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Blackburn DG, Hughes DF. Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes. Biol Rev Camb Philos Soc 2024; 99:1314-1356. [PMID: 38562006 DOI: 10.1111/brv.13070] [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: 08/23/2023] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
The reproductive diversity of extant cartilaginous fishes (class Chondrichthyes) is extraordinarily broad, reflecting more than 400 million years of evolutionary history. Among their many notable reproductive specialisations are viviparity (live-bearing reproduction) and matrotrophy (maternal provision of nutrients during gestation). However, attempts to understand the evolution of these traits have yielded highly discrepant conclusions. Here, we compile and analyse the current knowledge on the evolution of reproductive diversity in Chondrichthyes with particular foci on the frequency, phylogenetic distribution, and directionality of evolutionary changes in their modes of reproduction. To characterise the evolutionary transformations, we amassed the largest empirical data set of reproductive parameters to date covering nearly 800 extant species and analysed it via a comprehensive molecular-based phylogeny. Our phylogenetic reconstructions indicated that the ancestral pattern for Chondrichthyes is 'short single oviparity' (as found in extant holocephalans) in which females lay successive clutches (broods) of one or two eggs. Viviparity has originated at least 12 times, with 10 origins among sharks, one in batoids, and (based on published evidence) another potential origin in a fossil holocephalan. Substantial matrotrophy has evolved at least six times, including one origin of placentotrophy, three separate origins of oophagy (egg ingestion), and two origins of histotrophy (uptake of uterine secretions). In two clades, placentation was replaced by histotrophy. Unlike past reconstructions, our analysis reveals no evidence that viviparity has ever reverted to oviparity in this group. Both viviparity and matrotrophy have arisen by a variety of evolutionary sequences. In addition, the ancestral pattern of oviparity has given rise to three distinct egg-laying patterns that increased clutch (brood) size and/or involved deposition of eggs at advanced stages of development. Geologically, the ancestral oviparous pattern arose in the Paleozoic. Most origins of viviparity and matrotrophy date to the Mesozoic, while a few that are represented at low taxonomic levels are of Cenozoic origin. Coupled with other recent work, this review points the way towards an emerging consensus on reproductive evolution in chondrichthyans while offering a basis for future functional and evolutionary analyses. This review also contributes to conservation efforts by highlighting taxa whose reproductive specialisations reflect distinctive evolutionary trajectories and that deserve special protection and further investigation.
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Affiliation(s)
- Daniel G Blackburn
- Department of Biology & Electron Microscopy Center, Trinity College, 300 Summit St, Hartford, Connecticut, 06106, USA
| | - Daniel F Hughes
- Department of Biology, Coe College, 1220 First Avenue NE, Cedar Rapids, Iowa, 52402, USA
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2
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Matos A, Vilas-Arrondo N, Gomes-dos-Santos A, Veríssimo A, Román-Marcote E, Baldó F, Moreno-Aguilar J, Pérez M, Lopes-Lima M, Froufe E, Castro LFC. The complete mitogenome of the Atlantic longnose chimaera Rhinochimaera atlantica (Holt & Byrne, 1909). Mitochondrial DNA B Resour 2024; 9:886-891. [PMID: 39027115 PMCID: PMC11257016 DOI: 10.1080/23802359.2024.2378127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024] Open
Abstract
Holocephali is a subclass of chondrichthyans with ample geographic distribution in marine ecosystems. Holocephalan species are organized into three families: Callorhinchidae, Chimaeridae, and Rhinochimaeridae. Despite the critical ecological and evolutionary importance, genomic information from holocephalans is still scarce, particularly from rhinochimaerids. The present study provides the first complete mitogenome of the Atlantic longnose chimaera Rhinochimaera atlantica (Holt & Byrne, 1909). The whole mitogenome was sequenced from an R. atlantica specimen, collected on the Porcupine Bank (NE Atlantic), by Illumina high-throughput sequencing. The R. atlantica mitogenome has 17,852 nucleotides with 13 protein-coding genes, 22 transfer RNA, and two ribosomal RNA genes. Nine of these genes are in the complementary strand. This mitogenome has a GC content of 41.5% and an AT content of 58.5%. The phylogenetic reconstruction provided here, using all the available complete and partial Holocephali mitogenomes, places R. atlantica in the Rhinochimaeridae family, as expected. This genomic resource will be useful in the genomic characterization of this species.
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Affiliation(s)
- Ana Matos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Nair Vilas-Arrondo
- Programa de Doctorado “Ciencias marinas, Tecnología y Gestión” (Do*MAR), Universidad de Vigo, Vigo, Spain
- Centro Oceanográfico de Vigo (COV), Instituto Español de Oceanografía (IEO), CSIC, Vigo, Spain
| | - André Gomes-dos-Santos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Esther Román-Marcote
- Centro Oceanográfico de Vigo (COV), Instituto Español de Oceanografía (IEO), CSIC, Vigo, Spain
| | - Francisco Baldó
- Centro Oceanográfico de Cádiz (COCAD), Instituto Español de Oceanografía (IEO), CSIC, Cádiz, Spain
| | - Jaime Moreno-Aguilar
- Tecnologías y Servicios Agrarios, S.A. (TRAGSATEC), C/ Orient, Ciutadella, Spain
| | - Montse Pérez
- Centro Oceanográfico de Vigo (COV), Instituto Español de Oceanografía (IEO), CSIC, Vigo, Spain
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - L. Filipe C. Castro
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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3
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Brownstein CD, Near TJ. Colonization of the ocean floor by jawless vertebrates across three mass extinctions. BMC Ecol Evol 2024; 24:79. [PMID: 38867201 PMCID: PMC11170801 DOI: 10.1186/s12862-024-02253-y] [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: 01/16/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The deep (> 200 m) ocean floor is often considered to be a refugium of biodiversity; many benthic marine animals appear to share ancient common ancestry with nearshore and terrestrial relatives. Whether this pattern holds for vertebrates is obscured by a poor understanding of the evolutionary history of the oldest marine vertebrate clades. Hagfishes are jawless vertebrates that are either the living sister to all vertebrates or form a clade with lampreys, the only other surviving jawless fishes. RESULTS We use the hagfish fossil record and molecular data for all recognized genera to construct a novel hypothesis for hagfish relationships and diversification. We find that crown hagfishes persisted through three mass extinctions after appearing in the Permian ~ 275 Ma, making them one of the oldest living vertebrate lineages. In contrast to most other deep marine vertebrates, we consistently infer a deep origin of continental slope occupation by hagfishes that dates to the Paleozoic. Yet, we show that hagfishes have experienced marked body size diversification over the last hundred million years, contrasting with a view of this clade as morphologically stagnant. CONCLUSION Our results establish hagfishes as ancient members of demersal continental slope faunas and suggest a prolonged accumulation of deep sea jawless vertebrate biodiversity.
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Affiliation(s)
- Chase Doran Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA.
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
- Yale Peabody Museum, Yale University, New Haven, CT, 06511, USA
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Manzanares-Guzmán A, Lugo-Fabres PH, Camacho-Villegas TA. vNARs as Neutralizing Intracellular Therapeutic Agents: Glioblastoma as a Target. Antibodies (Basel) 2024; 13:25. [PMID: 38534215 DOI: 10.3390/antib13010025] [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: 11/27/2023] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Glioblastoma is the most prevalent and fatal form of primary brain tumors. New targeted therapeutic strategies for this type of tumor are imperative given the dire prognosis for glioblastoma patients and the poor results of current multimodal therapy. Previously reported drawbacks of antibody-based therapeutics include the inability to translocate across the blood-brain barrier and reach intracellular targets due to their molecular weight. These disadvantages translate into poor target neutralization and cancer maintenance. Unlike conventional antibodies, vNARs can permeate tissues and recognize conformational or cryptic epitopes due to their stability, CDR3 amino acid sequence, and smaller molecular weight. Thus, vNARs represent a potential antibody format to use as intrabodies or soluble immunocarriers. This review comprehensively summarizes key intracellular pathways in glioblastoma cells that induce proliferation, progression, and cancer survival to determine a new potential targeted glioblastoma therapy based on previously reported vNARs. The results seek to support the next application of vNARs as single-domain antibody drug-conjugated therapies, which could overcome the disadvantages of conventional monoclonal antibodies and provide an innovative approach for glioblastoma treatment.
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Affiliation(s)
- Alejandro Manzanares-Guzmán
- Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara 44270, Mexico
| | - Pavel H Lugo-Fabres
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)-Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara 44270, Mexico
| | - Tanya A Camacho-Villegas
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)-Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara 44270, Mexico
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Wang C, Ye P, Pillans R, Chen X, Wang J, Feutry P. Evolution of the Critically Endangered Green Sawfish Pristis zijsron (Rhinopristiformes, Pristidae), Inferred from the Whole Mitochondrial Genome. Genes (Basel) 2023; 14:2052. [PMID: 38002995 PMCID: PMC10671267 DOI: 10.3390/genes14112052] [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: 09/29/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The green sawfish Pristis zijsron (Bleeker, 1851), a species of sawfish in the family Pristidae (Rhinopristiformes), mainly inhabits the Indo-West Pacific region. In this study, the complete mitochondrial genome of the critically endangered green sawfish is first described. The length of the genome is 16,804 bp, with a nucleotide composition of 32.0% A, 24.8% C, 13.1% G, and 30.0% T. It contains 37 genes in the typical gene order of fish. Two start (GTG and ATG) and two stop (TAG and TAA/T-) codons are found in the thirteen protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Ser) to 75 bp (tRNA-Leu). The ratio of nonsynonymous substitution (Ka) and synonymous substitution (Ks) indicates that the family Pristidae are suffering a purifying selection. The reconstruction of Bayesian inference and the maximum likelihood phylogenetic tree show the same topological structure, and the family Pristidae is a monophyletic group with strong posterior probability. Pristis zijsron and P. pectinata form a sister group in the terminal clade. And the divergence time of Rhinopristiformes show that P. zijsron and P. pectinata diverged as two separate species in about Paleogene 31.53 Mya. Complete mitochondrial genomes of all five sawfishes have been published and phylogenetic relationships have been analyzed. The results of our study will provide base molecular information for subsequent research (e.g., distribution, conservation, phylogenetics, etc.) on this endangered group.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Peiyuan Ye
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Richard Pillans
- CSIRO Environment, Boggo Road, Dutton Park, QLD 4102, Australia;
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Pierre Feutry
- CSIRO Environment, Castray Esplanade, Hobart, TAS 7000, Australia
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6
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Jones RC, Hall K, Crow KD. Are vertebrates constrained to two sets of paired appendages? The morphology, development, and evolution of pre-pelvic claspers in the Holocephali. J Morphol 2023; 284:e21632. [PMID: 37585230 DOI: 10.1002/jmor.21632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/10/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023]
Abstract
Holocephalans exhibit auxiliary appendages called pre-pelvic claspers (PPCs) that are located anterior to the pelvic fins, while pelvic claspers are pelvic fin modifications located posteriorly as modified metapterygia. Articulation points of the PPCs have not previously been imaged or evaluated in a comparative context, therefore, they may represent modified pelvic fin structures if they articulate with the propterygium. Alternatively, they could represent the only example of an independent third set of paired appendages in an extant taxon, if they articulate independently from any pelvic fin basal cartilages, challenging the current paradigm that extant jawed vertebrates are constrained to two sets of paired appendages. Two extinct groups, including Placoderms and Acanthodians, exhibit variation in the number of paired appendages, suggesting this may be a plesiomorphic trait. We evaluated PPC developmental growth rates, morphology, and articulation points in spotted ratfish (Hydrolagus Colliei, Holocephali). We also compared variation in PPC morphology among representatives of the three extant holocephalan families. Both, the pre-pelvic and pelvic claspers exhibit a dramatic surge in growth at sexual maturity, and then level off, suggesting synchronous development via shared hormonal regulation. While mature females are larger than males, pelvic fin growth and development is faster in males, suggesting a selective advantage to larger fins with faster development. Finally, microcomputed tomography scans revealed that PPCs are not modified propterygia, nor do they articulate with the propterygium. They articulate with the anterior pre-pelvic process on the anterior puboischiadic bar (or pelvic girdle), suggesting that while they are associated with the pelvic girdle, they may indeed represent a third, independent set of paired appendages in extant holocephalans.
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Affiliation(s)
- Riley C Jones
- Department of Biology, San Francisco State University, San Francisco, California, USA
- Department of Biology, California State University, Northridge, California, USA
| | - Kayla Hall
- Department of Biology, University of Washington, Washington, USA
| | - Karen D Crow
- Department of Biology, San Francisco State University, San Francisco, California, USA
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7
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Wang X, Fang C, Wang C. Complete mitochondrial genome of Hydrolagus mitsukurii (Jordan & Snyder, 1904). Mitochondrial DNA B Resour 2023; 8:682-685. [PMID: 37346173 PMCID: PMC10281295 DOI: 10.1080/23802359.2023.2222852] [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: 11/16/2022] [Accepted: 06/02/2023] [Indexed: 06/23/2023] Open
Abstract
Holocephali has foreseeable value to help our understanding of vertebrate genome evolution due to its phylogenetic position. In this study, we reported a complete mitochondrial genome of Hydrolagus mitsukurii, a species of holocephalans. The mitochondrial genome is 20,486 bp in length and comprised 13 PCGs, 2 rRNA, 22 tRNA, and 1 control region (D-loop), as well as a long noncoding insertion between tRNAThr and tRNAPro. A phylogenetic tree based on 13 PCGs showed that Hydrolagus mitsukurii was grouped with the members of the family Chimaeridae. Furthermore, the phylogenetic tree further supported the paraphyletic clades of Hydrolagus and Chimera.
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Affiliation(s)
- Xiaogu Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, P.R. China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, P.R. China
- College of Oceanography, Hohai University, Nanjing, P.R. China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, P.R. China
- College of Oceanography, Hohai University, Nanjing, P.R. China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, P.R. China
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8
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Zhou J, Liu A, He F, Zhang Y, Shen L, Yu J, Zhang X. Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:501-514. [PMID: 36470576 PMCID: PMC10787021 DOI: 10.1016/j.gpb.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
The white-blotched river stingray (Potamotrygon leopoldi) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available, P. leopoldi provides the evolutionary details in fish phylogeny, niche adaptation, and skeleton formation. In this study, we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds, with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size. Our analysis shows that P. leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago. Moreover, two gene families related to the immune system (immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes) exhibit expansion in P. leopoldi only. We also identified the Hox gene clusters in P. leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P. leopoldi. The RNA sequencing data from P. leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals. Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes (both P. leopoldi and Callorhinchus milii) could partly explain the absence of hard bone in their endoskeleton. Overall, this genome resource provides new insights into the niche adaptation, body plan, and skeleton formation of P. leopoldi, as well as the genome evolution in cartilaginous fishes.
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Affiliation(s)
- Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Funan He
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Yunbin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Libing Shen
- International Human Phenome Institutes (Shanghai), Shanghai 200433, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiang Zhang
- Shanghai Nanmulin Biotechnology Company Limited, Shanghai 200031, China.
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Mera-Rodríguez D, Jourdan H, Ward PS, Shattuck S, Cover SP, Wilson EO, Rabeling C. Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics. Mol Phylogenet Evol 2023:107825. [PMID: 37244505 DOI: 10.1016/j.ympev.2023.107825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Studying the historical biogeography and life history transitions from eusocial colony life to social parasitism contributes to our understanding of the evolutionary mechanisms generating biodiversity in eusocial insects. The ants in the genus Myrmecia are a well-suited system for testing evolutionary hypotheses about how their species diversity was assembled through time because the genus is endemic to Australia with the single exception of the species M. apicalis inhabiting the Pacific Island of New Caledonia, and because at least one social parasite species exists in the genus. However, the evolutionary mechanisms underlying the disjunct biogeographic distribution of M. apicalis and the life history transition(s) to social parasitism remain unexplored. To study the biogeographic origin of the isolated, oceanic species M. apicalis and to reveal the origin and evolution of social parasitism in the genus, we reconstructed a comprehensive phylogeny of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements (UCEs) as molecular markers to generate a comprehensive molecular genetic dataset consisting of 2,287 loci per taxon on average for 66 out of the 93 known Myrmecia species as well as for the sister lineage Nothomyrmecia macrops and selected outgroups. Our time-calibrated phylogeny inferred that: (i) stem Myrmeciinae originated during the Paleocene ∼58 Ma ago; (ii) the current disjunct biogeographic distribution of M. apicalis was driven by long-distance dispersal from Australia to New Caledonia during the Miocene ∼14 Ma ago; (iii) the single social parasite species, M. inquilina, evolved directly from one of the two known host species, M. nigriceps, in sympatry via the intraspecific route of social parasite evolution; and (iv) 5 of the 9 previously established taxonomic species groups are non-monophyletic. We suggest minor changes to reconcile the molecular phylogenetic results with the taxonomic classification. Our study enhances our understanding of the evolution and biogeography of Australian bulldog ants, contributes to our knowledge about the evolution of social parasitism in ants, and provides a solid phylogenetic foundation for future inquiries into the biology, taxonomy, and classification of Myrmeciinae.
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Affiliation(s)
- Daniela Mera-Rodríguez
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany.
| | - Hervé Jourdan
- Institute of Research for Development. Promenade Roger Laroque, Nouméa 98848, New Caledonia
| | - Philip S Ward
- Department of Entomology and Nematology, University of California, Davis, CA 95616, United States of America
| | - Steven Shattuck
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Stefan P Cover
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Edward O Wilson
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Christian Rabeling
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany; Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America.
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10
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Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023; 33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten-Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA;
| | - Edward Rice
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Kremitzki Milin
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Ronald B Walter
- Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
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11
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Guo S, Gao W, Zeng M, Liu F, Yang Q, Chen L, Wang Z, Jin Y, Xiang P, Chen H, Wen Z, Shi Q, Song Z. Characterization of TLR1 and expression profiling of TLR signaling pathway related genes in response to Aeromonas hydrophila challenge in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂). Front Immunol 2023; 14:1163781. [PMID: 37056759 PMCID: PMC10086376 DOI: 10.3389/fimmu.2023.1163781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Toll‐like receptor 1 (TLR1) mediates the innate immune response to a variety of microbes through recognizing cell wall components (such as bacterial lipoproteins) in mammals. However, the detailed molecular mechanism of TLR1 involved in pathogen immunity in the representative hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂) has not been well studied. In the present study, we identified the TLR1 gene from the hybrid yellow catfish, and further comparative synteny data from multiple species confirmed that the TLR1 gene is highly conserved in teleosts. Phylogenetic analysis revealed distinguishable TLR1s in diverse taxa, suggesting consistence in evolution of the TLR1 proteins with various species. Structural prediction indicated that the three-dimensional structures of TLR1 proteins are relatively conserved among different taxa. Positive selection analysis showed that purifying selection dominated the evolutionary process of TLR1s and TLR1-TIR domain in both vertebrates and invertebrates. Expression pattern analysis based on the tissue distribution showed that TLR1 mainly transcribed in the gonad, gallbladder and kidney, and the mRNA levels of TLR1 in kidney were remarkably up-regulated after Aeromonas hydrophila stimulation, indicating that TLR1 participates in the inflammatory responses to exogenous pathogen infection in hybrid yellow catfish. Homologous sequence alignment and chromosomal location indicated that the TLR signaling pathway is very conserved in the hybrid yellow catfish. The expression patterns of TLR signaling pathway related genes (TLR1- TLR2 - MyD88 - FADD - Caspase 8) were consistent after pathogen stimulation, revealing that the TLR signaling pathway is triggered and activated after A. hydrophila infection. Our findings will lay a solid foundation for better understanding the immune roles of TLR1 in teleosts, as well as provide basic data for developing strategies to control disease outbreak in hybrid yellow catfish.
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Affiliation(s)
- Shengtao Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenxue Gao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengsha Zeng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fenglin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Qingzhuoma Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zesong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanjun Jin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Peng Xiang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hanxi Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhengyong Wen
- Key Laboratory of Sichuan for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- *Correspondence: Zhengyong Wen, ; Qiong Shi, ; Zhaobin Song,
| | - Qiong Shi
- Key Laboratory of Sichuan for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- *Correspondence: Zhengyong Wen, ; Qiong Shi, ; Zhaobin Song,
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Zhengyong Wen, ; Qiong Shi, ; Zhaobin Song,
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12
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Klug C, Coates M, Frey L, Greif M, Jobbins M, Pohle A, Lagnaoui A, Haouz WB, Ginter M. Broad snouted cladoselachian with sensory specialization at the base of modern chondrichthyans. SWISS JOURNAL OF PALAEONTOLOGY 2023; 142:2. [PMID: 37009301 PMCID: PMC10050047 DOI: 10.1186/s13358-023-00266-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/11/2023] [Indexed: 06/19/2023]
Abstract
UNLABELLED Throughout the Silurian and Devonian, cartilaginous fish successively evolved their specialized skeletal and dental characteristics, and increasingly refined their sensory systems. The Late Devonian shark taxon Maghriboselache mohamezanei gen. et sp. n. from the eastern Anti-Atlas of Morocco is known from multiple specimens preserving most of its skeletal features, which in some instances are preserved in three dimensions. Key details of the dentition, jaws, and pectoral skeleton are shared with the iconic genus Cladoselache. Phylogenetic analyses place the family Cladoselachidae as the sister group of symmoriiforms and these groups as sister group of the holocephalans. Further phylogenetic results corroborate that the initial evolutionary radiation of crown chondrichthyans occurred within or before the Late Devonian. Remarkably, this new stem holocephalan is equipped with a wide snout and large laterally separated nasal capsules: the earliest known example of this condition in the chondrichthyan and (perhaps) gnathostome record. This suggests sensory specialization approaching that of extant broad-rostrum elasmobranchs and represents a significant addition to increasingly apparent ecomorphological diversity among early chondrichthyans. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s13358-023-00266-6.
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Affiliation(s)
- Christian Klug
- Paläontologisches Institut und Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Michael Coates
- Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57Th St., Chicago, 60637 USA
| | - Linda Frey
- Paläontologisches Institut und Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Merle Greif
- Paläontologisches Institut und Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Melina Jobbins
- Paläontologisches Institut und Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Alexander Pohle
- Institute for Geology, Mineralogy, and Geophysics, Ruhr University Bochum, Universitätsstraβe 150, 44801 Bochum, Germany
| | - Abdelouahed Lagnaoui
- Interdisciplinary Research Laboratory in Sciences, Education and Training, Higher School of Education and Training Berrechid (ESEFB), Hassan First University, Avenue de l’Université, B.P:218, 26100 Berrechid, Morocco
- Laboratory of Stratigraphy of Oil-and-Gas Bearing Reservoirs, Department of Paleontology and Stratigraphy, Institute of Geology and Petroleum Technologies, Federal University, Kremlyovskaya Str. 18, 420008 Kazan, Volga Region Russia
| | - Wahiba Bel Haouz
- Laboratory of Stratigraphy of Oil-and-Gas Bearing Reservoirs, Department of Paleontology and Stratigraphy, Institute of Geology and Petroleum Technologies, Federal University, Kremlyovskaya Str. 18, 420008 Kazan, Volga Region Russia
- Geosciences Laboratory, Department of Geology, Faculty of Sciences Ain Chock, Hassan II University, Km 8 Route d’El Jadida, 20100 Casablanca, Morocco
| | - Michal Ginter
- Faculty of Geology, University of Warsaw, Al. Żwirki I Wigury 93, 02-089 Warsaw, Poland
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13
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Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Parrotfishes (Perciformes: Scaridae). BIOLOGY 2023; 12:biology12030410. [PMID: 36979102 PMCID: PMC10044791 DOI: 10.3390/biology12030410] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
In order to investigate the molecular evolution of mitogenomes among the family Scaridae, the complete mitogenome sequences of twelve parrotfish species were determined and compared with those of seven other parrotfish species. The comparative analysis revealed that the general features and organization of the mitogenome were similar among the 19 parrotfish species. The base composition was similar among the parrotfishes, with the exception of the genus Calotomus, which exhibited an unusual negative AT skew in the whole mitogenome. The PCGs showed similar codon usage, and all of them underwent a strong purifying selection. The gene rearrangement typical of the parrotfishes was detected, with the tRNAMet inserted between the tRNAIle and tRNAGln, and the tRNAGln was followed by a putative tRNAMet pseudogene. The parrotfish mitogenomes displayed conserved gene overlaps and secondary structure in most tRNA genes, while the non-coding intergenic spacers varied among species. Phylogenetic analysis based on the thirteen PCGs and two rRNAs strongly supported the hypothesis that the parrotfishes could be subdivided into two clades with distinct ecological adaptations. The early divergence of the sea grass and coral reef clades occurred in the late Oligocene, probably related to the expansion of sea grass habitat. Later diversification within the coral reef clade could be dated back to the Miocene, likely associated with the geomorphology alternation since the closing of the Tethys Ocean. This work provided fundamental molecular data that will be useful for species identification, conservation, and further studies on the evolution of parrotfishes.
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14
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da Silva JPCB, Vaz DFB. Morphology and phylogenetic significance of the pelvic articular region in elasmobranchs (Chondrichthyes). Cladistics 2023; 39:155-197. [PMID: 36856203 DOI: 10.1111/cla.12528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 03/02/2023] Open
Abstract
The morphology of paired fins is commonly overlooked in morphological studies, particularly the pelvic girdle and fins. Consequently, previous phylogenetic studies incorporating morphological data used few skeletal characters from this complex. In this paper, the phylogenetic significance of pelvic articular characters for elasmobranchs is discussed in light of the morphological variation observed in 130 species, the most comprehensive study exploring the morphology of the pelvic girdle done so far. The 10 morphological characters proposed herein for the pelvic articulation were incorporated into a molecular matrix of NADH2 sequences and submitted to an analysis of maximum parsimony employing extended implied weighting. The most stable tree was selected based on the distortion coefficients, SPR distances (subtree pruning and regrafting) and fit values. Some of the striking synapomorphies recovered within elasmobranchs include the presence of an articular surface for the first enlarged pelvic radial supporting Elasmobranchii and the pelvic articular region for the basipterygium extending from the posterolatral margin of the pelvic girdle over its lateral surface in Echinorhinus + Hexanchiformes. Additionally, the proposed characters and their distributions are discussed considering the relationships recovered and also compared with previous morphological and molecular phylogenetic hypotheses.
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Affiliation(s)
- João Paulo C B da Silva
- Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Castelo Branco, João Pessoa, 58051-900, Brazil
| | - Diego F B Vaz
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, 02143, USA.,Biorepository Collaboratorium Guam EPSCoR, Marine Laboratory, University of Guam, 303 University Dr, UOG Station, Mangilao, GU, 96923, USA
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15
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Identification of Cartilaginous Fish Endogenous Foamy Virus Rooting to Vertebrate Counterparts. J Virol 2023; 97:e0181622. [PMID: 36651746 PMCID: PMC9972966 DOI: 10.1128/jvi.01816-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Foamy viruses (FVs) are ideal models for studying the long-term evolutionary history between viruses and their hosts. Currently, FVs have been documented in nearly all major taxa of vertebrates, but evidence is lacking for true FV infiltration in cartilaginous fish, the most basal living vertebrates with jaws. Here, we screened 11 available genomes and 10 transcriptome sequence assemblies of cartilaginous fish and revealed a novel endogenous foamy virus, termed cartilaginous fish endogenous foamy virus (CFEFV), in the genomes of sharks and rays. Genomic analysis of CFEFVs revealed feature motifs that were retained among canonical FVs. Phylogenetic analysis using polymerase sequences revealed the rooting nature of CFEFVs to vertebrate FVs, indicating their deep origin. Interestingly, three viral lineages were found in a shark (Scyliorhinus torazame), one of which was clustered with ray-finned fish foamy-like viruses, indicating that multiple episodes of viral infiltrations had occurred in this species. These findings fill a major gap in the Spumaretrovirinae taxon and reveal the aquatic origin of FVs found in terrestrial vertebrates. IMPORTANCE Although foamy viruses (FVs) have been found in major branches of vertebrates, the presence of these viruses in cartilaginous fish, the most basal living vertebrates with jaws, remains to be explored. This study revealed a collection of cartilaginous endogenous FVs in sharks and rays through in silico genomic mining. These viruses were rooted in the polymerase (POL) phylogeny, indicating the ancient aquatic origin of FVs. However, their envelope (ENV) protein grouped with those of amphibian FVs, suggesting different evolutionary histories of different FV genes. Overall, we provide the last missing gap for the taxonomic investigation of Spumaretrovirinae and provide concrete support for the aquatic origin of FVs.
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16
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Li W, Wang Z, Liang Y, Huang W, Huang B. The origin and loss of interferon regulatory factor 10 (IRF10) in different lineages of vertebrates. Gene 2023; 854:147083. [PMID: 36481278 DOI: 10.1016/j.gene.2022.147083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
The vertebrate IFN regulatory factor (IRF) family consists of 11 members that exert distinct roles in a variety of biological processes, including antiviral defense, regulation of cell proliferation, differentiation and apoptosis. Of these, IRF10 is widely present in different vertebrate lineages, but appears to have been lost in primates and rodents. To understand the evolutionary occurrence of IRF10, we performed comparative analyses of currently available genomic data in a taxonomically diverse set of vertebrates, and found that IRF10 originated after the divergence of chondrichthyans from gnathostomes. Phylogenetically, vertebrate IRF10 is much more closely related to IRF4 than to IRF8 or IRF9, although these four IRFs may have a common ancestor. In addition, the loss of IRF10 in Euarchontoglires might be resulted from mutation accumulation, and the rate of mutations in rodents appears to be higher than in the primate lineage. In primates, the gene-disruptive mutations may have occurred at least prior to the separation of new world monkey and old world primates, roughly 40 million years ago. Overall, we propose a detailed evolutionary scenario for IRF10, which may help us understand the evolutionary mechanisms in the expansion and contraction of the IRF family.
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Affiliation(s)
- Wenxing Li
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Zhixuan Wang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Ying Liang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Wenshu Huang
- Fisheries College, Jimei University, Xiamen 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, China
| | - Bei Huang
- Fisheries College, Jimei University, Xiamen 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, China.
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17
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Fujimori C, Umatani C, Chimura M, Ijiri S, Bando H, Hyodo S, Kanda S. In vitro and in vivo gene transfer in the cloudy catshark Scyliorhinus torazame. Dev Growth Differ 2022; 64:558-565. [PMID: 36376176 PMCID: PMC10099843 DOI: 10.1111/dgd.12824] [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: 08/01/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022]
Abstract
Cartilaginous fishes have various unique physiological features such as a cartilaginous skeleton and a urea-based osmoregulation strategy for adaptation to their marine environment. Also, because they are a sister group of bony vertebrates, understanding their unique features is important from an evolutionary perspective. However, genetic engineering based on gene functions as well as cellular behavior has not been effectively utilized in cartilaginous fishes. This is partly because their reproductive strategy involves internal fertilization, which results in difficulty in microinjection into fertilized eggs at the early developmental stage. Here, to identify efficient gene transfer methods in cartilaginous fishes, we examined the effects of various methods both in vitro and in vivo using the cloudy catshark, a candidate model cartilaginous fish species. In all methods, green fluorescent protein (GFP) expression was used to evaluate exogenous gene transfer. First, we examined gene transfer into primary cultured cells from cloudy catshark embryos by lipofection, polyethylenimine (PEI) transfection, adenovirus infection, baculovirus infection, and electroporation. Among the methods tested, lipofection, electroporation, and baculovirus infection enabled the successful transfer of exogenous genes into primary cultured cells. We then attempted in vivo transfection into cloudy catshark embryos by electroporation and baculovirus infection. Although baculovirus-injected groups did not show GFP fluorescence, electroporation successfully introduced GFP into muscle cells. Furthermore, we succeeded in GFP transfer into adult tissues by electroporation. The in vitro and in vivo gene transfer methods that worked in this study may open ways for genetic manipulation including knockout experiments and cellular lineage analysis in cartilaginous fishes.
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Affiliation(s)
- Chika Fujimori
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Chie Umatani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Misaki Chimura
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Shigeho Ijiri
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Hisanori Bando
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Susumu Hyodo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shinji Kanda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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18
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Mitogenome of a monotypic genus, Oliotius Kottelat, 2013 (Cypriniformes: Cyprinidae): Genomic characterization and phylogenetic position. Gene 2022; 851:147035. [DOI: 10.1016/j.gene.2022.147035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022]
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19
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Song L, Chen XJ, Zhang S, Wang Q. Complete mitochondrial genome of Devario kakhienensis (Cypriniformes: Danionidae: Danioninae): genome characterization and phylogenetic consideration. Mitochondrial DNA B Resour 2022; 7:1685-1687. [PMID: 36147361 PMCID: PMC9487915 DOI: 10.1080/23802359.2022.2122749] [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] [Indexed: 11/24/2022] Open
Abstract
Complete mitochondrial genome and phylogenetic analysis of Devario kakhienensis, endemic minnow from southwest China, for the first time was presented. It was determined to be a 16,777 bp long circular molecule and the genome organization was consistent with that of Danioninae species published previously. Based on PCGs, the maximum likelihood phylogenetic analysis supported the close genetic relationship between D. kakhienensis and Devario interruptus. These data would contribute toward the genetic resource enrichment, and provide a valuable framework for future research in completely resolving phylogenetic relationships with the family Danionidae.
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Affiliation(s)
- Lin Song
- College of Fisheries Science and technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou City, Jiangsu Province, P. R. China
| | - Xiao Jiang Chen
- College of Fisheries Science and technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou City, Jiangsu Province, P. R. China
| | - Sai Zhang
- College of Fisheries Science and technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou City, Jiangsu Province, P. R. China
| | - Quan Wang
- College of Fisheries Science and technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou City, Jiangsu Province, P. R. China
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20
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Katsu Y, Oana S, Lin X, Hyodo S, Bianchetti L, Baker ME. Cloning of nine glucocorticoid receptor isoforms from the slender African lungfish (Protopterus dolloi). PLoS One 2022; 17:e0272219. [PMID: 35913912 PMCID: PMC9342798 DOI: 10.1371/journal.pone.0272219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
We wanted to clone the glucocorticoid receptor (GR) from slender African lungfish (Protopterus dolloi) for comparison to the P. dolloi mineralocorticoid receptor (MR), which we had cloned and were characterizing, as well as for comparison to the GRs from humans, elephant shark and zebrafish. However, although sequencing of the genome of the Australian lungfish (Neoceratodus forsteri), as well as, that of the West African lungfish (Protopterus annectens) were reported in the first three months of 2021, we could not retrieve a GR sequence with a BLAST search of GenBank, when we submitted our research for publication in July 2021. Moreover, we were unsuccessful in cloning the GR from slender African lungfish using a cDNA from the ovary of P. dolloi and PCR primers that had successfully cloned a GR from elephant shark, Xenopus and gar GRs. On October 21, 2021 the nucleotide sequence of West African lungfish (P. annectens) GR was deposited in GenBank. We used this GR sequence to construct PCR primers that successfully cloned the GR from the slender spotted lungfish. Here, we report the sequences of nine P. dolloi GR isoforms and explain the basis for the previous failure to clone a GR from slender African lungfish using PCR primers that cloned the GR from elephant shark, Xenopus and gar. Studies are underway to determine corticosteroid activation of these slender African lungfish GRs.
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Affiliation(s)
- Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Faculty of Science, Hokkaido University, Sapporo, Japan
- * E-mail: (YK); (MEB)
| | - Shin Oana
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Xiaozhi Lin
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Laurent Bianchetti
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104—Inserm U1258, Université de Strasbourg, Illkirch, France
| | - Michael E. Baker
- Division of Nephrology-Hypertension, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (YK); (MEB)
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21
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Huang Y, Li J, Bian C, Li R, You X, Shi Q. Evolutionary Genomics Reveals Multiple Functions of Arylalkylamine N-Acetyltransferase in Fish. Front Genet 2022; 13:820442. [PMID: 35664299 PMCID: PMC9160868 DOI: 10.3389/fgene.2022.820442] [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: 11/23/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
As an important hormone, melatonin participates in endocrine regulation of diverse functions in vertebrates. Its biosynthesis is catalyzed by four cascaded enzymes, among them, arylalkylamine N-acetyltransferase (AANAT) is the most critical one. Although only single aanat gene has been identified in most groups of vertebrates, researchers including us have determined that fish have the most diverse of aanat genes (aanat1a, aanat1b, and aanat2), playing various potential roles such as seasonal migration, amphibious aerial vision, and cave or deep-sea adaptation. With the rapid development of genome and transcriptome sequencing, more and more putative sequences of fish aanat genes are going to be available. Related phylogeny and functional investigations will enrich our understanding of AANAT functions in various fish species.
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Affiliation(s)
- Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-Ugent Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ruihan Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
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Vilas-Arrondo N, Gomes-dos-Santos A, Pérez M, Baldó F, Veríssimo A, Catarino D, Machado AM, Román-Marcote E, Bañón R, Froufe E, Castro LFC. A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads. Mitochondrial DNA B Resour 2022; 7:434-437. [PMID: 35274036 PMCID: PMC8903783 DOI: 10.1080/23802359.2022.2044403] [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] [Indexed: 11/22/2022] Open
Abstract
Chondrichthyans (sharks, rays and chimeras) are a fascinating and highly vulnerable group of early branching gnathostomes. However, they remain comparatively poorly sampled from the point of view of molecular resources, with deep water taxa being particularly data deficient. The development of long-read sequencing technologies enables the analysis of phylogenetic relationships through a precise and reliable assembly of complete mtDNA genomes. The sequencing and characterization of the complete mitogenome of the opal chimera Chimera opalescens Luchetti, Iglésias et Sellos 2011, using the long-read technique PacBio HiFi is presented. The entire mitogenome was 23,411 bp long and shows the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes, as all other examined Chondrichthyan mitogenomes. Phylogenetic reconstructions using all available Chondrichthyan mitogenomes, including 11 Holocephali (chimeras and ratfishes), places C. opalescens within the Chimaeridae family. Furthermore, the results reinforce previous findings, showing the genus Chimera as paraphyletic and thus highlighting the need to expand molecular approaches in this group of cartilaginous fishes.
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Affiliation(s)
- Nair Vilas-Arrondo
- AQUACOV, Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Vigo, Vigo, Spain
- UVIGO, PhD Program “Marine Science, Technology and Management” (Do*MAR), Faculty of Biology, University of Vigo, Vigo, Spain
| | - André Gomes-dos-Santos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Montse Pérez
- AQUACOV, Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Vigo, Vigo, Spain
| | - Francisco Baldó
- Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Cádiz, Cádiz, Spain
| | - Ana Veríssimo
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Diana Catarino
- Ocean Sciences Institute - Okeanos, Universidade dos Açores, Horta, Portugal
| | - André M. Machado
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Esther Román-Marcote
- Servizo de Planificación, Consellería do Mar, Xunta de Galicia, Santiago de Compostela, Spain; BIOPESLE, Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de Vigo, Vigo, Spain
| | - Rafael Bañón
- Ocean Sciences Institute - Okeanos, Universidade dos Açores, Horta, Portugal
- Grupo de Estudos do Medio Mariño (GEMM), Ribeira, Spain
| | - Elsa Froufe
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - L. Filipe C. Castro
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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23
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Pears JB, Tillett C, Tahara R, Larsson HCE, Boisvert CA. Imaging With the Past: Revealing the Complexity of Chimaeroid Pelvic Musculature Anatomy and Development. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.812561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chondrichthyans are now widely adopted as models for examining the development and evolution of the stem gnathostome body plan. The fins of some cartilaginous fish are recognized for their plesiomorphic form and mode of muscular development, i.e., epithelial extension. Despite detailed molecular and descriptive examinations of these developmental mechanisms, there has been little contemporary examination of the ontogeny and morphology of the musculature in chondrichthyans including that of the paired fins. This gap represents a need for further examination of the developmental morphology of these appendicular musculatures to gain insight into their evolution in gnathostomes. The elephant shark is a Holocephalan, the sister group of all other chondrichthyans (Holocephali: Callorhinchus milii). Here, we use nano-CT imaging and 3D reconstructions to describe the development of the pelvic musculature of a growth series of elephant shark embryos. We also use historical descriptions from the nineteenth century and traditional dissection methods to describe the adult anatomy. This combined approach, using traditional methods and historical knowledge with modern imaging techniques, has enabled a more thorough examination of the anatomy and development of the pelvic musculature revealing that chimaeroid musculatures are more complex than previously thought. These data, when compared to extant and extinct sister taxa, are essential for interpreting and reconstructing fossil musculatures as well as understanding the evolution of paired fins.
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24
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Khalid Z, Chen Y, Yu D, Abbas M, Huan M, Naz Z, Mengist HM, Cao MJ, Jin T. IgNAR antibody: Structural features, diversity and applications. FISH & SHELLFISH IMMUNOLOGY 2022; 121:467-477. [PMID: 35077867 DOI: 10.1016/j.fsi.2022.01.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
In response to the invasion of exogenous microorganisms, one of the defence strategies of the immune system is to produce antibodies. Cartilaginous fish is among those who evolved the earliest humoral immune system that utilizes immunoglobulin-type antibodies. The cartilaginous fish antibodies fall into three categories: IgW, IgM, and IgNAR. The shark Immunoglobulin Novel Antigen Receptor (IgNAR) constitutes disulfide-bonded dimers of two protein chains, similar to the heavy chain of mammalian IgGs. Shark IgNAR is the primary antibody of a shark's adaptive immune system with a serum concentration of 0.1-1.0 mg/mL. Its structure comprises of one variable (V) domain (VNAR) and five constant (C1 -C5) domains in the secretory form. VNARs are classified into several subclasses based on specific properties such as the quantity and position of additional non-canonical cysteine (Cys) residues in the VNAR. The VDJ recombination in IgNAR comprises various fragments; one variable component, three diverse sections, one joining portion, and a solitary arrangement of constant fragments framed in each IgNAR gene cluster. The re-arrangement happens just inside this gene cluster bringing about a VD1D2D3J segment. Therefore, four re-arrangement procedures create the entire VNAR space. IgNAR antibody can serve as an excellent diagnostic, therapeutic, and research tool because it has a smaller size, high specificity for antigen-binding, and perfect stability. The domain characterization, structural features, types, diversity and therapeutic applications of IgNAR molecules are highlighted in this review. It would be helpful for further research on IgNAR antibodies acting as an essential constituent of the adaptive immune system and a potential therapeutic agent.
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Affiliation(s)
- Zunera Khalid
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yulei Chen
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, China
| | - Du Yu
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Misbah Abbas
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Ma Huan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Zara Naz
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Hylemariam Mihiretie Mengist
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, China.
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, 200031, China.
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25
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Katsu Y, Oana S, Lin X, Hyodo S, Baker ME. Aldosterone and dexamethasone activate African lungfish mineralocorticoid receptor: Increased activation after removal of the amino-terminal domain. J Steroid Biochem Mol Biol 2022; 215:106024. [PMID: 34774724 DOI: 10.1016/j.jsbmb.2021.106024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/28/2021] [Accepted: 11/09/2021] [Indexed: 12/18/2022]
Abstract
Aldosterone, the main physiological mineralocorticoid in humans and other terrestrial vertebrates, first appears in lungfish, which are lobe-finned fish that are forerunners of terrestrial vertebrates. Aldosterone activation of the MR regulates internal homeostasis of water, sodium and potassium, which was critical in the conquest of land by vertebrates. We studied transcriptional activation of the slender African lungfish MR by aldosterone, other corticosteroids and progesterone and find that aldosterone, 11-deoxycorticosterone, 11-deoxycortisol and progesterone have half-maximal responses (EC50 s) below 1 nM and are potential physiological mineralocorticoids. In contrast, EC50 s for corticosterone and cortisol were 23 nM and 66 nM, respectively. Unexpectedly, truncated lungfish MR, consisting of the DNA-binding, hinge and steroid-binding domains, had a stronger response to corticosteroids and progesterone than full-length lungfish MR, indicating that the N-terminal domain represses steroid activation of lungfish MR, unlike human MR in which the N-terminal domain contains an activation function. BLAST searches of GenBank did not retrieve a GR ortholog, leading us to test dexamethasone and triamcinolone for activation of lungfish MR. At 10 nM, both synthetic glucocorticoids are about 4-fold stronger than 10 nM aldosterone in activating full-length lungfish MR, leading us to propose that lungfish MR also functions as a GR.
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Affiliation(s)
- Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Faculty of Sciences, Hokkaido University, Sapporo, Japan.
| | - Shin Oana
- Faculty of Sciences, Hokkaido University, Sapporo, Japan
| | - Xiaozhi Lin
- Faculty of Sciences, Hokkaido University, Sapporo, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Michael E Baker
- Division of Nephrology-Hypertension, Department of Medicine, 0693, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0693, United States; Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA, 92093, United States.
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26
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Atake OJ, Eames BF. Mineralized Cartilage and Bone-Like Tissues in Chondrichthyans Offer Potential Insights Into the Evolution and Development of Mineralized Tissues in the Vertebrate Endoskeleton. Front Genet 2021; 12:762042. [PMID: 35003210 PMCID: PMC8727550 DOI: 10.3389/fgene.2021.762042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
The impregnation of biominerals into the extracellular matrix of living organisms, a process termed biomineralization, gives rise to diverse mineralized (or calcified) tissues in vertebrates. Preservation of mineralized tissues in the fossil record has provided insights into the evolutionary history of vertebrates and their skeletons. However, current understanding of the vertebrate skeleton and of the processes underlying its formation is biased towards biomedical models such as the tetrapods mouse and chick. Chondrichthyans (sharks, skates, rays, and chimaeras) and osteichthyans are the only vertebrate groups with extant (living) representatives that have a mineralized skeleton, but the basal phylogenetic position of chondrichthyans could potentially offer unique insights into skeletal evolution. For example, bone is a vertebrate novelty, but the internal supporting skeleton (endoskeleton) of extant chondrichthyans is commonly described as lacking bone. The molecular and developmental basis for this assertion is yet to be tested. Subperichondral tissues in the endoskeleton of some chondrichthyans display mineralization patterns and histological and molecular features of bone, thereby challenging the notion that extant chondrichthyans lack endoskeletal bone. Additionally, the chondrichthyan endoskeleton demonstrates some unique features and others that are potentially homologous with other vertebrates, including a polygonal mineralization pattern, a trabecular mineralization pattern, and an unconstricted perichordal sheath. Because of the basal phylogenetic position of chondrichthyans among all other extant vertebrates with a mineralized skeleton, developmental and molecular studies of chondrichthyans are critical to flesh out the evolution of vertebrate skeletal tissues, but only a handful of such studies have been carried out to date. This review discusses morphological and molecular features of chondrichthyan endoskeletal tissues and cell types, ultimately emphasizing how comparative embryology and transcriptomics can reveal homology of mineralized skeletal tissues (and their cell types) between chondrichthyans and other vertebrates.
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Affiliation(s)
| | - B. Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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27
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Qi J, Shi F, Zhang B, Chen X, Jie X, Furumitsu K, Corush JB, Yamaguchi A, Zhang J. Insights into genetic variation and demographic history of sharpnose rays: Examinations of three species of Telatrygon (Elasmobranchii, Dasyatidae) from the Indo-West Pacific. Integr Zool 2021; 17:1063-1077. [PMID: 34932875 DOI: 10.1111/1749-4877.12614] [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] [Indexed: 11/30/2022]
Abstract
Coastal and demersal chondrichthyans (sharks, rays, and skates) are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology. Population genetic studies investigating the extent to which demographic history shapes the genetic structure of these fishes are rare. Here, we combination mitochondrial DNA (Cytb and ND2) and eight nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the three Indo-West Pacific species of sharpnose rays (Telatrygon zugei, Telatrygon biasa, and Trygon crozieri). High levels of genetic variation both within and between species was identified. Phylogenetic analysis partitioned haplotypes into two lineages supporting divergence of T. zugei from T. crozieri and T. biasa during the Pleistocene. Furthermore, microsatellite-based clustering analyses identified four genetic groups (i.e., T. zugei from Japan, T. zugei from coastal China, T. biasa from Gulf of Thailand, and T. crozieri from the Andaman Sea. Measurements of genetic differentiation also support these four groups. Additionally, Pleistocene demographic expansions were examined in all genetic groups. The climate oscillations and current hydrologic cycles in the Indo-West Pacific appear to be coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays. Considering the species group has, until recently, been thought to be one species, these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jiwei Qi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fanglei Shi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baowei Zhang
- School of Life Science, Anhui University, Hefei, Anhui, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xing Jie
- East China Sea Centre of Standard and Metrology, SOA, Shanghai, China
| | | | - Joel B Corush
- Illinois Natural History Survey, University of Illinois Champaign-Urbana, Champaign, IL, 61820
| | | | - Jie Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
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28
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Lin X, Takagi W, Hyodo S, Ijiri S, Katsu Y, Baker ME. Regulation by Progestins, Corticosteroids, and RU486 of Transcriptional Activation of Elephant Shark and Human Progesterone Receptors: An Evolutionary Perspective. ACS Pharmacol Transl Sci 2021; 5:52-61. [DOI: 10.1021/acsptsci.1c00191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaozhi Lin
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Wataru Takagi
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan
| | - Shigeho Ijiri
- Graduate School of Fisheries Science, Hokkaido University, Hakodate 041-8611, Japan
| | - Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
- Faculty of Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Michael E. Baker
- Division of Nephrology, Department of Medicine, University of California, San Diego, California 92093, United States
- Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, California 92093, United States
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29
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Enzymatic Approach in Calcium Phosphate Biomineralization: A Contribution to Reconcile the Physicochemical with the Physiological View. Int J Mol Sci 2021; 22:ijms222312957. [PMID: 34884758 PMCID: PMC8657759 DOI: 10.3390/ijms222312957] [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: 10/22/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 01/22/2023] Open
Abstract
Biomineralization is the process by which organisms produce hard inorganic matter from soft tissues with outstanding control of mineral deposition in time and space. For this purpose, organisms deploy a sophisticated "toolkit" that has resulted in significant evolutionary innovations, for which calcium phosphate (CaP) is the biomineral selected for the skeleton of vertebrates. While CaP mineral formation in aqueous media can be investigated by studying thermodynamics and kinetics of phase transitions in supersaturated solutions, biogenic mineralization requires coping with the inherent complexity of biological systems. This mainly includes compartmentalization and homeostatic processes used by organisms to regulate key physiological factors, including temperature, pH and ion concentration. A detailed analysis of the literature shows the emergence of two main views describing the mechanism of CaP biomineralization. The first one, more dedicated to the study of in vivo systems and supported by researchers in physiology, often involves matrix vesicles (MVs). The second one, more investigated by the physicochemistry community, involves collagen intrafibrillar mineralization particularly through in vitro acellular models. Herein, we show that there is an obvious need in the biological systems to control both where and when the mineral forms through an in-depth survey of the mechanism of CaP mineralization. This necessity could gather both communities of physiologists and physicochemists under a common interest for an enzymatic approach to better describe CaP biomineralization. Both homogeneous and heterogeneous enzymatic catalyses are conceivable for these systems, and a few preliminary promising results on CaP mineralization for both types of enzymatic catalysis are reported in this work. Through them, we aim to describe the relevance of our point of view and the likely findings that could be obtained when adding an enzymatic approach to the already rich and creative research field dealing with CaP mineralization. This complementary approach could lead to a better understanding of the biomineralization mechanism and inspire the biomimetic design of new materials.
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30
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Anumukonda K, Francis M, Currie P, Tulenko F, Hsu E. Heavy chain-only antibody genes in fish evolved to generate unique CDR3 repertoire. Eur J Immunol 2021; 52:247-260. [PMID: 34708869 DOI: 10.1002/eji.202149588] [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: 08/18/2021] [Revised: 10/08/2021] [Accepted: 10/26/2021] [Indexed: 11/11/2022]
Abstract
In addition to conventional immunoglobulin, camelids and cartilaginous fish express a special class of antibody that consists only of heavy (H) chain (HCAbs). In the holocephalan elephantfish, there are two HCAb classes, one of which has evolved surprising features. The H-chain genes in cartilaginous fish are organized as 20-200 minigenes, or clusters, each consisting of VH, 1-3 DH, JH gene segments with one set of constant region exons. We report that HHC2 (holocephalan H-chain antibody 2) evolved from IgM H-chain clusters, but its DH gene segments have diverged considerably. The three DH in HHC2 clusters are A-rich, so that one to three potential reading frames for each DH encode lysine and arginine. All three are incorporated into the rearranged VDJ, ensuring that the ligand-binding site carries multiple basic residues, as cDNA sequences demonstrate. The electropositive character in HHC2 CDR3 is accompanied by a paucity of aromatic amino acids, the latter feature at variance to the established, interactive role of tyrosine not only in ligand-binding but generally at interfaces of protein complexes. The selection for these divergent HHC2 features challenges currently accepted ideas on what determines antibody reactivity and molecular recognition.
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Affiliation(s)
- Kamala Anumukonda
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, 11203, USA
| | - Malcolm Francis
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Peter Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, 11203, USA
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31
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Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution. Nat Commun 2021; 12:4489. [PMID: 34301952 PMCID: PMC8302630 DOI: 10.1038/s41467-021-24573-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.
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32
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Ancient fishes and the functional evolution of the corticosteroid stress response in vertebrates. Comp Biochem Physiol A Mol Integr Physiol 2021; 260:111024. [PMID: 34237466 DOI: 10.1016/j.cbpa.2021.111024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022]
Abstract
The neuroendocrine mechanism underlying stress responses in vertebrates is hypothesized to be highly conserved and evolutionarily ancient. Indeed, elements of this mechanism, from the brain to steroidogenic tissue, are present in all vertebrate groups; yet, evidence of the function and even identity of some elements of the hypothalamus-pituitary-adrenal/interrenal (HPA/I) axis is equivocal among the most basal vertebrates. The purpose of this review is to discuss the functional evolution of the HPA/I axis in vertebrates with a focus on our understanding of this neuroendocrine mechanism in the most ancient vertebrates: the agnathan (i.e., hagfish and lamprey) and chondrichthyan fishes (i.e., sharks, rays, and chimeras). A review of the current literature presents evidence of a conserved HPA/I axis in jawed vertebrates (i.e., gnathostomes); yet, available data in jawless (i.e., agnathan) and chondrichthyan fishes are limited. Neuroendocrine regulation of corticosteroidogenesis in agnathans and chondrichthyans appears to function through similar pathways as in bony fishes and tetrapods; however, key elements have yet to be identified and the involvement of melanotropins and gonadotropin-releasing hormone in the stress axis in these ancient fishes warrants further investigation. Further, the identities of physiological glucocorticoids are uncertain in hagfishes, chondrichthyans, and even coelacanths. Resolving these and other knowledge gaps in the stress response of ancient fishes will be significant for advancing knowledge of the evolutionary origins of the vertebrate stress response.
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33
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Katsu Y, Shariful IMD, Lin X, Takagi W, Urushitani H, Kohno S, Hyodo S, Baker ME. N-terminal domain regulates steroid activation of elephant shark glucocorticoid and mineralocorticoid receptors. J Steroid Biochem Mol Biol 2021; 210:105845. [PMID: 33652098 DOI: 10.1016/j.jsbmb.2021.105845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/29/2020] [Accepted: 02/04/2021] [Indexed: 12/23/2022]
Abstract
Orthologs of human glucocorticoid receptor (GR) and human mineralocorticoid receptor (MR) first appear in cartilaginous fishes. Subsequently, the MR and GR diverged to respond to different steroids: the MR to aldosterone and the GR to cortisol and corticosterone. We report that cortisol, corticosterone and aldosterone activate full-length elephant shark GR, and progesterone, which activates elephant shark MR, does not activate elephant shark GR. However, progesterone inhibits steroid binding to elephant shark GR, but not to human GR. Together, this indicates partial functional divergence of elephant shark GR from the MR. Deletion of the N-terminal domain (NTD) from elephant shark GR (truncated GR) reduced the response to corticosteroids, while truncated and full-length elephant shark MR had similar responses to corticosteroids. Swapping of NTDs of elephant shark GR and MR yielded an elephant shark MR chimera with full-length GR-like increased activation by corticosteroids and progesterone compared to full-length elephant shark MR. Elephant shark MR NTD fused to GR DBD + LBD had similar activation as full-length MR, indicating that the MR NTD lacked GR-like NTD activity. We propose that NTD activation of human GR evolved early in GR divergence from the MR.
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Affiliation(s)
- Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Xiaozhi Lin
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Wataru Takagi
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Hiroshi Urushitani
- Department of Food and Nutrition, The University of Aizu, Junior College Division, Fukushima, Japan
| | - Satomi Kohno
- Department of Biology, St. Cloud State University, St. Cloud, MN, USA
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Michael E Baker
- Division of Nephrology-Hypertension, Department of Medicine, University of California, San Diego, CA, USA.
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Schluessel V, Rick IP, Seifert FD, Baumann C, Lee Davies WI. Not just shades of grey: life is full of colour for the ocellate river stingray (Potamotrygon motoro). J Exp Biol 2021; 224:237826. [PMID: 33771913 DOI: 10.1242/jeb.226142] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 03/19/2021] [Indexed: 12/14/2022]
Abstract
Previous studies have shown that marine stingrays have the anatomical and physiological basis for colour vision, with cone spectral sensitivity in the blue to green range of the visible spectrum. Behavioural studies on Glaucostegus typus also showed that blue and grey can be perceived and discriminated. The present study is the first to assess visual opsin genetics in the ocellate river stingray (Potamotrygon motoro) and test whether individuals perceive colour in two alternative forced choice experiments. Retinal transcriptome profiling using RNA-Seq and quantification demonstrated the presence of lws and rh2 cone opsin genes and a highly expressed single rod (rh1) opsin gene. Spectral tuning analysis predicted these vitamin A1-based visual photopigments to exhibit spectral absorbance maxima at 461 nm (rh2), 496 nm (rh1) and 555 nm (lws); suggesting the presence of dichromacy in this species. Indeed, P. motoro demonstrates the potential to be equally sensitive to wavelengths from 380 to 600 nm of the visible spectrum. Behavioural results showed that red and green plates, as well as blue and yellow plates, were readily discriminated based on colour; however, brightness differences also played a part in the discrimination of blue and yellow. Red hues of different brightness were distinguished significantly above chance level from one another. In conclusion, the genetic and behavioural results support prior data on marine stingrays. However, this study suggests that freshwater stingrays of the family Potamotrygonidae may have a visual colour system that has ecologically adapted to a riverine habitat.
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Affiliation(s)
- Vera Schluessel
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115 Bonn, Germany
| | - Ingolf P Rick
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115 Bonn, Germany
| | - Friederike Donata Seifert
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115 Bonn, Germany
| | - Christina Baumann
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115 Bonn, Germany
| | - Wayne Iwan Lee Davies
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115 Bonn, Germany.,Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden.,School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne Campus, Melbourne, VIC 3086, Australia
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35
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Gonçalves-Carneiro D, Takata MA, Ong H, Shilton A, Bieniasz PD. Origin and evolution of the zinc finger antiviral protein. PLoS Pathog 2021; 17:e1009545. [PMID: 33901262 PMCID: PMC8102003 DOI: 10.1371/journal.ppat.1009545] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 05/06/2021] [Accepted: 04/08/2021] [Indexed: 01/24/2023] Open
Abstract
The human zinc finger antiviral protein (ZAP) recognizes RNA by binding to CpG dinucleotides. Mammalian transcriptomes are CpG-poor, and ZAP may have evolved to exploit this feature to specifically target non-self viral RNA. Phylogenetic analyses reveal that ZAP and its paralogue PARP12 share an ancestral gene that arose prior to extensive eukaryote divergence, and the ZAP lineage diverged from the PARP12 lineage in tetrapods. Notably, the CpG content of modern eukaryote genomes varies widely, and ZAP-like genes arose subsequent to the emergence of CpG-suppression in vertebrates. Human PARP12 exhibited no antiviral activity against wild type and CpG-enriched HIV-1, but ZAP proteins from several tetrapods had antiviral activity when expressed in human cells. In some cases, ZAP antiviral activity required a TRIM25 protein from the same or related species, suggesting functional co-evolution of these genes. Indeed, a hypervariable sequence in the N-terminal domain of ZAP contributed to species-specific TRIM25 dependence in antiviral activity assays. Crosslinking immunoprecipitation coupled with RNA sequencing revealed that ZAP proteins from human, mouse, bat and alligator exhibit a high degree of CpG-specificity, while some avian ZAP proteins appear more promiscuous. Together, these data suggest that the CpG- rich RNA directed antiviral activity of ZAP-related proteins arose in tetrapods, subsequent to the onset of CpG suppression in certain eukaryote lineages, with subsequent species-specific adaptation of cofactor requirements and RNA target specificity. To control viral infections, cells have evolved a variety of mechanisms that detect, modify and sometimes eliminate viral components. One of such mechanism is the Zinc Finger Antiviral Protein (ZAP) which binds RNA sequences that are rich in elements composed of a cytosine followed by a guanine. Selection of viral RNA can only be achieved because such elements are sparse in RNAs encoded by human genes. Here, we traced the molecular evolution of ZAP. We found that ZAP and a closely related gene, PARP12, originated from the same ancestral gene that existed in a predecessor of vertebrates and invertebrates. We found that ZAP proteins from mammals, birds and reptiles have antiviral activity but only in the presence of a co-factor, TRIM25, from the same species. ZAP proteins from birds were particularly interesting since they demonstrated a broader antiviral activity, primarily driven by relaxed requirement for cytosine-guanine. Our findings suggest that viruses that infect birds–which are important vectors for human diseases–are under differential selective pressures and this property may influence the outcome of interspecies transmission.
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Affiliation(s)
- Daniel Gonçalves-Carneiro
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Matthew A. Takata
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Heley Ong
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Amanda Shilton
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York City, New York, United States of America
- * E-mail:
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36
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Berio F, Debiais-Thibaud M. Evolutionary developmental genetics of teeth and odontodes in jawed vertebrates: a perspective from the study of elasmobranchs. JOURNAL OF FISH BIOLOGY 2021; 98:906-918. [PMID: 31820456 DOI: 10.1111/jfb.14225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Most extant vertebrates display a high variety of tooth and tooth-like organs (odontodes) that vary in shape, position over the body and nature of composing tissues. The development of these structures is known to involve similar genetic cascades and teeth and odontodes are believed to share a common evolutionary history. Gene expression patterns have previously been compared between mammalian and teleost tooth development but we highlight how the comparative framework was not always properly defined to deal with different tooth types or tooth developmental stages. Larger-scale comparative analyses also included cartilaginous fishes: sharks display oral teeth and dermal scales for which the gene expression during development started to be investigated in the small-spotted catshark Scyliorhinus canicula during the past decade. We report several descriptive approaches to analyse the embryonic tooth and caudal scale gene expressions in S. canicula. We compare these expressions wih the ones reported in mouse molars and teleost oral and pharyngeal teeth and highlight contributions and biases that arise from these interspecific comparisons. We finally discuss the evolutionary processes that can explain the observed intra and interspecific similarities and divergences in the genetic cascades involved in tooth and odontode development in jawed vertebrates.
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Affiliation(s)
- Fidji Berio
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
- University of Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Institut de Génomique Fonctionnelle de Lyon, UMR5242, 46 Allée d'Italie, Lyon, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
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37
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Gomes-Dos-Santos A, Machado AM, Aranha SG, Dias E, Veríssimo A, Castro LFC, Froufe E. The complete mitochondrial genome of the endemic Iberian pygmy skate Neoraja iberica Stehmann, Séret, Costa, & Baro 2008 (Elasmobranchii, Rajidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:848-850. [PMID: 33796653 PMCID: PMC7971246 DOI: 10.1080/23802359.2021.1884030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Skates, Chondrichthyes fishes from order Rajiformes, are the most species-rich group of all Batoidea. However, their phylogenetic relationships and systematics is still a highly discussed and controversial subject. The use of complete mitogenome has shown to be a promising tool to fill this gap of knowledge. Here, the complete mitogenome of the Iberian pygmy skate Neoraja iberica (Stehmann, Séret, Costa & Baro 2008) was sequenced and assembled. The mitogenome is 16,723 bp long and its gene content (i.e. 13 protein-coding genes, 22 transfer RNA, and 2 ribosomal RNA genes) and arrangement are the expected for Batoidea. Phylogenetic reconstructions, including 89 Rajiformes and two outgroup Rhinopristiformes, recovered family Rajidae as monophyletic, and further divided in the monophyletic tribe Rajini, sister to tribes Amblyrajini and Rostrorajini. The newly sequenced N. iberica mitogenome is the first representative of the tribe Rostrorajini.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal
| | - Sofia Graça Aranha
- CCMAR - Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Ester Dias
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO - Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Universityof Porto, Matosinhos, Portugal
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38
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Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs. Genes (Basel) 2021; 12:genes12030324. [PMID: 33668210 PMCID: PMC7995966 DOI: 10.3390/genes12030324] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.
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39
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Gomes-Dos-Santos A, Vilas-Arrondo N, Machado AM, Veríssimo A, Pérez M, Baldó F, Castro LFC, Froufe E. Shedding light on the Chimaeridae taxonomy: the complete mitochondrial genome of the cartilaginous fish Hydrolagus mirabilis (Collett, 1904) (Holocephali: Chimaeridae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:420-422. [PMID: 33659699 PMCID: PMC7872578 DOI: 10.1080/23802359.2020.1870887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Cartilaginous fish are fascinating taxa, present in the folklore and art of many different cultures. Moreover, they display several unique anatomical, physiological, molecular, and behavioral characteristics making them extremely interesting from a biological perspective. Nevertheless, some crucial knowledge gaps remain, including phylogenetic relationships among extant species. Here, we produced the complete mitogenome sequence of the large-eyed rabbitfish, Hydrolagus mirabilis (Chimaeriformes). The complete mitogenome is 19,435 bp long and shows the same overall content, i.e. 13 protein-coding genes, 22 transfer RNA, and two ribosomal RNA genes, as all other examined Chondrichthyan mitogenomes. Phylogenetic reconstructions including 12 Holocephalan and three outgroup Elasmobranch mitogenomes place the H. mirabilis within the family Chimaeridae but revealed paraphyletic Hydrolagus and Chimaera, in line with a previous study, highlighting the importance for collecting additional molecular data to improve phylogenetic reconstruction in this group of vertebrates.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nair Vilas-Arrondo
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Vigo, Spain.,Faculty of Biology, UVIGO, PhD Program "Marine Science, Technology and Management" (Do MAR), University of Vigo, Vigo, Spain
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO - Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
| | - Montse Pérez
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Vigo, Spain
| | - Francisco Baldó
- Instituto Español de Oceanografía, Centro Oceanográfico de Cádiz, Puerto Pesquero, Muelle de Levante s/n, Cádiz, Spain
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros de Leixões, Av. General Norton De Matos s/n, University of Porto, Matosinhos, Portugal
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40
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Matz H, Munir D, Logue J, Dooley H. The immunoglobulins of cartilaginous fishes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 115:103873. [PMID: 32979434 PMCID: PMC7708420 DOI: 10.1016/j.dci.2020.103873] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 05/12/2023]
Abstract
Cartilaginous fishes, comprising the chimeras, sharks, skates, and rays, split from the common ancestor with other jawed vertebrates approx. 450 million years ago. Being the oldest extant taxonomic group to possess an immunoglobulin (Ig)-based adaptive immune system, examination of this group has taught us much about the evolution of adaptive immunity, as well as the conserved and taxon-specific characteristics of Igs. Significant progress has been made analyzing sequences from numerous genomic and transcriptomic data sets. These findings have been supported by additional functional studies characterizing the Igs and humoral response of sharks and their relatives. This review will summarize what we have learned about the genomic organization, protein structure, and in vivo function of these Ig isotypes in cartilaginous fishes and highlight the areas where our knowledge is still lacking.
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Affiliation(s)
- Hanover Matz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - Danish Munir
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Helen Dooley
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Institute of Marine and Environmental Technology, Baltimore, MD, USA.
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41
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Dearden RP, Mansuit R, Cuckovic A, Herrel A, Didier D, Tafforeau P, Pradel A. The morphology and evolution of chondrichthyan cranial muscles: A digital dissection of the elephantfish Callorhinchus milii and the catshark Scyliorhinus canicula. J Anat 2021; 238:1082-1105. [PMID: 33415764 PMCID: PMC8053583 DOI: 10.1111/joa.13362] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022] Open
Abstract
The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups-holocephalans and elasmobranchs-have played a pivotal role in the formation of evolutionary hypotheses targeting major cranial structures such as the jaws and pharynx. However, despite the advent of digital dissections as a means of easily visualizing and sharing the results of anatomical studies in three dimensions, information on the musculoskeletal systems of the chondrichthyan head remains largely limited to traditional accounts, many of which are at least a century old. Here, we use synchrotron tomographic data to carry out a digital dissection of a holocephalan and an elasmobranch widely used as model species: the elephantfish, Callorhinchus milii, and the small-spotted catshark, Scyliorhinus canicula. We describe and figure the skeletal anatomy of the head, labial, mandibular, hyoid, and branchial cartilages in both taxa as well as the muscles of the head and pharynx. In Callorhinchus, we make several new observations regarding the branchial musculature, revealing several previously unreported or ambiguously characterized muscles, likely homologous to their counterparts in the elasmobranch pharynx. We also identify a previously unreported structure linking the pharyngohyal of Callorhinchus to the neurocranium. Finally, we review what is known about the evolution of chondrichthyan cranial muscles from their fossil record and discuss the implications for muscle homology and evolution, broadly concluding that the holocephalan pharynx is likely derived from a more elasmobranch-like form which is plesiomorphic for the chondrichthyan crown group. This dataset has great potential as a resource, particularly for researchers using these model species for zoological research, functional morphologists requiring models of musculature and skeletons, as well as for palaeontologists seeking comparative models for extinct taxa.
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Affiliation(s)
- Richard P Dearden
- CR2P, Centre de Recherche en Paléontologie-Paris, Muséum national d'Histoire naturelle, Sorbonne Université, Centre National de la Recherche Scientifique, Paris cedex 05, France
| | - Rohan Mansuit
- CR2P, Centre de Recherche en Paléontologie-Paris, Muséum national d'Histoire naturelle, Sorbonne Université, Centre National de la Recherche Scientifique, Paris cedex 05, France.,UMR 7179 (MNHN-CNRS) MECADEV, Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, Paris, France
| | | | - Anthony Herrel
- UMR 7179 (MNHN-CNRS) MECADEV, Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, Paris, France
| | - Dominique Didier
- Department of Biology, Millersville University, Millersville, PA, USA
| | - Paul Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France
| | - Alan Pradel
- CR2P, Centre de Recherche en Paléontologie-Paris, Muséum national d'Histoire naturelle, Sorbonne Université, Centre National de la Recherche Scientifique, Paris cedex 05, France
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Hart NS, Lamb TD, Patel HR, Chuah A, Natoli RC, Hudson NJ, Cutmore SC, Davies WIL, Collin SP, Hunt DM. Visual Opsin Diversity in Sharks and Rays. Mol Biol Evol 2020; 37:811-827. [PMID: 31770430 DOI: 10.1093/molbev/msz269] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.
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Affiliation(s)
- Nathan S Hart
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Hardip R Patel
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Riccardo C Natoli
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Nicholas J Hudson
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Scott C Cutmore
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Wayne I L Davies
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
| | - Shaun P Collin
- School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - David M Hunt
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, The University of Western Australia, Crawley, WA, Australia
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43
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Iijima M, Ishiyama M. A unique mineralization mode of hypermineralized pleromin in the tooth plate of Chimaera phantasma contributes to its microhardness. Sci Rep 2020; 10:18591. [PMID: 33122684 PMCID: PMC7596707 DOI: 10.1038/s41598-020-75545-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/14/2020] [Indexed: 11/15/2022] Open
Abstract
Tooth plates of the chimaeroids, holocephalian fishes, are unique dental hard tissues. Unlike the teeth of other animals, the tooth plates are located on the roof of the mouth and in the lower jaw. Their tooth plates consist, to a large extent, of lightly mineralized tissue (osteodentin) and hypermineralized tissue (pleromin). Notably, the mineral phase of pleromin is whitlockite, while that of other animals is apatite. Dietary habits of chimaeroids and wearing features of their tooth plates suggest an extreme hardness of pleromin, but this has never been investigated. We examined the microhardness of the tooth plate of Chimaera phantasma and found that pleromin in the biting region was extremely hard, comparable with the hardness of mature tooth enamel, whereas the hardness of immature pleromin was lower than that of bovine dentin. The hardness of osteodentin, on the other hand, was equivalent to that of bovine dentin and almost the same throughout the tooth plate. Immature pleromin was sparsely packed with oval crystals of whitlockite and, as pleromin matures, the space between crystals was filled with small intercrystalline materials. The maturing process of pleromin could partly contribute to its remarkable hardness and have some implications for designing novel biomaterials.
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Affiliation(s)
- Mayumi Iijima
- Department of Applied Biological Chemistry, Graduated School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Mikio Ishiyama
- Department of Histology, The Nippon Dental University School of Life Dentistry at Niigata, 1-8 Hamaura-cho, Chuou-ku, Niigata, 951-8580, Japan
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Abstract
Over the last few decades, an increasing number of vertebrate taxa have been identified that undergo programmed genome rearrangement, or programmed DNA loss, during development. In these organisms, the genome of germ cells is often reproducibly different from the genome of all other cells within the body. Although we clearly have not identified all vertebrate taxa that undergo programmed genome loss, the list of species known to undergo loss now represents ∼10% of vertebrate species, including several basally diverging lineages. Recent studies have shed new light on the targets and mechanisms of DNA loss and their association with canonical modes of DNA silencing. Ultimately, expansion of these studies into a larger collection of taxa will aid in reconstructing patterns of shared/independent ancestry of programmed DNA loss in the vertebrate lineage, as well as more recent evolutionary events that have shaped the structure and content of eliminated DNA.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
| | | | - Cody Saraceno
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
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Fonseca E, Machado AM, Vilas-Arrondo N, Gomes-Dos-Santos A, Veríssimo A, Esteves P, Almeida T, Themudo G, Ruivo R, Pérez M, da Fonseca R, Santos MM, Froufe E, Román-Marcote E, Venkatesh B, Castro LFC. Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes. Gen Comp Endocrinol 2020; 295:113527. [PMID: 32526329 DOI: 10.1016/j.ygcen.2020.113527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Nuclear receptors (NRs) are key transcription factors that originated in the common ancestor of metazoans. The vast majority of NRs are triggered by binding to either endogenous (e.g. retinoic acid) or exogenous (e.g. xenobiotics) ligands, and their evolution and expansion is tightly linked to the function of endocrine systems. Importantly, they represent classic targets of physiological exploitation by endocrine disrupting chemicals. The NR gene repertoire in different lineages has been shaped by gene loss, duplication and mutation, denoting a dynamic evolutionary route. As the earliest diverging class of gnathostomes (jawed vertebrates), cartilaginous fishes offer an exceptional opportunity to address the early diversification of NR gene families and the evolution of the endocrine system in jawed vertebrates. Here we provide an exhaustive analysis into the NR gene composition in five elasmobranch (sharks and rays) and two holocephalan (chimaeras) species. For this purpose, we generated also a low coverage draft genome assembly of the chimaera small-eyed rabbitfish, Hydrolagus affinis. We show that cartilaginous fish retain an archetypal NR gene repertoire, similar to that of mammals and coincident with the two rounds of whole genome duplication that occurred in the gnathostome ancestor. Furthermore, novel gene members of the non-canonical NR0B receptors were found in the genomes of this lineage. Our findings provide an essential view into the early diversification of NRs in gnathostomes, paving the way for functional studies.
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Affiliation(s)
- Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Nair Vilas-Arrondo
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain; UVIGO, phD Program "Marine Science, Tehchology and Management" (Do *MAR), Faculty of Biology, University of Vigo, 36200 Vigo, Spain
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - Ana Veríssimo
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, U.Porto, 4485-661 Vairão, Portugal
| | - Pedro Esteves
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; UVIGO, phD Program "Marine Science, Tehchology and Management" (Do *MAR), Faculty of Biology, University of Vigo, 36200 Vigo, Spain
| | - Tereza Almeida
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, U.Porto, 4485-661 Vairão, Portugal
| | - Gonçalo Themudo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Raquel Ruivo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Montse Pérez
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain
| | - Rute da Fonseca
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Denmark
| | - Miguel M Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Esther Román-Marcote
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore.
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal.
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Crawford L, Bart H, Harold EL, Huckaba TM, Davenport IR. Tube-like structures within the ovarian follicle of Hydrolagus colliei indicate the early origins of follicle cell processes. JOURNAL OF FISH BIOLOGY 2020; 97:691-695. [PMID: 32506516 DOI: 10.1111/jfb.14423] [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: 04/21/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Follicle cell processes (FCP) are actin-based, tube-like structures that connect the developing oocyte to the follicle cells throughout oogenesis. They were first described in Selachians (sharks) where their suggested roles were facilitating the transport of metabolites to the developing oocyte and providing structural support to the large egg cells of sharks, an early stage in the evolution of viviparity. Subsequent studies found that FCP are absent in Rajiformes (skates), suggesting that FCP may have been novel structures specific to the sharks. Here, FCP in Hydrolagus colliei, a Chimaeriform, were described. The FCP of H. colliei differ morphologically from those previously described in sharks, but as they also contain actin, they presumably play similar roles provisioning the developing oocyte and providing structural support. The presence of FCP in the order Chimaeriformes suggests that their origin predates the split of the elasmobranchs and the holocephalans.
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Affiliation(s)
- Lydia Crawford
- Ecology and Evolutionary Biology Department, Tulane University, New Orleans, Louisiana, USA
| | - Henry Bart
- Ecology and Evolutionary Biology Department, Tulane University, New Orleans, Louisiana, USA
| | - Enrique L Harold
- Department of Biology, Xavier University of Louisiana, New Orleans, Louisiana, USA
| | - Thomas M Huckaba
- Department of Biology, Xavier University of Louisiana, New Orleans, Louisiana, USA
| | - Ian R Davenport
- Department of Biology, Xavier University of Louisiana, New Orleans, Louisiana, USA
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Babarinde IA, Saitou N. The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences. Genome Biol Evol 2020; 12:1444-1458. [PMID: 32835375 DOI: 10.1093/gbe/evaa157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae-Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.
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Affiliation(s)
- Isaac Adeyemi Babarinde
- Department of Biological Sciences, Southern University of Science and Technology, Shenzhen, China.,Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan.,School of Medicine, University of the Ryukyus, Okinawa, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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Molecular circumscription of new species of Gyrocotyle Diesing, 1850 (Cestoda) from deep-sea chimaeriform holocephalans in the North Atlantic. Syst Parasitol 2020; 97:285-296. [PMID: 32328809 DOI: 10.1007/s11230-020-09912-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/01/2020] [Indexed: 10/24/2022]
Abstract
Chimaeras, or ratfishes, are the only extant group of holocephalan fishes and are the sole host group of gyrocotylidean cestodes, which represent a sister group of the true tapeworms (Eucestoda). These unique, non-segmented cestodes have been known since the 1850s and multiple species and genera have been erected despite a general agreement that the delineation of species on the basis of morphology is effectively impossible. Thus, in the absence of molecular studies, the validity of gyrocotylid taxa and their specific host associations has remained highly speculative. Here we report the presence of Gyrocotyle spp. from rarely-caught deep-sea chimaeras collected in the North-East Atlantic, and describe two new species: G. haffii n. sp. from the bent-nose chimaera, Harriota raleighana Goode & Bean, and G. discoveryi n. sp. from the large-eyed rabbit fish, Hydrolagus mirabilis (Collett). Nuclear ribosomal sequence data were generated for individual parasites taken from different host species collected on different dates and from different localities and were combined with previously published sequences. Phylogenetic analyses supported the recognition of independent lineages and clusters, indicative of species, but were indecisive in recovering the root of the tree in analyses that included non-gyrocotylid outgroup taxa. The molecular data reveal variation not reflected in morphology and point to a complex picture of genetic divergence shaped by both isolation and migration in the deep-sea environment.
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Vision in sharks and rays: Opsin diversity and colour vision. Semin Cell Dev Biol 2020; 106:12-19. [PMID: 32331993 DOI: 10.1016/j.semcdb.2020.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 01/11/2023]
Abstract
The visual sense of elasmobranch fishes is poorly studied compared to their bony cousins, the teleosts. Nevertheless, the elasmobranch eye features numerous specialisations that have no doubt facilitated the diversification and evolutionary success of this fascinating taxon. In this review, I highlight recent discoveries on the nature and phylogenetic distribution of visual pigments in sharks and rays. Whereas most rays appear to be cone dichromats, all sharks studied to date are cone monochromats and, as a group, have likely abandoned colour vision on multiple occasions. This situation in sharks mirrors that seen in other large marine predators, the pinnipeds and cetaceans, which leads us to reassess the costs and benefits of multiple cone pigments and wavelength discrimination in the marine environment.
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Baker ME, Katsu Y. Progesterone: An enigmatic ligand for the mineralocorticoid receptor. Biochem Pharmacol 2020; 177:113976. [PMID: 32305433 DOI: 10.1016/j.bcp.2020.113976] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/10/2020] [Indexed: 12/21/2022]
Abstract
The progesterone receptor (PR) mediates progesterone regulation of female reproductive physiology, as well as gene transcription in non-reproductive tissues, such as brain, bone, lung and vasculature, in both women and men. An unusual property of progesterone is its high affinity for the mineralocorticoid receptor (MR), which regulates electrolyte transport in the kidney in humans and other terrestrial vertebrates. In humans, rats, alligators and frogs, progesterone antagonizes activation of the MR by aldosterone, the physiological mineralocorticoid in terrestrial vertebrates. In contrast, in elephant shark, ray-finned fishes and chickens, progesterone activates the MR. Interestingly, cartilaginous fishes and ray-finned fishes do not synthesize aldosterone, raising the question of which steroid(s) activate the MR in cartilaginous fishes and ray-finned fishes. The simpler synthesis of progesterone, compared to cortisol and other corticosteroids, makes progesterone a candidate physiological activator of the MR in elephant sharks and ray-finned fishes. Elephant shark and ray-finned fish MRs are expressed in diverse tissues, including heart, brain and lung, as well as, ovary and testis, two reproductive tissues that are targets for progesterone, which together suggests a multi-faceted physiological role for progesterone activation of the MR in elephant shark and ray-finned fish. The functional consequences of progesterone as an antagonist of some terrestrial vertebrate MRs and as an agonist of fish and chicken MRs are not fully understood. The physiological activities of progesterone through binding to vertebrate MRs merits further investigation.
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Affiliation(s)
- Michael E Baker
- Division of Nephrology-Hypertension, Department of Medicine, 0735, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0735, United States.
| | - Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.
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