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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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Liu GY, Jouandin P, Bahng RE, Perrimon N, Sabatini DM. An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.541239. [PMID: 37292894 PMCID: PMC10245982 DOI: 10.1101/2023.05.25.541239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Animals must sense and respond to nutrient availability in their local niche. This task is coordinated in part by the mTOR complex 1 (mTORC1) pathway, which regulates growth and metabolism in response to nutrients1-5. In mammals, mTORC1 senses specific amino acids through specialized sensors that act through the upstream GATOR1/2 signaling hub6-8. To reconcile the conserved architecture of the mTORC1 pathway with the diversity of environments that animals can occupy, we hypothesized that the pathway might maintain plasticity by evolving distinct nutrient sensors in different metazoan phyla1,9,10. Whether such customization occurs-and how the mTORC1 pathway might capture new nutrient inputs-is not known. Here, we identify the Drosophila melanogaster protein Unmet expectations (Unmet, formerly CG11596) as a species-restricted nutrient sensor and trace its incorporation into the mTORC1 pathway. Upon methionine starvation, Unmet binds to the fly GATOR2 complex to inhibit dTORC1. S-adenosylmethionine (SAM), a proxy for methionine availability, directly relieves this inhibition. Unmet expression is elevated in the ovary, a methionine-sensitive niche11, and flies lacking Unmet fail to maintain the integrity of the female germline under methionine restriction. By monitoring the evolutionary history of the Unmet-GATOR2 interaction, we show that the GATOR2 complex evolved rapidly in Dipterans to recruit and repurpose an independent methyltransferase as a SAM sensor. Thus, the modular architecture of the mTORC1 pathway allows it to co-opt preexisting enzymes and expand its nutrient sensing capabilities, revealing a mechanism for conferring evolvability on an otherwise highly conserved system.
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Affiliation(s)
- Grace Y. Liu
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology; 455 Main Street, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Patrick Jouandin
- Department of Genetics, Blavatnik Institute, Harvard Medical School; Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA 02115, USA
- Present address: Institut de Recherche en Cancérologie de Montpellier, Inserm U1194-UM-ICM; Campus Val d’Aurelle, F-34298 Montpellier Cedex 5, France
| | - Raymond E. Bahng
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology; 455 Main Street, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School; Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA 02115, USA
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Saxena H, Negi H, Sharma B. Role of F-box E3-ubiquitin ligases in plant development and stress responses. PLANT CELL REPORTS 2023:10.1007/s00299-023-03023-8. [PMID: 37195503 DOI: 10.1007/s00299-023-03023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/27/2023] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.
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Affiliation(s)
- Harshita Saxena
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia Griffin Campus, 1109 Experiment Street, Griffin, GA, 30223, USA
| | - Harshita Negi
- Department of Biological Sciences, University of South Carolina, 715 Sumter Street, Columbia, SC, 29208, USA
| | - Bhaskar Sharma
- School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Geelong, VIC, 3216, Australia.
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA, 92521, USA.
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Kusová A, Steinbachová L, Přerovská T, Drábková LZ, Paleček J, Khan A, Rigóová G, Gadiou Z, Jourdain C, Stricker T, Schubert D, Honys D, Schrumpfová PP. Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions. PLANT MOLECULAR BIOLOGY 2023; 112:61-83. [PMID: 37118559 PMCID: PMC10167121 DOI: 10.1007/s11103-023-01348-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/02/2023] [Indexed: 05/09/2023]
Abstract
Telomere repeat binding proteins (TRBs) belong to a family of proteins possessing a Myb-like domain which binds to telomeric repeats. Three members of this family (TRB1, TRB2, TRB3) from Arabidopsis thaliana have already been described as associated with terminal telomeric repeats (telomeres) or short interstitial telomeric repeats in gene promoters (telo-boxes). They are also known to interact with several protein complexes: telomerase, Polycomb repressive complex 2 (PRC2) E(z) subunits and the PEAT complex (PWOs-EPCRs-ARIDs-TRBs). Here we characterize two novel members of the TRB family (TRB4 and TRB5). Our wide phylogenetic analyses have shown that TRB proteins evolved in the plant kingdom after the transition to a terrestrial habitat in Streptophyta, and consequently TRBs diversified in seed plants. TRB4-5 share common TRB motifs while differing in several others and seem to have an earlier phylogenetic origin than TRB1-3. Their common Myb-like domains bind long arrays of telomeric repeats in vitro, and we have determined the minimal recognition motif of all TRBs as one telo-box. Our data indicate that despite the distinct localization patterns of TRB1-3 and TRB4-5 in situ, all members of TRB family mutually interact and also bind to telomerase/PRC2/PEAT complexes. Additionally, we have detected novel interactions between TRB4-5 and EMF2 and VRN2, which are Su(z)12 subunits of PRC2.
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Affiliation(s)
- Alžbeta Kusová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tereza Přerovská
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Paleček
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahamed Khan
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Gabriela Rigóová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Zuzana Gadiou
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Claire Jourdain
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tino Stricker
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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55
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Sun X, Liu W, Peng Y, Meng L, Zhang J, Pan Y, Wang D, Zhu J, Wang C, Yan C. Genome-wide analyses of Glutathione S-transferase gene family and expression profiling under deltamethrin exposure in non-biting midge Propsilocerus akamusi. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101081. [PMID: 37150092 DOI: 10.1016/j.cbd.2023.101081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023]
Abstract
Glutathione S-transferases (GSTs) are major enzymes in detoxification phase II, and have been functioned in resistance to various insecticides or oxidative stress. Herein, we selected the non-biting midge, Propsilocerus akamusi, widespread in Asian aquatic ecosystems, to uncover the gene location, structure, and phylogenetics relationship of GSTs at genome scale first time. Thirty-three cytosolic and four microsomal GST genes were identified and located on the four chromosomes. The cytosolic GSTs involved in the eight subclasses and five GST genes were unclassified. The expansion of GST genes in P. akamusi experienced duplication events on the delta, theta, xi, iota, and unclassified subclasses. The RNA-Seq analyses and RT-qPCR validation showed that the expression of PaGSTt2 gene is significantly elevated, with deltamethrin concentration increasing. The tertiary structure of PaGSTt2 enzyme was reconstructed, which was different from the other theta gene in the active site. In addition, the GST genes of six chironomids were first described based on the assembled genomes to explore the difference of those in the adaptation to kinds of environments. The GST frame for P. akmusi and its expression profiles provide valuable resources to understand their role in insecticide resistance of this species, as well as those of other biting midges.
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Affiliation(s)
- Xiaoya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Wenbin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Yuanyuan Peng
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Lingfei Meng
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Junyu Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Yahan Pan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Deyu Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Junhao Zhu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Chengyan Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Chuncai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China.
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Su H, Xu J, Li J, Yi Z. Four ciliate-specific expansion events occurred during actin gene family evolution of eukaryotes. Mol Phylogenet Evol 2023; 184:107789. [PMID: 37105243 DOI: 10.1016/j.ympev.2023.107789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Actin gene family is a divergent and ancient eukaryotic cellular cytoskeletal gene family, and participates in many essential cellular processes. Ciliated protists offer us an excellent opportunity to investigate gene family evolution, since their gene families evolved faster in ciliates than in other eukaryotes. Nonetheless, actin gene family is well studied in few model ciliate species but little is known about its evolutionary patterns in ciliates. Here, we analyzed the evolutionary pattern of eukaryotic actin gene family based on genomes/transcriptomes of 36 species covering ten ciliate classes, as well as those of nine non-ciliate eukaryotic species. Results showed: (1) Except for conventional actins and actin-related proteins (Arps) shared by various eukaryotes, at least four ciliate-specific subfamilies occurred during evolution of actin gene family. Expansions of Act2 and ArpC were supposed to have happen in the ciliate common ancestor, while expansions of ActI and ActII may have occurred in the ancestor of Armophorea, Muranotrichea, and Spirotrichea. (2) The number of actin isoforms varied greatly among ciliate species. Environmental adaptability, whole genome duplication (WGD) or segmental duplication events, distinct spatial and temporal patterns of expression might play driving forces for the increasement of isoform numbers. (3) The 'birth and death' model of evolution could explain the evolution of actin gene family in ciliates. And actin genes have been generally under strong negative selection to maintain protein structures and physiological functions. Collectively, we provided meaningful information for understanding the evolution of eukaryotic actin gene family.
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Affiliation(s)
- Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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57
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Schelle L, Côrte-Real JV, Esteves PJ, Abrantes J, Baldauf HM. Functional cross-species conservation of guanylate-binding proteins in innate immunity. Med Microbiol Immunol 2023; 212:141-152. [PMID: 35416510 PMCID: PMC9005921 DOI: 10.1007/s00430-022-00736-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Abstract
Guanylate binding proteins (GBPs) represent an evolutionary ancient protein family widely distributed among eukaryotes. They are interferon (IFN)-inducible guanosine triphosphatases that belong to the dynamin superfamily. GBPs are known to have a major role in the cell-autonomous innate immune response against bacterial, parasitic and viral infections and are also involved in inflammasome activation. Evolutionary studies depicted that GBPs present a pattern of gain and loss of genes in each family with several genes pseudogenized and some genes more divergent, indicative for the birth-and-death evolution process. Most species harbor large GBP gene clusters encoding multiple paralogs. Previous functional studies mainly focused on mouse and human GBPs, but more data are becoming available, broadening the understanding of this multifunctional protein family. In this review, we will provide new insights and give a broad overview about GBP evolution, conservation and their roles in all studied species, including plants, invertebrates and vertebrates, revealing how far the described features of GBPs can be transferred to other species.
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Affiliation(s)
- Luca Schelle
- Faculty of Medicine, Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - João Vasco Côrte-Real
- Faculty of Medicine, Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Pedro José Esteves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- CITS-Center of Investigation in Health Technologies, CESPU, 4585-116, Gandra, Portugal
| | - Joana Abrantes
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Hanna-Mari Baldauf
- Faculty of Medicine, Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
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58
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Zhang S, Liu F, Yang B, Liu Y, Wang GR. Functional characterization of sex pheromone receptors in Spodoptera frugiperda, S. exigua, and S. litura moths. INSECT SCIENCE 2023; 30:305-320. [PMID: 35932282 DOI: 10.1111/1744-7917.13098] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Moths possess an extremely sensitive and diverse sex pheromone processing system, in which pheromone receptors (PRs) are essential to ensure communication between mating partners. Functional properties of some PRs are conserved among species, which is important for reproduction. However, functional differentiation has occurred in some homologous PR genes, which may drive species divergence. Here, using genome analysis, 17 PR genes were identified from Spodoptera frugiperda, S. exigua, and S. litura, which belong to 6 homologous groups (odorant receptor [OR]6, 11, 13, 16, 56, and 62); of which 6 PR genes (OR6, OR11, OR13, OR16, OR56, and OR62) were identified in S. frugiperda and S. exigua, and 5 PR genes were identified in S. litura, excluding OR62. Using heterologous expression in Xenopus oocytes, we characterized the functions of PR orthologs including OR6, OR56, and OR62, which have not been clarified in previous studies. OR6 orthologs were specifically tuned to (Z,E)-9,12-tetradecadienyl acetate (Z9,E12-14:OAc), and OR62 orthologs were robustly tuned to Z7-12:OAc in S. frugiperda and S. exigua. The optimal ligand for OR56 was Z7-12:OAc in S. frugiperda, but responses were minimal in S. exigua and S. litura. In addition, SfruOR6 was male antennae-specific, whereas SfruOR56 and SfruOR62 were male antennae-biased. Our study further clarified the functional properties of PRs in 3 Spodoptera moth species, providing a comprehensive understanding of the mechanisms of intraspecific communication and interspecific isolation in Spodoptera.
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Affiliation(s)
- Sai Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Fang Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Bin Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gui-Rong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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59
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Jia C, Mohamed A, Cattaneo AM, Huang X, Keyhani NO, Gu M, Zang L, Zhang W. Odorant-Binding Proteins and Chemosensory Proteins in Spodoptera frugiperda: From Genome-Wide Identification and Developmental Stage-Related Expression Analysis to the Perception of Host Plant Odors, Sex Pheromones, and Insecticides. Int J Mol Sci 2023; 24:ijms24065595. [PMID: 36982668 PMCID: PMC10056595 DOI: 10.3390/ijms24065595] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Spodoptera frugiperda is a worldwide generalist pest with remarkable adaptations to environments and stresses, including developmental stage-related behavioral and physiological adaptations, such as diverse feeding preferences, mate seeking, and pesticide resistance. Insects’ odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are essential for the chemical recognition during behavioral responses or other physiological processes. The genome-wide identification and the gene expression patterns of all these identified OBPs and CSPs across developmental stage-related S. frugiperda have not been reported. Here, we screened for genome-wide SfruOBPs and SfruCSPs, and analyzed the gene expression patterns of SfruOBPs and SfruCSPs repertoires across all developmental stages and sexes. We found 33 OBPs and 22 CSPs in the S. frugiperda genome. The majority of the SfruOBP genes were most highly expressed in the adult male or female stages, while more SfruCSP genes were highly expressed in the larval or egg stages, indicating their function complementation. The gene expression patterns of SfruOBPs and SfruCSPs revealed strong correlations with their respective phylogenic trees, indicating a correlation between function and evolution. In addition, we analyzed the chemical-competitive binding of a widely expressed protein, SfruOBP31, to host plant odorants, sex pheromones, and insecticides. Further ligands binding assay revealed a broad functional related binding spectrum of SfruOBP31 to host plant odorants, sex pheromones, and insecticides, suggesting its potential function in food, mate seeking, and pesticide resistance. These results provide guidance for future research on the development of behavioral regulators of S. frugiperda or other environmentally friendly pest-control strategies.
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Affiliation(s)
- Chen Jia
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Amr Mohamed
- Department of Entomology, Faculty of Science, Cairo University, Giza 12613, Egypt
- Division of Invertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Alberto Maria Cattaneo
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, Lomma—Campus Alnarp, 234 22 Lomma, Sweden
| | - Xiaohua Huang
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Nemat O. Keyhani
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Maiqun Gu
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Liansheng Zang
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Wei Zhang
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
- Correspondence:
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60
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Rojrung R, Kuamsab N, Putaporntip C, Jongwutiwes S. Analysis of sequence diversity in Plasmodium falciparum glutamic acid-rich protein (PfGARP), an asexual blood stage vaccine candidate. Sci Rep 2023; 13:3951. [PMID: 36894624 PMCID: PMC9996596 DOI: 10.1038/s41598-023-30975-4] [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: 01/09/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Glutamic acid-rich protein of Plasmodium falciparum (PfGARP) binds to erythrocyte band 3 and may enhance cytoadherence of infected erythrocytes. Naturally acquired anti-PfGARP antibodies could confer protection against high parasitemia and severe symptoms. While whole genome sequencing analysis has suggested high conservation in this locus, little is known about repeat polymorphism in this vaccine candidate antigen. Direct sequencing was performed from the PCR-amplified complete PfGARP gene of 80 clinical isolates from four malaria endemic provinces in Thailand and an isolate from a Guinean patient. Publicly available complete coding sequences of this locus were included for comparative analysis. Six complex repeat (RI-RVI) and two homopolymeric glutamic acid repeat (E1 and E2) domains were identified in PfGARP. The erythrocyte band 3-binding ligand in domain RIV and the epitope for mAB7899 antibody eliciting in vitro parasite killing property were perfectly conserved across isolates. Repeat lengths in domains RIII and E1-RVI-E2 seemed to be correlated with parasite density of the patients. Sequence variation in PfGARP exhibited genetic differentiation across most endemic areas of Thailand. Phylogenetic tree inferred from this locus has shown that most Thai isolates formed closely related lineages, suggesting local expansion/contractions of repeat-encoding regions. Positive selection was observed in non-repeat region preceding domain RII which corresponded to a helper T cell epitope predicted to be recognized by a common HLA class II among Thai population. Predicted linear B cell epitopes were identified in both repeat and non-repeat domains. Besides length variation in some repeat domains, sequence conservation in non-repeat regions and almost all predicted immunogenic epitopes have suggested that PfGARP-derived vaccine may largely elicit strain-transcending immunity.
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Affiliation(s)
- Rattanaporn Rojrung
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Medical Sciences Program, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Napaporn Kuamsab
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Community Public Health Program, Faculty of Health Science and Technology, Southern College of Technology, Nakorn Si Thammarat, Thailand
| | - Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Somchai Jongwutiwes
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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61
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Extensive MHC class IIβ diversity across multiple loci in the small-spotted catshark (Scyliorhinus canicula). Sci Rep 2023; 13:3837. [PMID: 36882519 PMCID: PMC9992475 DOI: 10.1038/s41598-023-30876-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
The major histocompatibility complex (MHC) is a multigene family responsible for pathogen detection, and initiation of adaptive immune responses. Duplication, natural selection, recombination, and their resulting high functional genetic diversity spread across several duplicated loci are the main hallmarks of the MHC. Although these features were described in several jawed vertebrate lineages, a detailed MHC IIβ characterization at the population level is still lacking for chondrichthyans (chimaeras, rays and sharks), i.e. the most basal lineage to possess an MHC-based adaptive immune system. We used the small-spotted catshark (Scyliorhinus canicula, Carcharhiniformes) as a case-study species to characterize MHC IIβ diversity using complementary molecular tools, including publicly available genome and transcriptome datasets, and a newly developed high-throughput Illumina sequencing protocol. We identified three MHC IIβ loci within the same genomic region, all of which are expressed in different tissues. Genetic screening of the exon 2 in 41 individuals of S. canicula from a single population revealed high levels of sequence diversity, evidence for positive selection, and footprints of recombination. Moreover, the results also suggest the presence of copy number variation in MHC IIβ genes. Thus, the small-spotted catshark exhibits characteristics of functional MHC IIβ genes typically observed in other jawed vertebrates.
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62
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Past, Present, and Future of Naturally Occurring Antimicrobials Related to Snake Venoms. Animals (Basel) 2023; 13:ani13040744. [PMID: 36830531 PMCID: PMC9952678 DOI: 10.3390/ani13040744] [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: 12/15/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/22/2023] Open
Abstract
This review focuses on proteins and peptides with antimicrobial activity because these biopolymers can be useful in the fight against infectious diseases and to overcome the critical problem of microbial resistance to antibiotics. In fact, snakes show the highest diversification among reptiles, surviving in various environments; their innate immunity is similar to mammals and the response of their plasma to bacteria and fungi has been explored mainly in ecological studies. Snake venoms are a rich source of components that have a variety of biological functions. Among them are proteins like lectins, metalloproteinases, serine proteinases, L-amino acid oxidases, phospholipases type A2, cysteine-rich secretory proteins, as well as many oligopeptides, such as waprins, cardiotoxins, cathelicidins, and β-defensins. In vitro, these biomolecules were shown to be active against bacteria, fungi, parasites, and viruses that are pathogenic to humans. Not only cathelicidins, but all other proteins and oligopeptides from snake venom have been proteolyzed to provide short antimicrobial peptides, or for use as templates for developing a variety of short unnatural sequences based on their structures. In addition to organizing and discussing an expressive amount of information, this review also describes new β-defensin sequences of Sistrurus miliarius that can lead to novel peptide-based antimicrobial agents, using a multidisciplinary approach that includes sequence phylogeny.
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63
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Dos Santos CEV, Almeida BRRD, Tavares FDS, Frade LFDS, Cardoso AL, de Sá ALA, Nagamachi CY, de Sousa LM, Pieczarka JC, Noronha RCR. Chromosomal Mapping of the Histone Multigene Family and U2 snRNA in Hypancistrus Species (Siluriformes, Loricariidae) from the Brazilian Amazon. Zebrafish 2023; 20:28-36. [PMID: 36795616 DOI: 10.1089/zeb.2022.0030] [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: 02/17/2023] Open
Abstract
Loricariidae (Siluriformes) comprises ∼1026 species of neotropical fish, being considered the most diverse among the Siluriformes. Studies on repetitive DNA sequences have provided important data on the evolution of the genomes of members of this family, especially of the Hypostominae subfamily. In this study, the chromosomal mapping of the histone multigene family and U2 snRNA was performed in two species belonging to the Hypancistrus genus, Hypancistrus sp. "pão" (2n = 52, 22m + 18sm +12st) and Hypancistrus zebra (2n = 52, 16m + 20sm +16st). The presence of dispersed signals of histones H2A, H2B, H3, and H4 in the karyotype of both species, with each sequence displaying a varied level of accumulation and dispersion of these sequences between them was observed; in addition, U2 snDNA probe only showed positive results in H. zebra, which present this multigene in the terminal region of three chromosomal pairs. The obtained results resemble data already analyzed in the literature, in which the action of transposable elements interfere in the organization of these multigene families, in addition to other evolutionary processes that shape the evolution of the genome, such as circular or ectopic recombination. This study also shows that the dispersion of the multigene histone family is quite complex, and from this, these data serve as a point of discussion for the evolutionary processes that occur in the Hypancistrus karyotype.
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Affiliation(s)
| | | | - Flávia Dos Santos Tavares
- Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Luan Felipe da Silva Frade
- Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Adauto Lima Cardoso
- Laboratório Genômica Integrativa, Departamento de Biologia Funcional e Estrutural, Instituto de Biociências, Universidade Estadual Paulista, Campus Botucatu, São Paulo, Brazil
| | - André Luiz Alves de Sá
- Laboratório de Genética Aplicada, Instituto Socioambiental e dos Recursos Hídricos, Universidade Federal Rural da Amazônia, Campus Belém, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Genética Aplicada, Instituto Socioambiental e dos Recursos Hídricos, Universidade Federal Rural da Amazônia, Campus Belém, Belém, Brazil.,Pesquisador CNPq, Brazil
| | - Leandro Melo de Sousa
- Faculdade de Ciências Biológicas, Universidade Federal do Pará, Campus de Altamira, Altamira, Brazil.,Pesquisador CNPq, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Genética Aplicada, Instituto Socioambiental e dos Recursos Hídricos, Universidade Federal Rural da Amazônia, Campus Belém, Belém, Brazil.,Pesquisador CNPq, Brazil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Genética Aplicada, Instituto Socioambiental e dos Recursos Hídricos, Universidade Federal Rural da Amazônia, Campus Belém, Belém, Brazil.,Pesquisador CNPq, Brazil
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64
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Wcisel DJ, Dornburg A, McConnell SC, Hernandez KM, Andrade J, de Jong JLO, Litman GW, Yoder JA. A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors. Immunogenetics 2023; 75:53-69. [PMID: 35869336 PMCID: PMC9845131 DOI: 10.1007/s00251-022-01270-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/01/2022] [Indexed: 01/21/2023]
Abstract
Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout, and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversity, thereby limiting our predictions for their evolutionary origin and function. In order to better understand the diversity of NILTs and their possible roles in immune function, we identified five NILT loci in the Atlantic salmon (Salmo salar) genome, defined 86 NILT Ig domains within a 3-Mbp region of zebrafish (Danio rerio) chromosome 1, and described 41 NILT Ig domains as part of an alternative haplotype for this same genomic region. We then identified transcripts encoded by 43 different NILT genes which reflect an unprecedented diversity of Ig domain sequences and combinations for a family of non-recombining receptors within a single species. Zebrafish NILTs include a sole putative activating receptor but extensive inhibitory and secreted forms as well as membrane-bound forms with no known signaling motifs. These results reveal a higher level of genetic complexity, interindividual variation, and sequence diversity for NILTs than previously described, suggesting that this gene family likely plays multiple roles in host immunity.
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Affiliation(s)
- Dustin J Wcisel
- Department of Molecular Biomedical Sciences, Comparative Medicine Institute, and Center for Human Health and the Environment, North Carolina State University, Raleigh, 27607, NC, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, 28223, NC, USA
| | - Sean C McConnell
- Section of Hematology-Oncology and Stem Cell Transplant, Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Kyle M Hernandez
- Center for Translational Data Science and Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jorge Andrade
- Center for Research Informatics, University of Chicago, Chicago, IL, USA
- Current Affiliation: Kite Pharma, Santa Monica, 90404, CA, USA
| | - Jill L O de Jong
- Section of Hematology-Oncology and Stem Cell Transplant, Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, 33701, FL, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, Comparative Medicine Institute, and Center for Human Health and the Environment, North Carolina State University, Raleigh, 27607, NC, USA.
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65
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Cao L, Chen P, Hou X, Ma J, Yang N, Xu Y, Zhang Y, Zhao A, Zhang J, Li X, Huang H. Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) × Epinephelus polyphekadion (male). JOURNAL OF FISH BIOLOGY 2023; 102:328-339. [PMID: 36317644 DOI: 10.1111/jfb.15263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Hybridization is one of the primary methods used to cultivate farmed grouper species. The hybrid grouper derived from crossing Epinephelus fuscoguttatus (♀) and E. polyphekadion (♂) exhibits growth superiority over its parents. The genetic characteristics and growth patterns of the hybrid grouper have not yet been defined. This study confirms the ploidy level of the hybrid grouper (2n = 48) using chromosome count analysis and flow cytometry. The 5S rDNA family was used to evaluate genetic diversity. Only one 5S class (~400 bp) was detected in the hybrid grouper, which could be used to distinguish between two different types based on nucleotide sequences, likely representing homologous unit classes from the female and male parental species. Growth patterns of 5-8-month-old hybrid groupers were also monitored. In this phase, a positive allometric growth pattern in body mass with total length was found. Body height and body mass were significantly correlated based on correlation and path coefficient, suggesting that body height could serve as an excellent index to increase body mass. These results aid our understanding of the genetic evolution of the hybrid grouper and inform the development of improved rearing techniques.
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Affiliation(s)
- Liu Cao
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Pan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Xingrong Hou
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Jun Ma
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Ning Yang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Yanping Xu
- Hainan Tropical Ocean University, Sanya, China
| | | | - Anqi Zhao
- Hainan Tropical Ocean University, Sanya, China
| | | | - Xinyu Li
- Hainan Tropical Ocean University, Sanya, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
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66
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Opazo JC, Vandewege MW, Hoffmann FG, Zavala K, Meléndez C, Luchsinger C, Cavieres VA, Vargas-Chacoff L, Morera FJ, Burgos PV, Tapia-Rojas C, Mardones GA. How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member. Mol Biol Evol 2023; 40:6993039. [PMID: 36656997 PMCID: PMC9897032 DOI: 10.1093/molbev/msad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.
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Affiliation(s)
| | - Michael W Vandewege
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Catalina Meléndez
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Charlotte Luchsinger
- Department of Physiology, School of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Luis Vargas-Chacoff
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Applied Biochemistry Laboratory, Facultad de Ciencias Veterinarias, Instituto de Farmacología y Morfofisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Cheril Tapia-Rojas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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67
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Bizarria R, Pietrobon TDC, Ferreira H, Rodrigues A. Polymorphisms of rDNA genes in Cyberlindnera yeast suggest birth-and-death evolution events. FEMS Yeast Res 2023; 23:foad032. [PMID: 37291697 DOI: 10.1093/femsyr/foad032] [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: 01/20/2023] [Revised: 04/28/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023] Open
Abstract
In eukaryotes, the ribosome machinery is encoded by repeats of the ribosomal RNA genes: 26/28S, 18S, 5.8S, and 5S, structured in tandem arrays and frequently homogenized within a genome. This homogenization is thought to be driven by concerted evolution, evolving as a unit, which contributes to its target as the species barcode in modern taxonomy. However, high heterogeneity of rDNA genes has been reported, including in Saccharomycotina yeasts. Here, we describe the polymorphisms and heterogeneity of D1/D2 domains (26S rRNA) and the intergenic transcribed spacer of a new yeast species with affinities to the genus Cyberlindnera and their evolution. Both regions are not homogenized, failing the prediction of concerted evolution. Phylogenetic network analysis of cloned sequences revealed that Cyberlindnera sp. rDNAs are diverse and evolved by reticulation rather than by bifurcating tree evolution model. Predicted rRNA secondary structures also confirmed structural differences, except for some conserved hairpin loops. We hypothesize that some rDNA is inactive within this species and evolves by birth-and-death rather than concerted evolution. Our findings propel further investigation into the evolution of rDNA genes in yeasts.
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Affiliation(s)
- Rodolfo Bizarria
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Tatiane de Castro Pietrobon
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Henrique Ferreira
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
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68
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Seike T, Niki H. Pheromone Response and Mating Behavior in Fission Yeast. Microbiol Mol Biol Rev 2022; 86:e0013022. [PMID: 36468849 PMCID: PMC9769774 DOI: 10.1128/mmbr.00130-22] [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] [Indexed: 12/12/2022] Open
Abstract
Most ascomycete fungi, including the fission yeast Schizosaccharomyces pombe, secrete two peptidyl mating pheromones: C-terminally modified and unmodified peptides. S. pombe has two mating types, plus and minus, which secrete two different pheromones, P-factor (unmodified) and M-factor (modified), respectively. These pheromones are specifically recognized by receptors on the cell surface of cells of opposite mating types, which trigger a pheromone response. Recognition between pheromones and their corresponding receptors is important for mate discrimination; therefore, genetic changes in pheromone or receptor genes affect mate recognition and cause reproductive isolation that limits gene flow between populations. Such genetic variation in recognition via the pheromone/receptor system may drive speciation. Our recent studies reported that two pheromone receptors in S. pombe might have different stringencies in pheromone recognition. In this review, we focus on the molecular mechanism of pheromone response and mating behavior, emphasizing pheromone diversification and its impact on reproductive isolation in S. pombe and closely related fission yeast species. We speculate that the "asymmetric" system might allow flexible adaptation to pheromone mutational changes while maintaining stringent recognition of mating partners. The loss of pheromone activity results in the extinction of an organism's lineage. Therefore, genetic changes in pheromones and their receptors may occur gradually and/or coincidently before speciation. Our findings suggest that the M-factor plays an important role in partner discrimination, whereas P-factor communication allows flexible adaptation to create variations in S. pombe. Our inferences provide new insights into the evolutionary mechanisms underlying pheromone diversification.
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Affiliation(s)
- Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
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69
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Neves F, Muñoz-Mérida A, Machado AM, Almeida T, Gaigher A, Esteves PJ, Castro LFC, Veríssimo A. Uncovering a 500 million year old history and evidence of pseudogenization for TLR15. Front Immunol 2022; 13:1020601. [PMID: 36605191 PMCID: PMC9808068 DOI: 10.3389/fimmu.2022.1020601] [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: 08/16/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Toll like receptors (TLRs) are at the front line of pathogen recognition and host immune response. Many TLR genes have been described to date with some being found across metazoans while others are restricted to specific lineages. A cryptic member of the TLR gene family, TLR15, has a unique phylogenetic distribution. Initially described in extant species of birds and reptiles, an ortholog has been reported for cartilaginous fish. Methods Here, we significantly expanded the evolutionary analysis of TLR15 gene evolution, taking advantage of large genomic and transcriptomic resources available from different lineages of vertebrates. Additionally, we objectively search for TLR15 in lobe-finned and ray-finned fish, as well as in cartilaginous fish and jawless vertebrates. Results and discussion We confirm the presence of TLR15 in early branching jawed vertebrates - the cartilaginous fish, as well as in basal Sarcopterygii - in lungfish. However, within cartilaginous fish, the gene is present in Holocephalans (all three families) but not in Elasmobranchs (its sister-lineage). Holocephalans have long TLR15 protein sequences that disrupt the typical TLR structure, and some species display a pseudogene sequence due to the presence of frameshift mutations and early stop codons. Additionally, TLR15 has low expression levels in holocephalans when compared with other TLR genes. In turn, lungfish also have long TLR15 protein sequences but the protein structure is not compromised. Finally, TLR15 presents several sites under negative selection. Overall, these results suggest that TLR15 is an ancient TLR gene and is experiencing ongoing pseudogenization in early-branching vertebrates.
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Affiliation(s)
- Fabiana Neves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,*Correspondence: Fabiana Neves,
| | - Antonio Muñoz-Mérida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M. Machado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Tereza Almeida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Pedro J. Esteves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - L. Filipe C. Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Belyakov EA, Mikhaylova YV, Machs EM, Zhurbenko PM, Rodionov AV. Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing. Sci Rep 2022; 12:21610. [PMID: 36517537 PMCID: PMC9750990 DOI: 10.1038/s41598-022-25954-0] [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: 05/31/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Sparganium is an emergent aquatic macrophyte widely spread in temperate and subtropical zones. Taxa of this genus feature high phenotypic plasticity and can produce interspecific hybrids. By means of high-throughput sequencing of the internal transcribed spacer (ITS1) of 35S rDNA, the status of 15 Eurasian Sparganium species and subspecies was clarified and the role of hybridization events in the recent evolution of the genus was investigated. It has been shown that a number of species such as S. angustifolium, S. fallax and S. subglobosum have homogenized rDNA represented by one major ribotype. The rDNA of other taxa is represented by two or more major ribotypes. Species with high rDNA heterogeneity are apparently of hybrid origin. Based on the differences in rDNA patterns, intraspecific diversity was identified in S. probatovae and S. emersum. Thus, we have concluded that Sparganium has extensive interspecific hybridization at the subgenus level, and there may also be occasional hybridization between species from different subgenera.
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Affiliation(s)
- Evgeny A. Belyakov
- grid.464570.40000 0001 1092 3616Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl Region, Nekouz District, 109, Borok, Russia 152742 ,grid.446199.70000 0000 8543 3323Cherepovets State University, Lunacharsky Ave., 5, Cherepovets, Russia 162600
| | - Yulia V. Mikhaylova
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Eduard M. Machs
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Peter M. Zhurbenko
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
| | - Aleksandr V. Rodionov
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
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71
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Rapid molecular diversification and homogenization of clustered major ampullate silk genes in Argiope garden spiders. PLoS Genet 2022; 18:e1010537. [PMID: 36508456 PMCID: PMC9779670 DOI: 10.1371/journal.pgen.1010537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/22/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
The evolutionary diversification of orb-web weaving spiders is closely tied to the mechanical performance of dragline silk. This proteinaceous fiber provides the primary structural framework of orb web architecture, and its extraordinary toughness allows these structures to absorb the high energy of aerial prey impact. The dominant model of dragline silk molecular structure involves the combined function of two highly repetitive, spider-specific, silk genes (spidroins)-MaSp1 and MaSp2. Recent genomic studies, however, have suggested this framework is overly simplistic, and our understanding of how MaSp genes evolve is limited. Here we present a comprehensive analysis of MaSp structural and evolutionary diversity across species of Argiope (garden spiders). This genomic analysis reveals the largest catalog of MaSp genes found in any spider, driven largely by an expansion of MaSp2 genes. The rapid diversification of Argiope MaSp genes, located primarily in a single genomic cluster, is associated with profound changes in silk gene structure. MaSp2 genes, in particular, have evolved complex hierarchically organized repeat units (ensemble repeats) delineated by novel introns that exhibit remarkable evolutionary dynamics. These repetitive introns have arisen independently within the genus, are highly homogenized within a gene, but diverge rapidly between genes. In some cases, these iterated introns are organized in an alternating structure in which every other intron is nearly identical in sequence. We hypothesize that this intron structure has evolved to facilitate homogenization of the coding sequence. We also find evidence of intergenic gene conversion and identify a more diverse array of stereotypical amino acid repeats than previously recognized. Overall, the extreme diversification found among MaSp genes requires changes in the structure-function model of dragline silk performance that focuses on the differential use and interaction among various MaSp paralogs as well as the impact of ensemble repeat structure and different amino acid motifs on mechanical behavior.
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72
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Novel selectively amplified DNA sequences in the germline genome of the Japanese hagfish, Eptatretus burgeri. Sci Rep 2022; 12:21373. [PMID: 36494570 PMCID: PMC9734144 DOI: 10.1038/s41598-022-26007-2] [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: 07/16/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
In the Japanese hagfish Eptatretus burgeri, 16 chromosomes (eliminated [E]-chromosomes) have been lost in somatic cells (2n = 36), which is equivalent to approx. 21% of the genomic DNA in germ cells (2n = 52). At least seven of the 12 eliminated repetitive DNA families isolated in eight hagfish species were selectively amplified in the germline genome of this species. One of them, EEEb1 (eliminated element of E. burgeri 1) is exclusively localized on all E-chromosomes. Herein, we identified four novel eliminated repetitive DNA families (named EEEb3-6) through PCR amplification and suppressive subtractive hybridization (SSH) combined with Southern-blot hybridization. EEEb3 was mosaic for 5S rDNA and SINE elements. EEEb4 was GC-rich repeats and has one pair of direct and inverted repeats, whereas EEEb5 and EEEb6 were AT-rich repeats with one pair and two pairs of sub-repeats, respectively. Interestingly, all repeat classes except EEEb3 were transcribed in the testes, although no open reading frames (ORF) were identified. We conducted fluorescence in situ hybridization (FISH) to examine the chromosomal localizations of EEEb3-6 and EEEb2, which was previously isolated from the germline genome of E. burgeri. All sequences were only found on all EEEb1-positive E-chromosomes. Copy number estimation of the repeated elements by slot-blot hybridization revealed that (i) the EEEb1-6 family members occupied 39.9% of the total eliminated DNA, and (ii) a small number of repeats were retained in somatic cells, suggesting that there is incomplete elimination of the repeated elements. These results provide new insights into the mechanisms involved in the chromosome elimination and the evolution of E-chromosomes.
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73
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Dearborn DC, Warren S, Hailer F. Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species. Mol Ecol 2022; 31:6390-6406. [PMID: 36208104 PMCID: PMC9729452 DOI: 10.1111/mec.16726] [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: 03/21/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analysed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future studies should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.
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Affiliation(s)
- Donald C Dearborn
- Biology Department, Bates College, 44 Campus Ave, Lewiston, Maine, USA,Roux Institute, Northeastern University, Fore St, Portland, Maine, USA,Co-corresponding authors: and
| | - Sophie Warren
- Biology Department, Bates College, 44 Campus Ave, Lewiston, Maine, USA,Present address: Department of Health Policy, London School of Economics and Political Science, Houghton Street, London WC2A 2AE, UK
| | - Frank Hailer
- Organisms and Environment, School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK,Co-corresponding authors: and
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74
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Sultanov D, Hochwagen A. Varying strength of selection contributes to the intragenomic diversity of rRNA genes. Nat Commun 2022; 13:7245. [PMID: 36434003 PMCID: PMC9700816 DOI: 10.1038/s41467-022-34989-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Ribosome biogenesis in eukaryotes is supported by hundreds of ribosomal RNA (rRNA) gene copies that are encoded in the ribosomal DNA (rDNA). The multiple copies of rRNA genes are thought to have low sequence diversity within one species. Here, we present species-wide rDNA sequence analysis in Saccharomyces cerevisiae that challenges this view. We show that rDNA copies in this yeast are heterogeneous, both among and within isolates, and that many variants avoided fixation or elimination over evolutionary time. The sequence diversity landscape across the rDNA shows clear functional stratification, suggesting different copy-number thresholds for selection that contribute to rDNA diversity. Notably, nucleotide variants in the most conserved rDNA regions are sufficiently deleterious to exhibit signatures of purifying selection even when present in only a small fraction of rRNA gene copies. Our results portray a complex evolutionary landscape that shapes rDNA sequence diversity within a single species and reveal unexpectedly strong purifying selection of multi-copy genes.
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Affiliation(s)
- Daniel Sultanov
- grid.137628.90000 0004 1936 8753Department of Biology, New York University, New York, NY 10003 USA
| | - Andreas Hochwagen
- grid.137628.90000 0004 1936 8753Department of Biology, New York University, New York, NY 10003 USA
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75
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Volonté M, Traverso L, Estivalis JML, Almeida FC, Ons S. Comparative analysis of detoxification-related gene superfamilies across five hemipteran species. BMC Genomics 2022; 23:757. [PMCID: PMC9670383 DOI: 10.1186/s12864-022-08974-y] [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: 05/17/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022] Open
Abstract
Background Hemiptera is one of the most speciose orders of insects, and the most speciose considering Hemimetabola. Through their evolutive history, hemipterans with different feeding habits have adapted to deal with different chemical challenges. Three major gene families are involved in xenobiotic detoxification in insects: the cytochromes P450 (CYPs), carboxyl/cholinesterases (CCEs), and glutathione transferases (GSTs). Here we perform a comparative analysis on the complement of these gene superfamilies across five hemipteran species; four heteropterans (the pentatomid plant feeders Nezara viridula and Halyomorpha halys; the hematophagous Cimex lectularius, Cimicidae, and Rhodnius prolixus, Reduviidae), and one Auchenorrhyncha plant feeder (Nilaparvata lugens). Results Our results point to an expansion of several enzyme families associated with xenobiotic detoxification in heteropterans with respect to other species and the existence of a dynamic evolution pattern including CYP3 clan, hormone and pheromone processing class in the CCE superfamily, and sigma class in GST superfamily. Other detoxification-related families are reduced in the hemipteran species analyzed here: reduction or even absence of epsilon class and reduced delta class in GST superfamily; absence of mitochondrial CYP12 family; absence of CYP9 family in CYP3 clan; and reduction or even absence of some dietary/detoxification groups of CCEs. Interestingly, the most polyphagous species analyzed here (H. halys) is also the one that presents the largest repertoire of detoxification enzymes. Gene cluster analysis suggests that this could be due to gene duplication events. Conclusions The evolutionary analysis performed here reveals characteristics that are both common and particular for heteropterans. The composition and organization of detoxification-related gene families could shed light on evolutionary forces that shaped their divergence. These families are important for both the detoxification of diet products and for conferring tolerance or resistance to synthetic insecticides. Furthermore, we present the first comprehensive analysis of detoxification gene superfamilies in N. viridula, an understudied species in spite of its economic relevance as a crop pest. The information obtained is of interest for basic insect science as well as for the control of harmful species and the management of insecticide resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08974-y.
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Affiliation(s)
- Mariano Volonté
- grid.9499.d0000 0001 2097 3940Laboratorio de Neurobiología de Insectos (LNI), Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CENEXA, CONICET, La Plata, Buenos Aires Argentina
| | - Lucila Traverso
- grid.9499.d0000 0001 2097 3940Laboratorio de Neurobiología de Insectos (LNI), Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CENEXA, CONICET, La Plata, Buenos Aires Argentina
| | - Jose Manuel Latorre Estivalis
- grid.7345.50000 0001 0056 1981Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias, Universidad de Buenos Aires – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Francisca Cunha Almeida
- grid.7345.50000 0001 0056 1981Grupo de Investigación en Filogeografía y Filogenias Moleculares, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sheila Ons
- grid.9499.d0000 0001 2097 3940Laboratorio de Neurobiología de Insectos (LNI), Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CENEXA, CONICET, La Plata, Buenos Aires Argentina
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76
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Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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LaJeunesse TC, Casado-Amezúa P, Hume BCC, Butler CC, Mordret S, Piredda R, De Luca P, Pannone R, Sarno D, Wiedenmann J, D’Ambra I. Mutualistic dinoflagellates with big disparities in ribosomal DNA variation may confound estimates of symbiont diversity and ecology in the jellyfish Cotylorhiza tuberculata. Symbiosis 2022. [DOI: 10.1007/s13199-022-00880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Yohe LR, Fabbri M, Lee D, Davies KTJ, Yohe TP, Sánchez MKR, Rengifo EM, Hall RP, Mutumi G, Hedrick BP, Sadier A, Simmons NB, Sears KE, Dumont E, Rossiter SJ, Bhullar BAS, Dávalos LM. Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats. Evolution 2022; 76:2347-2360. [PMID: 35904467 DOI: 10.1111/evo.14591] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 01/22/2023]
Abstract
Although evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant visiting from a presumed insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants-a potential ecological constraint on sensory evolution.
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Affiliation(s)
- Laurel R Yohe
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Deaprtment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA.,North Carolina Research Campus, Kannapolis, North Carolina, 28081, USA
| | - Matteo Fabbri
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Daniela Lee
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Harvard School of Medicine, Cambridge, Massachusetts, 02115, USA
| | - Kalina T J Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | | | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, 20004, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13416-970, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, 15073, Peru
| | - Ronald P Hall
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Gregory Mutumi
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Brandon P Hedrick
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, New York, 10024, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Elizabeth Dumont
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Bhart-Anjan S Bhullar
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Yale Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06511, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Center for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, 11794, USA
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Targueta CP, Gatto KP, Vittorazzi SE, Recco-Pimentel SM, Lourenço LB. High diversity of 5S ribosomal DNA and evidence of recombination with the satellite DNA PcP190 in frogs. Gene 2022; 851:147015. [DOI: 10.1016/j.gene.2022.147015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/25/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
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Jeckel AM, Beran F, Züst T, Younkin G, Petschenka G, Pokharel P, Dreisbach D, Ganal-Vonarburg SC, Robert CAM. Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches. Front Physiol 2022; 13:1001032. [PMID: 36237530 PMCID: PMC9552321 DOI: 10.3389/fphys.2022.1001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Herbivorous insects encounter diverse plant specialized metabolites (PSMs) in their diet, that have deterrent, anti-nutritional, or toxic properties. Understanding how they cope with PSMs is crucial to understand their biology, population dynamics, and evolution. This review summarizes current and emerging cutting-edge methods that can be used to characterize the metabolic fate of PSMs, from ingestion to excretion or sequestration. It further emphasizes a workflow that enables not only to study PSM metabolism at different scales, but also to tackle and validate the genetic and biochemical mechanisms involved in PSM resistance by herbivores. This review thus aims at facilitating research on PSM-mediated plant-herbivore interactions.
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Affiliation(s)
- Adriana Moriguchi Jeckel
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Franziska Beran
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tobias Züst
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Gordon Younkin
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Georg Petschenka
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Prayan Pokharel
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Domenic Dreisbach
- Institute for Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Stephanie Christine Ganal-Vonarburg
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Christelle Aurélie Maud Robert
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
- *Correspondence: Christelle Aurélie Maud Robert,
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81
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Krause DJ, Hittinger CT. Functional Divergence in a Multi-gene Family Is a Key Evolutionary Innovation for Anaerobic Growth in Saccharomyces cerevisiae. Mol Biol Evol 2022; 39:6711080. [PMID: 36134526 PMCID: PMC9551191 DOI: 10.1093/molbev/msac202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The amplification and diversification of genes into large multi-gene families often mark key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression of seven serine/threonine-rich anaerobically-induced cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here, we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event. Based on synteny and their phylogeny, we separate the anCWMPs into four gene subfamilies. To resolve prior inconclusive genetic investigations of these genes, we constructed a set of combinatorial deletion mutants to determine their contributions toward anaerobic growth in S. cerevisiae. We found that two genes, TIR1 and TIR3, were together necessary and sufficient for the anCWMP contribution to anaerobic growth. Overexpressing either gene alone was insufficient for anaerobic growth, implying that they encode non-overlapping functional roles in the cell during anaerobic growth. We infer from the phylogeny of the anCWMP genes that these two important genes derive from an ancient duplication that predates the WGD event, whereas the TIR1 subfamily experienced gene family amplification after the WGD event. Taken together, the genetic and molecular evidence suggests that one key anCWMP gene duplication event, several auxiliary gene duplication events, and functional divergence underpin the evolution of anaerobic growth in budding yeasts.
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Affiliation(s)
- David J Krause
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI
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82
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Li T, Bian J, Tang M, Shangguan H, Zeng Y, Luo R, Sun H, Ke Q, Nie X, Li Y, Cui L. BGFD: an integrated multi-omics database of barley gene families. BMC PLANT BIOLOGY 2022; 22:454. [PMID: 36131236 PMCID: PMC9490965 DOI: 10.1186/s12870-022-03846-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND A gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies. Systematic identification and annotation of gene families are key for studies of molecular function and evolutionary history. RESULTS We constructed a multi-omics database containing 5593 genes of 77 gene families called the Barley Gene Family Database (BGFD: http://barleygfdb.com ). BGFD is a free, user-friendly, and web-accessible platform that provides data on barley family genes. BGFD provides intuitive visual displays to facilitate studies of the physicochemical properties, gene structure, phylogenetic relationships, and motif organization of genes. Massive multi-omics datasets have been acquired and processed to generate an atlas of expression pattern profiles and genetic variation in BGFD. The platform offers several practical toolkits to conduct searches, browse, and employ BLAST functions, and the data are downloadable. CONCLUSIONS BGFD will aid research on the domestication and adaptive evolution of barley; it will also facilitate the screening of candidate genes and exploration of important agronomic traits in barley.
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Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong China
| | - Minqiang Tang
- College of Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Hongbin Shangguan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Huifan Sun
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Qinglin Ke
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
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83
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Immunoglobulin heavy constant gamma gene evolution is modulated by both the divergent and birth-and-death evolutionary models. Primates 2022; 63:611-625. [DOI: 10.1007/s10329-022-01019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022]
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84
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Fu Q, Hu J, Zhang P, Li Y, Zhao S, Cao M, Yang N, Li C. CC and CXC chemokines in turbot (Scophthalmus maximus L.): Identification, evolutionary analyses, and expression profiling after Aeromonas salmonicida infection. FISH & SHELLFISH IMMUNOLOGY 2022; 127:82-98. [PMID: 35690275 DOI: 10.1016/j.fsi.2022.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 05/06/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Chemokines are a superfamily of structurally related cytokines, which exert essential roles in guiding cell migration in development, homeostasis, and immunity. CC and CXC chemokines are the two major subfamilies in teleost species. In this study, a total of seventeen CC and CXC chemokines, with inclusion of twelve CC and five CXC chemokines, were systematically identified from the turbot genome, making turbot the teleost harboring the least number of CC and CXC chemokines among all teleost species ever reported. Phylogeny, synteny, and genomic organization analyses were performed to annotate these genes, and multiple chemokine genes were identified in the turbot genome, due to the tandem duplications (CCL19 and CCL20), the whole genome duplications (CCL20, CCL25, and CXCL12), and the teleost-specific members (CCL34-36, CCL44, and CXCL18). In addition, chemokines were ubiquitously expressed in nine examined healthy tissues, with high expression levels observed in liver, gill, and spleen. Moreover, most chemokines were significantly differentially expressed in gill and spleen after Aeromonas salmonicida infection, and exhibited tissue-specific and time-dependent manner. Finally, protein-protein interaction network (PPI) analysis indicated that turbot chemokines interacted with a few immune-related genes such as interleukins, cathepsins, stats, and TLRs. These results should be valuable for comparative immunological studies and provide insights for further functional characterization of chemokines in teleost.
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Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Hu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Pei Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuqing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shoucong Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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85
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Meslin C, Mainet P, Montagné N, Robin S, Legeai F, Bretaudeau A, Johnston JS, Koutroumpa F, Persyn E, Monsempès C, François MC, Jacquin-Joly E. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae. G3 (BETHESDA, MD.) 2022; 12:6598846. [PMID: 35652787 PMCID: PMC9339325 DOI: 10.1093/g3journal/jkac131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022]
Abstract
The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.
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Affiliation(s)
- Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Pauline Mainet
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Stéphanie Robin
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, 35042 Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes 5042, France
| | - Fabrice Legeai
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, 35042 Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes 5042, France
| | - Anthony Bretaudeau
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, 35042 Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes 5042, France
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Fotini Koutroumpa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France.,Present address: INRAE, Université Tours, Infectiologie et Santé Publique (ISP), 37380 Nouzilly, France
| | - Emma Persyn
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France.,CIRAD, UMR PVBMT, Réunion, France
| | - Christelle Monsempès
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Marie-Christine François
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
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86
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Xue M, Huang X, Xue J, He R, Liang G, Liang H, Liu J, Wen C. Comparative Genomic Analysis of Seven Vibrio alginolyticus Strains Isolated From Shrimp Larviculture Water With Emphasis on Chitin Utilization. Front Microbiol 2022; 13:925747. [PMID: 35966654 PMCID: PMC9364117 DOI: 10.3389/fmicb.2022.925747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
The opportunistic pathogen Vibrio alginolyticus is gaining attention because of its disease-causing risks to aquatic animals and humans. In this study, seven Vibrio strains isolated from different shrimp hatcheries in Southeast China were subjected to genome sequencing and subsequent comparative analysis to explore their intricate relationships with shrimp aquaculture. The seven isolates had an average nucleotide identity of ≥ 98.3% with other known V. alginolyticus strains. The species V. alginolyticus had an open pan-genome, with the addition of ≥ 161 novel genes following each new genome for seven isolates and 14 publicly available V. alginolyticus strains. The percentages of core genes of the seven strains were up to 83.1–87.5%, indicating highly conserved functions, such as chitin utilization. Further, a total of 14 core genes involved in the chitin degradation pathway were detected on the seven genomes with a single copy, 12 of which had undergone significant purifying selection (dN/dS < 1). Moreover, the seven strains could utilize chitin as the sole carbon-nitrogen source. In contrast, mobile genetic elements (MGEs) were identified in seven strains, including plasmids, prophages, and genomic islands, which mainly encoded accessory genes annotated as hypothetical proteins. The infection experiment showed that four of the seven strains might be pathogenic because the survival rates of Litopenaeus vannamei postlarvae were significantly reduced (P < 0.05) when compared to the control. However, no obvious correlation was noted between the number of putative virulence factors and toxic effects of the seven strains. Collectively, the persistence of V. alginolyticus in various aquatic environments may be attributed to its high genomic plasticity via the acquisition of novel genes by various MGEs. In view of the strong capability of chitin utilization by diverse vibrios, the timely removal of massive chitin-rich materials thoroughly in shrimp culture systems may be a key strategy to inhibit proliferation of vibrios and subsequent infection of shrimp. In addition, transcontinental transfer of potentially pathogenic V. alginolyticus strains should receive great attention to avoid vibriosis.
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87
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Copy number changes in co-expressed odorant receptor genes enable selection for sensory differences in drosophilid species. Nat Ecol Evol 2022; 6:1343-1353. [PMID: 35864227 DOI: 10.1038/s41559-022-01830-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
Despite numerous examples of chemoreceptor gene family expansions and contractions, how these relate to modifications in the sensory neuron populations in which they are expressed remains unclear. Drosophila melanogaster's odorant receptor (Or) family is ideal for addressing this question because most Ors are expressed in distinct olfactory sensory neuron (OSN) types. Between-species changes in Or copy number may therefore indicate increases or reductions in the number of OSN populations. Here we investigated the Or67a subfamily, which exhibits copy number variation in D. melanogaster and its closest relatives: D. simulans, D. sechellia and D. mauritiana. These species' common ancestor had three Or67a paralogues that had already diverged adaptively. Following speciation, two Or67a paralogues were lost independently in D. melanogaster and D. sechellia, with ongoing positive selection shaping the intact genes. Unexpectedly, the functionally diverged Or67a paralogues in D. simulans are co-expressed in a single neuron population, which projects to a glomerulus homologous to that innervated by Or67a neurons in D. melanogaster. Thus, while sensory pathway neuroanatomy is conserved, independent selection on co-expressed receptors has contributed to species-specific peripheral coding. This work reveals a type of adaptive change largely overlooked for olfactory evolution, raising the possibility that similar processes influence other cases of insect Or co-expression.
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88
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Noronha RCR, Almeida BRR, Chagas MCS, Tavares FS, Cardoso AL, Bastos CEMC, Silva NKN, Klautau AGCM, Luna FO, Attademo FLN, Lima DS, Sabioni LA, Sampaio MIC, Oliveira JM, do Nascimento LAS, Martins C, Vicari MR, Nagamachi CY, Pieczarka JC. Karyotypes of Manatees: New Insights into Hybrid Formation ( Trichechus inunguis × Trichechus m. manatus) in the Amazon Estuary. Genes (Basel) 2022; 13:1263. [PMID: 35886048 PMCID: PMC9323068 DOI: 10.3390/genes13071263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Great efforts have been made to preserve manatees. Recently, a hybrid zone was described between Trichechus inunguis (TIN) and the Trichechus manatus manatus (TMM) in the Amazon estuary. Cytogenetic data on these sirenians are limited, despite being fundamental to understanding the hybridization/introgression dynamics and genomic organization in Trichechus. We analyzed the karyotype of TMM, TIN, and two hybrid specimens ("Poque" and "Vitor") by classical and molecular cytogenetics. G-band analysis revealed that TMM (2n = 48) and TIN (2n = 56) diverge by at least six Robertsonian translocations and a pericentric inversion. Hybrids had 2n = 50, however, with Autosomal Fundamental Number (FNA) = 88 in "Poque" and FNA = 74 in "Vitor", and chromosomal distinct pairs in heterozygous; additionally, "Vitor" exhibited heteromorphisms and chromosomes whose pairs could not be determined. The U2 snDNA and Histone H3 multi genes are distributed in small clusters along TIN and TMM chromosomes and have transposable Keno and Helitron elements (TEs) in their sequences. The different karyotypes observed among manatee hybrids may indicate that they represent different generations formed by crossing between fertile hybrids and TIN. On the other hand, it is also possible that all hybrids recorded represent F1 and the observed karyotype differences must result from mechanisms of elimination.
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Affiliation(s)
- Renata C. R. Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Bruno R. R. Almeida
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
- Campus Itaituba, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Itaituba 68183-300, PA, Brazil
| | - Monique C. S. Chagas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Flávia S. Tavares
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Adauto L. Cardoso
- Laboratório Genômica Integrativa, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brazil; (A.L.C.); (C.M.)
| | - Carlos E. M. C. Bastos
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Natalia K. N. Silva
- Campus Tucuruí, Universidade do Estado do Pará, Tucuruí 68455-210, PA, Brazil;
| | - Alex G. C. M. Klautau
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte, Instituto Chico Mendes de Conservação da Biodiversidade, Belém 66635-110, PA, Brazil;
| | - Fábia O. Luna
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Instituto Chico Mendes de Conservação de Biodiversidade, Santos 11050-031, SP, Brazil; (F.O.L.); (F.L.N.A.)
| | - Fernanda L. N. Attademo
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Instituto Chico Mendes de Conservação de Biodiversidade, Santos 11050-031, SP, Brazil; (F.O.L.); (F.L.N.A.)
- Departamento de Zoologia, Programa de Pós-Graduação em Biologia Animal/PPBA, Laboratório de Ecologia Comportamento e Conservação/LECC, Universidade Federal de Pernambuco/UFPE, Recife 50670-901, PE, Brazil
| | - Danielle S. Lima
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos, Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, Tefé 69553-225, AM, Brazil; (D.S.L.); (L.A.S.)
- Rede de Pesquisa e Conservação de Sirênios no Estuário Amazônico, Macapá 68903-197, AP, Brazil
| | - Luiz A. Sabioni
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos, Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, Tefé 69553-225, AM, Brazil; (D.S.L.); (L.A.S.)
- Rede de Pesquisa e Conservação de Sirênios no Estuário Amazônico, Macapá 68903-197, AP, Brazil
- Campus Porto Grande, Instituto Federal de Educação Ciência e Tecnologia do Amapá, Rodovia BR 210, Km 103, s/n, Zona Rural, Porto Grande 68997-000, AP, Brazil
| | - Maria I. C. Sampaio
- Instituto de Estudos Costeiros, Campus Bragança, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil;
| | - Jairo Moura Oliveira
- Zoological Park of Santarém, ZOOUNAMA, Universidade da Amazônia, Santarém 68030-150, PA, Brazil;
| | | | - Cesar Martins
- Laboratório Genômica Integrativa, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brazil; (A.L.C.); (C.M.)
| | - Marcelo R. Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil;
| | - Cleusa Y. Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Julio C. Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
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89
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Comparisons of chemosensory gene repertoires in human and non-human feeding Anopheles mosquitoes link olfactory genes to anthropophily. iScience 2022; 25:104521. [PMID: 35754720 PMCID: PMC9213756 DOI: 10.1016/j.isci.2022.104521] [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: 12/09/2021] [Revised: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/06/2022] Open
Abstract
We investigate the genetic basis of anthropophily (human host use) in a non-model mosquito species group, the Anopheles farauti complex from the southwest Pacific. This complex has experienced multiple transitions from anthropophily to zoophily, contrasting with well-studied systems (the global species Aedes aegypti and the African Anopheles gambiae complex) that have evolved to be specialist anthropophiles. By performing tests of selection and assessing evolutionary patterns for >200 olfactory genes from nine genomes, we identify several candidate genes associated with differences in anthropophily in this complex. Based on evolutionary patterns (phylogenetic relationships, fixed amino acid differences, and structural differences) as well as results from selection analyses, we identify numerous genes that are likely to play an important role in mosquitoes’ ability to detect humans as hosts. Our findings contribute to the understanding of the evolution of insect olfactory gene families and mosquito host preference as well as having potential applied outcomes. Genomes of Anopheles mosquitoes with differing host preferences were sequenced Evolutionary comparisons were performed on >200 insect chemosensory genes These comparisons revealed candidate genes involved in human feeding Two of the main candidates identified were co-receptor Ir8a and Or75
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90
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Shi Y, Sun S, Zhang Y, He Y, Du M, ÓReilly AO, Wu S, Yang Y, Wu Y. Single amino acid variations drive functional divergence of cytochrome P450s in Helicoverpa species. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 146:103796. [PMID: 35636594 DOI: 10.1016/j.ibmb.2022.103796] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Divergence of gene function is a hallmark of evolution, but assessing such divergence in one species or between species requires information on functional alterations of the alleles and homologs. Here, we explore the functional divergence of two paralogs, CYP6AE19 and CYP6AE20, from Helicoverpa armigera, and two close orthologs, CYP6B8 and CYP6B7, from two related species (Helicoverpa zea and H. armigera); although there is high sequence identity within each pair of enzymes, the latter P450 of each pair has lost metabolic competence towards the plant allelochemical xanthotoxin. Multiple chimeric and single/double site mutants were created by exchanging the diverse substrate recognition sites (SRSs) and amino acids within each pair of P450s. Heterologous expression in Sf9 cells and in vitro metabolism studies showed that the exchange of SRS4 swapped the activity of CYP6AE19 and CYP6AE20, and subsequent site-directed mutagenesis demonstrated that the CYP6AE20 V318M substitution causes a gain-of-function towards xanthotoxin. Meanwhile, a single amino acid substitution (L489P) in SRS6 was found to swap activity between the CYP6B orthologs. Sequence alignments of CYP6AE paralogs and all reported insect xanthotoxin-metabolizing P450s suggest M318 and P489 are essential for the catalytic activities of CYP6AE paralogs and CYP6B orthologs, respectively, but P450s in different subfamilies may have different mechanisms towards the same substrate. Our findings demonstrate that a single amino acid substitution can suffice to alter substrate metabolism and this functional divergence resulting from natural mutations will help to further our understanding of the process of natural selection of P450 genes and their role in insect-host plant interactions.
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Affiliation(s)
- Yu Shi
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shuo Sun
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yujun Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yingshi He
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Minghong Du
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Andrias O ÓReilly
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, UK.
| | - Shuwen Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yihua Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yidong Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
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91
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Cheng L, Song D, Yu X, Du X, Huo T. Endangered Schizothoracin Fish in the Tarim River Basin Are Threatened by Introgressive Hybridization. BIOLOGY 2022; 11:biology11070981. [PMID: 36101362 PMCID: PMC9311807 DOI: 10.3390/biology11070981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/17/2022] [Accepted: 06/24/2022] [Indexed: 11/23/2022]
Abstract
Simple Summary Interspecific hybridization and introgression may threaten the survival of endangered species. Big-head Schizothoracin (Aspiorhynchus laticeps) and Tarim Schizothoracin (Schizothorax biddulphi) are two recognized types of fish of Schizothoracinae which belong to the family Cyprinidae. Big-head Schizothoracin and Tarim Schizothoracin are sympatrically distributed in the Tarim River basin in Xinjiang, China, and have been listed as first-class and second-class national key protected animals, respectively. Based on morphological characteristics, Schizothorax esocinus (another Schizothoracin that occurs in the Tarim River basin) is speculated to be hybrid offspring of Big-head Schizothoracin and Tarim Schizothoracin, but there is no direct genetic evidence for this point. In this study, the hybridization status of Schizothorax esocinus was confirmed by comparing genetic constitutions of mitochondrial DNA (mtDNA) and inter transcribed spacer (ITS2) encoded by the nuclear genome. Extensive hybridization and introgression between Big-head Schizothoracin and Tarim Schizothoracin was detected. Since both Big-head Schizothoracin and Tarim Schizothoracin are critically endangered fishes, risk management due to hybridization is recommended to be considered as a part of current conservation programs. Abstract Big-head Schizothoracin (Aspiorhynchus laticeps) and Tarim Schizothoracin (Schizothorax biddulphi) are locally sympatric in the Tarim River Basin. Although another Schizothoracin (Schizothorax esocinus) in Tarim River basin has been speculated to be hybrid offspring of Big-head Schizothoracin and Tarim Schizothoracin, there was no genetic evidence. Previous studies on the genetics and evolution of Schizothoracins in Xinjiang Province were mostly based on mitochondrial DNA (mtDNA), whose characteristics of maternal inheritance made it hard to answer the question of whether there was hybridization and introgression between Big-head Schizothoracin and Tarim Schizothoracin. In this study, cytochrome b (cytb) gene of mtDNA and internal transcribed spacer 2 (ITS2) that is encoded by the nuclear genome were genotyped within the entire samples at the same time. Our results confirmed that Schizothorax esocinus was the hybrid offspring of Big-head Schizothoracin and Tarim Schizothoracin. The heterozygous ITS2 genotypes and/or Aspiorhynchus laticeps-like mtDNA were also detected in a subset of samples that should have been identified as pure Schizothorax biddulphi based on morphology. The ITS2 is characterized by multi-copy, concert evolution, and biparental inheritance. Thus, by comparing with mtDNA data, broad-scale bidirectional hybridization and introgression between Big-head Schizothoracin and Tarim Schizothoracin were revealed. Although interspecific hybridization may play a positive role in ecology and evolution, interspecific hybrids could threaten their parental species by the swamping of genetics and demography. As both parents of hybridization are critically endangered fishes, in this case, it is urgently necessary to strengthen the scientific assessment of the risks of the hybrids and the control of the hybridization and introgression between Aspiorhynchus laticeps and Schizothorax biddulphi in the Tarim River Basin.
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Affiliation(s)
| | | | | | - Xue Du
- Correspondence: (X.D.); (T.H.)
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92
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Haig D. Paradox lost: Concerted evolution and centromeric instability: Centromeres are hospitable habitats for repeats that evolve adaptations for proliferation within the nucleus sometimes at organismal cost.: Centromeres are hospitable habitats for repeats that evolve adaptations for proliferation within the nucleus sometimes at organismal cost. Bioessays 2022; 44:e2200023. [PMID: 35748194 DOI: 10.1002/bies.202200023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022]
Abstract
Homologous centromeres compete for segregation to the secondary oocyte nucleus at female meiosis I. Centromeric repeats also compete with each other to populate centromeres in mitotic cells of the germline and have become adapted to use the recombinational machinery present at centromeres to promote their own propagation. Repeats are not needed at centromeres, rather centromeres appear to be hospitable habitats for the colonization and proliferation of repeats. This is probably an indirect consequence of two distinctive features of centromeric DNA. Centromeres are subject to breakage by the mechanical forces exerted by microtubules and meiotic crossing-over is suppressed. Centromeric proteins acting in trans are under selection to mitigate the costs of centromeric repeats acting in cis. Collateral costs of mitotic competition at centromeres may help to explain the high rates of aneuploidy observed in early human embryos.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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93
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Solovyev VI, Dubatolov VV, Vavilova VY, Kosterin OE. Estimating range disjunction time of the Palearctic Admirals (Limenitis L.) with COI and histone H1 genes. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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94
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Azambuja M, Orane Schemberger M, Nogaroto V, Moreira-Filho O, Martins C, Ricardo Vicari M. Major and minor U small nuclear RNAs genes characterization in a neotropical fish genome: Chromosomal remodeling and repeat units dispersion in Parodontidae. Gene 2022; 826:146459. [PMID: 35358649 DOI: 10.1016/j.gene.2022.146459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/15/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Abstract
In association with many proteins, small nuclear RNAs (snRNAs) organize the spliceosomes that play a significant role in processing precursor mRNAs during gene expression. According to snRNAs genic arrangements, two kinds of spliceosomes (major and minor) can be organized into eukaryotic cells. Although in situ localization of U1 and U2 snDNAs have been performed in fish karyotypes, studies with genomic characterization and functionality of U snRNAs integrated into chromosomal changes on Teleostei are still scarce. This study aimed to achieve a genomic characterization of the U snRNAs genes in Apareiodon sp. (2n = 54, ZZ/ZW), apply these data to recognize functional/defective copies, and map chromosomal changes involving snDNAs in Parodontidae species karyotype diversification. Nine snRNA multigene families (U1, U2, U4, U5, U6, U11, U12, U4atac and U6atac) arranged in putatively functional copies in the genome were analyzed. Proximal Sequence Elements (PSE) and TATA-box promoters occurrence, besides an entire transcribed region and conserved secondary structures, qualify them for spliceosome activity. In addition, several defective copies or pseudogenes were identified for the snRNAs that make up the major spliceosome. In situ localization of snDNAs in five species of Parodontidae demonstrated that U1, U2, and U4 snDNAs were involved in chromosomal location changes or units dispersion. The U snRNAs defective/pseudogenes units dispersion could be favored by the probable occurrence of active retrotransposition enzymes in the Apareiodon genome. The U2 and U4 snDNAs sites were involved in independent events in the differentiation of sex chromosomes among Parodontidae lineages. The study characterized U snRNA genes that compose major and minor spliceosomes in the Apareiodon sp. genome and proposes that their defective copies trigger chromosome differentiation and diversification events in Parodontidae.
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Affiliation(s)
- Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil.
| | - Michelle Orane Schemberger
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil.
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, Paraná, Brazil.
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Carlos, São Paulo, Brazil.
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, s/n, 18618-689 Botucatu, São Paulo, Brazil.
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil; Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, Paraná, Brazil.
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95
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Roved J, Hansson B, Stervander M, Hasselquist D, Westerdahl H. MHCtools - an R package for MHC high-throughput sequencing data: genotyping, haplotype and supertype inference, and downstream genetic analyses in non-model organisms. Mol Ecol Resour 2022; 22:2775-2792. [PMID: 35587892 PMCID: PMC9543685 DOI: 10.1111/1755-0998.13645] [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: 03/12/2020] [Revised: 04/11/2022] [Accepted: 05/11/2022] [Indexed: 11/30/2022]
Abstract
The major histocompatibility complex (MHC) plays a central role in the vertebrate adaptive immune system and has been of long-term interest in evolutionary biology. While several protocols have been developed for MHC genotyping, there is a lack of transparent and standardized tools for downstream analysis of MHC data. Here, we present the R package MHCtools and demonstrate the use of its functions to (i) assist accurate MHC genotyping from high-throughput amplicon-sequencing data, (ii) infer functional MHC supertypes using bootstrapped clustering analysis, (iii) identify segregating MHC haplotypes from family data, and (iv) analyse functional and genetic distances between MHC sequences. We employed MHCtools to analyse MHC class I (MHC-I) amplicon data of 559 great reed warblers (Acrocephalus arundinaceus). We identified 390 MHC-I alleles which clustered into 14 functional supertypes. A phylogenetic analysis and analyses of positive selection suggested that the MHC-I alleles belonged to several distinct functional groups. We furthermore identified 107 segregating haplotypes among 116 families, and found substantial variation in diversity with 4-21 MHC-I alleles and 3-13 MHC-I supertypes per haplotype. Finally, we show that the great reed warbler haplotypes harboured combinations of MHC-I supertypes with greater functional divergence than observed in simulated populations of possible haplotypes, a result that is in accordance with the divergent allele advantage hypothesis. Our study demonstrates the power of MHCtools to support genotyping and analysis of MHC in non-model species, which we hope will encourage broad implementation among researchers in MHC genetics and evolution.
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Affiliation(s)
- Jacob Roved
- GLOBE Institute, Section for Evolutionary Genomics, University of Copenhagen, 1350, Copenhagen K, Denmark
| | - Bengt Hansson
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Martin Stervander
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62, Lund, Sweden.,Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, 391 82, Kalmar, Sweden.,Bird Group, Department of Life Sciences, Natural History Museum, Akeman Street, Hertfordshire, HP23 6AP, UK
| | - Dennis Hasselquist
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62, Lund, Sweden.,Bird Group, Department of Life Sciences, Natural History Museum, Akeman Street, Hertfordshire, HP23 6AP, UK
| | - Helena Westerdahl
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62, Lund, Sweden
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96
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Osakabe A, Molaro A. Histone renegades: Unusual H2A histone variants in plants and animals. Semin Cell Dev Biol 2022; 135:35-42. [PMID: 35570098 DOI: 10.1016/j.semcdb.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 12/27/2022]
Abstract
H2A variants are histones that carry out specialized nucleosome function during the eukaryote genome packaging. Most genes encoding H2A histone variants arose in the distant past, and have highly conserved domains and structures. Yet, novel H2A variants have continued to arise throughout the radiation of eukaryotes and disturbed the apparent tranquility of nucleosomes. These species-specific H2A variants contributed to the functional diversification of nucleosomes through changes in both their structure and expression patterns. In this short review, we discuss the evolutionary trajectories of these histone renegades in plants and animal genomes.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
| | - Antoine Molaro
- Genetics, Reproduction & Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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97
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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98
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TLR7 and TLR8 evolution in lagomorphs: different patterns in the different lineages. Immunogenetics 2022; 74:475-485. [PMID: 35419618 DOI: 10.1007/s00251-022-01262-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2022] [Indexed: 11/05/2022]
Abstract
Toll-like receptors (TLRs) are one of the most ancient and widely studied innate immune receptors responsible for host defense against invading pathogens. Among the known TLRs, TLR7 and TLR8 sense and recognize single-stranded (ss) RNAs with a dynamic evolutionary history. While TLR8 was lost in birds and duplicated in turtles and crocodiles, TLR7 is duplicated in some birds, but in other tetrapods, there is only one copy. In mammals, with the exception of lagomorphs, TLR7 and TLR8 are highly conserved. Here, we aim to study the evolution of TLR7 and TLR8 in mammals, with a special focus in the order Lagomorpha. By searching public sequence databases, conducting evolutionary analysis, and evaluating gene expression, we were able to confirm that TLR8 is absent in hares but widely expressed in the European rabbit. In contrast, TLR7 is absent in the European rabbit and quite divergent in hares. Our results suggest that, in lagomorphs, more in particular in leporids, TLR7 and TLR8 genes have evolved faster than in any other mammalian group. The long history of interaction with viruses and their location in highly dynamic telomeric regions might explain the pattern observed.
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99
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de la Fuente M, Novo M. Understanding Diversity, Evolution, and Structure of Small Heat Shock Proteins in Annelida Through in Silico Analyses. Front Physiol 2022; 13:817272. [PMID: 35530508 PMCID: PMC9075518 DOI: 10.3389/fphys.2022.817272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/22/2022] [Indexed: 12/04/2022] Open
Abstract
Small heat shock proteins (sHsps) are oligomeric stress proteins characterized by an α-crystallin domain (ACD). These proteins are localized in different subcellular compartments and play critical roles in the stress physiology of tissues, organs, and whole multicellular eukaryotes. They are ubiquitous proteins found in all living organisms, from bacteria to mammals, but they have never been studied in annelids. Here, a data set of 23 species spanning the annelid tree of life, including mostly transcriptomes but also two genomes, was interrogated and 228 novel putative sHsps were identified and manually curated. The analysis revealed very high protein diversity and showed that a significant number of sHsps have a particular dimeric architecture consisting of two tandemly repeated ACDs. The phylogenetic analysis distinguished three main clusters, two of them containing both monomeric sHsps, and ACDs located downstream in the dimeric sHsps, and the other one comprising the upstream ACDs from those dimeric forms. Our results support an evolutionary history of these proteins based on duplication events prior to the Spiralia split. Monomeric sHsps 76) were further divided into five subclusters. Physicochemical properties, subcellular location predictions, and sequence conservation analyses provided insights into the differentiating elements of these putative functional groups. Strikingly, three of those subclusters included sHsps with features typical of metazoans, while the other two presented characteristics resembling non-metazoan proteins. This study provides a solid background for further research on the diversity, evolution, and function in the family of the sHsps. The characterized annelid sHsps are disclosed as essential for improving our understanding of this important family of proteins and their pleotropic functions. The features and the great diversity of annelid sHsps position them as potential powerful molecular biomarkers of environmental stress for acting as prognostic tool in a diverse range of environments.
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Affiliation(s)
- Mercedes de la Fuente
- Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), Las Rozas, Spain
- *Correspondence: Mercedes de la Fuente,
| | - Marta Novo
- Faculty of Biology, Biodiversity, Ecology and Evolution Department, Complutense University of Madrid, Madrid, Spain
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100
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Côrte-Real JV, Baldauf HM, Melo-Ferreira J, Abrantes J, Esteves PJ. Evolution of Guanylate Binding Protein ( GBP) Genes in Muroid Rodents (Muridae and Cricetidae) Reveals an Outstanding Pattern of Gain and Loss. Front Immunol 2022; 13:752186. [PMID: 35222365 PMCID: PMC8863968 DOI: 10.3389/fimmu.2022.752186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/20/2022] [Indexed: 01/05/2023] Open
Abstract
Guanylate binding proteins (GBPs) are paramount in the host immunity by providing defense against invading pathogens. Multigene families related to the immune system usually show that the duplicated genes can either undergo deletion, gain new functions, or become non-functional. Here, we show that in muroids, the Gbp genes followed an unusual pattern of gain and loss of genes. Muroids present a high diversity and plasticity regarding Gbp synteny, with most species presenting two Gbp gene clusters. The phylogenetic analyses revealed seven different Gbps groups. Three of them clustered with GBP2, GBP5 and GBP6 of primates. Four new Gbp genes that appear to be exclusive to muroids were identified as Gbpa, b, c and d. A duplication event occurred in the Gbpa group in the common ancestor of Muridae and Cricetidae (~20 Mya), but both copies were deleted from the genome of Mus musculus, M. caroli and Cricetulus griseus. The Gbpb gene emerged in the ancestor of Muridae and Cricetidae and evolved independently originating Gbpb1 in Muridae, Gbpb2 and Gbpb3 in Cricetidae. Since Gbpc appears only in three species, we hypothesize that it was present in the common ancestor and deleted from most muroid genomes. The second Gbp gene cluster, Gbp6, is widespread across all muroids, indicating that this cluster emerged before the Muridae and Cricetidae radiation. An expansion of Gbp6 occurred in M. musculus and M. caroli probably to compensate the loss of Gbpa and b. Gbpd is divided in three groups and is present in most muroids suggesting that a duplication event occurred in the common ancestor of Muridae and Cricetidae. However, in Grammomys surdaster and Mus caroli, Gbpd2 is absent, and in Arvicanthis niloticus, Gbpd1 appears to have been deleted. Our results further demonstrated that primate GBP1, GBP3 and GBP7 are absent from the genome of muroids and showed that the Gbp gene annotations in muroids were incorrect. We propose a new classification based on the phylogenetic analyses and the divergence between the groups. Extrapolations to humans based on functional studies of muroid Gbps should be re-evaluated. The evolutionary analyses of muroid Gbp genes provided new insights about the evolution and function of these genes.
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Affiliation(s)
- João Vasco Côrte-Real
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany
| | - José Melo-Ferreira
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Joana Abrantes
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Pedro José Esteves
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal.,Center of Investigation in Health Technologies (CITS), CESPU, Gandra, Portugal
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