Affiliation(s)
- Thomas W P Wood
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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46
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Meng K, Wu Y. Footprints of divergent evolution in two Na+/H+ type antiporter gene families (NHX and SOS1) in the genus Populus. TREE PHYSIOLOGY 2018; 38:813-824. [PMID: 29394412 DOI: 10.1093/treephys/tpx173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/19/2017] [Indexed: 05/19/2023]
Abstract
Populus, a deciduous tree species of major economic and ecological value, grows across the range in which trees are distributed in the Northern Hemisphere. Patterns of DNA variation are often used to identify the evolutionary forces shaping the genotypes of distinctive species lineages. Sodium/hydrogen (Na+/H+) antiporter genes have been shown to play a central role in plant salt tolerance. Here, we analyzed DNA nucleotide polymorphisms in the Na+/H+ antiporter (NHX and SOS1) gene families across 30 different Populus species using several methods of phylogenetic analysis and functional verification. NHX and SOS1 gene families in the genus Populus have expanded from the state in their common ancestors by duplication events, and their distinct lineages have been retained. Signals of positive selection at certain amino acid sites in different members of the Na/H antiporter gene families show that the dynamics that drive the evolution of each gene vary. SOS1 has undergone duplication in Populus euphratica and been subjected to adaptive evolution in section Turanga; the paralog of PeSOS1 (PeSOS1.2) can complement the Escherichia coli mutant EP432; and the expression pattern of PeSOS1.2 is different from that of PeSOS1, a fact which may have been beneficial for P. euphratica, conferring a fitness advantage in saline habitats. The divergent evolution of the individual members of the NHX and SOS1 gene families is likely to have been influenced by the varied ecological and environmental niches occupied by the different poplar species, giving rise to evolutionary footprints that reflect the specific functions and subcellular localizations of the proteins encoded by these genes.
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Affiliation(s)
- Kuibin Meng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yuxia Wu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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47
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Lalonde RL, Akimenko MA. Effects of fin fold mesenchyme ablation on fin development in zebrafish. PLoS One 2018; 13:e0192500. [PMID: 29420592 PMCID: PMC5805328 DOI: 10.1371/journal.pone.0192500] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
Abstract
The evolution of the tetrapod limb involved an expansion and elaboration of the endoskeletal elements, while the fish fin rays were lost. Loss of fin-specific genes, and regulatory changes in key appendicular patterning genes have been identified as mechanisms of limb evolution, however their contributions to cellular organization and tissue differences between fins and limbs remains poorly understood. During early larval fin development, hoxa13a/hoxd13a-expressing fin fold mesenchyme migrate through the median and pectoral fin along actinotrichia fibrils, non-calcified skeletal elements crucial for supporting the fin fold. Fin fold mesenchyme migration defects have previously been proposed as a mechanism of fin dermal bone loss during tetrapod evolution as it has been shown they contribute directly to the fin ray osteoblast population. Using the nitroreductase/metronidazole system, we genetically ablated a subset of hoxa13a/hoxd13a-expressing fin fold mesenchyme to assess its contributions to fin development. Following the ablation of fin fold mesenchyme in larvae, the actinotrichia are unable to remain rigid and the median and pectoral fin folds collapse, resulting in a reduced fin fold size. The remaining cells following ablation are unable to migrate and show decreased actinodin1 mesenchymal reporter activity. Actinodin proteins are crucial structural component of the actinotrichia. Additionally, we show a decrease in hoxa13a, hoxd13a, fgf10a and altered shha, and ptch2 expression during larval fin development. A continuous treatment of metronidazole leads to fin ray defects at 30dpf. Fewer rays are present compared to stage-matched control larvae, and these rays are shorter and less defined. These results suggest the targeted hoxa13a/hoxd13a-expressing mesenchyme contribute to their own successful migration through their contributions to actinotrichia. Furthermore, due to their fate as fin ray osteoblasts, we propose their initial ablation, and subsequent disorganization produces truncated fin dermal bone elements during late larval stages.
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Affiliation(s)
- Robert L. Lalonde
- Department of Biology, University of Ottawa, 20 Marie-Curie, Ottawa, Ontario, Canada
| | - Marie-Andrée Akimenko
- Department of Biology, University of Ottawa, 20 Marie-Curie, Ottawa, Ontario, Canada
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Tulenko FJ, Massey JL, Holmquist E, Kigundu G, Thomas S, Smith SME, Mazan S, Davis MC. Fin-fold development in paddlefish and catshark and implications for the evolution of the autopod. Proc Biol Sci 2018; 284:rspb.2016.2780. [PMID: 28539509 DOI: 10.1098/rspb.2016.2780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 01/04/2023] Open
Abstract
The evolutionary origin of the autopod involved a loss of the fin-fold and associated dermal skeleton with a concomitant elaboration of the distal endoskeleton to form a wrist and digits. Developmental studies, primarily from teleosts and amniotes, suggest a model for appendage evolution in which a delay in the AER-to-fin-fold conversion fuelled endoskeletal expansion by prolonging the function of AER-mediated regulatory networks. Here, we characterize aspects of paired fin development in the paddlefish Polyodon spathula (a non-teleost actinopterygian) and catshark Scyliorhinus canicula (chondrichthyan) to explore aspects of this model in a broader phylogenetic context. Our data demonstrate that in basal gnathostomes, the autopod marker HoxA13 co-localizes with the dermoskeleton component And1 to mark the position of the fin-fold, supporting recent work demonstrating a role for HoxA13 in zebrafish fin ray development. Additionally, we show that in paddlefish, the proximal fin and fin-fold mesenchyme share a common mesodermal origin, and that components of the Shh/LIM/Gremlin/Fgf transcriptional network critical to limb bud outgrowth and patterning are expressed in the fin-fold with a profile similar to that of tetrapods. Together these data draw contrast with hypotheses of AER heterochrony and suggest that limb-specific morphologies arose through evolutionary changes in the differentiation outcome of conserved early distal patterning compartments.
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Affiliation(s)
- Frank J Tulenko
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA.,Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - James L Massey
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309, USA
| | - Elishka Holmquist
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Gabriel Kigundu
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sarah Thomas
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sylvie Mazan
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, UMR7232, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marcus C Davis
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
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Paço A, Freitas R. Hox D genes and the fin-to-limb
transition: Insights from fish studies. Genesis 2017; 56. [DOI: 10.1002/dvg.23069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/14/2017] [Accepted: 09/08/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Paço
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
| | - Renata Freitas
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
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50
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Amaral DB, Schneider I. Fins into limbs: Recent insights from sarcopterygian fish. Genesis 2017; 56. [PMID: 28834157 DOI: 10.1002/dvg.23052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/10/2017] [Accepted: 08/15/2017] [Indexed: 02/03/2023]
Abstract
Limbs with digits evolved as sarcopterygian fish transitioned to a terrestrial life, giving rise to modern tetrapods. Since the Devonian, most of the sarcopterygian fish diversity became extinct, with the only surviving representatives being two coelacanth and six lungfish species. As the sister group of tetrapods, sarcopterygian fish constitute the ideal models to address questions regarding the transition of vertebrates from water to land. However, distantly related yet experimentally amenable teleost fish species have instead become the organisms of choice for geneticists and developmental biologists. Comparative studies using teleosts, such as zebrafish, have greatly enriched our knowledge on the genetic and regulatory mechanisms underlying fin development. However, their highly derived fin anatomy provides limited insights on the origin of limbs and the teleost-specific whole-genome duplication represents a further complication to comparisons of gene function and regulation. In recent years, refined morphological and behavioral studies and access to lungfish embryos and availability of genetic resources have underscored the value of nontetrapod sarcopterygians as model organisms. Here we review recent studies using lungfishes and coelacanths that shed light on various aspects of the evolution of the tetrapod limb, including the origin of the tetrapod pelvis, limb musculature, digits, locomotion, and regenerative capacity.
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Affiliation(s)
- Danielson B Amaral
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01, Belém, 66075-900, Brazil
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01, Belém, 66075-900, Brazil
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