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Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
Downloaded from orbit.dtu.dk on: Oct 10, 2021 The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Li, Linzhou; Wang, Sibo; Wang, Hongli; Sahu, Sunil Kumar; Marin, Birger; Li, Haoyuan; Xu, Yan; Liang, Hongping; Li, Zhen; Cheng, Shifeng Total number of authors: 24 Published in: Nature Ecology & Evolution Link to article, DOI: 10.1038/s41559-020-1221-7 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Li, L., Wang, S., Wang, H., Sahu, S. K., Marin, B., Li, H., Xu, Y., Liang, H., Li, Z., Cheng, S., Reder, T., Çebi, Z., Wittek, S., Petersen, M., Melkonian, B., Du, H., Yang, H., Wang, J., Wong, G. K. S., ... Liu, H. (2020). The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nature Ecology & Evolution, 4, 1220-1231. https://doi.org/10.1038/s41559-020-1221-7 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. -
Molecular Phylogeny and Taxonomic Revision of Chaetophoralean Algae (Chlorophyta)
University of South Bohemia in České Budějovice Faculty of Science Molecular phylogeny and taxonomic revision of chaetophoralean algae (Chlorophyta) Ph.D. Thesis Mgr. Lenka Caisová Supervisor RNDr. Jiří Neustupa, Ph.D. Department of Botany, Faculty of Sciences, Charles University in Prague Formal supervisor Prof. RNDr. Jiří Komárek, DrSc. University of South Bohemia, Faculty of Science, Institute of Botany, Academy of Sciences, Třeboň Consultants Prof. Dr. Michael Melkonian Biozentrum Köln, Botanisches Institut, Universität zu Köln, Germany Mgr. Pavel Škaloud, Ph.D. Department of Botany, Faculty of Sciences, Charles University in Prague České Budějovice, 2011 Caisová, L. 2011: Molecular phylogeny and taxonomic revision of chaetophoralean algae (Chlorophyta). PhD. Thesis, composite in English. University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic, 110 pp, shortened version 30 pp. Annotation Since the human inclination to estimate and trace natural diversity, usable species definitions as well as taxonomical systems are required. As a consequence, the first proposed classification schemes assigned the filamentous and parenchymatous taxa to the green algal order Chaetophorales sensu Wille. The introduction of ultrastructural and molecular methods provided novel insight into algal evolution and generated taxonomic revisions based on phylogenetic inference. However, until now, the number of molecular phylogenetic studies focusing on the Chaetophorales s.s. is surprisingly low. To enhance knowledge about phylogenetic -
Non-Pollen Palynomorphs Notes: 2
Non-pollen palynomorphs notes: 2. Holocene record of Megalohypha aqua - dulces , its relation to the fossil form genus Fusiformisporites and association with lignicolous freshwater fungi Lyudmila Shumilovskikh, Astrid Ferrer, Frank Schlütz To cite this version: Lyudmila Shumilovskikh, Astrid Ferrer, Frank Schlütz. Non-pollen palynomorphs notes: 2. Holocene record of Megalohypha aqua - dulces , its relation to the fossil form genus Fusiformisporites and association with lignicolous freshwater fungi. Review of Palaeobotany and Palynology, Elsevier, 2017, 246, pp.167-176. 10.1016/j.revpalbo.2017.07.002. hal-01790616 HAL Id: hal-01790616 https://hal-amu.archives-ouvertes.fr/hal-01790616 Submitted on 14 May 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Review of Palaeobotany and Palynology 246 (2017) 167–176 Contents lists available at ScienceDirect Review of Palaeobotany and Palynology journal homepage: www.elsevier.com/locate/revpalbo Review papers Non-pollen palynomorphs notes: 2. Holocene record of Megalohypha aqua-dulces, its relation to the -
Structural Variation and Evolution of Chloroplast Trnas in Green Algae
Structural variation and evolution of chloroplast tRNAs in green algae Fangbing Qi, Yajing Zhao, Ningbo Zhao, Kai Wang, Zhonghu Li and Yingjuan Wang State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotech- nology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China ABSTRACT As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the 9-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. -
Peres Ck Dr Rcla.Pdf (2.769Mb)
UNIVERSIDADE ESTADUAL PAULISTA unesp “JÚLIO DE MESQUITA FILHO” INSTITUTO DE BIOCIÊNCIAS – RIO CLARO PROGRAMA DE PÓS-GRADUAÇÃO EM CIÊNCIAS BIOLÓGICAS (BIOLOGIA VEGETAL) TAXONOMIA, DISTRIBUIÇÃO AMBIENTAL E CONSIDERAÇÕES BIOGEOGRÁFICAS DE ALGAS VERDES MACROSCÓPICAS EM AMBIENTES LÓTICOS DE UNIDADES DE CONSERVAÇÃO DO SUL DO BRASIL CLETO KAVESKI PERES Tese apresentada ao Instituto de Biociências do Câmpus de Rio Claro, Universidade Estadual Paulista, como parte dos requisitos para obtenção do título de Doutor em Ciências Biológicas (Biologia Vegetal). Rio Claro Junho - 2011 CLETO KAVESKI PERES TAXONOMIA, DISTRIBUIÇÃO AMBIENTAL E CONSIDERAÇÕES BIOGEOGRÁFICAS DE ALGAS VERDES MACROSCÓPICAS EM AMBIENTES LÓTICOS DE UNIDADES DE CONSERVAÇÃO DO SUL DO BRASIL ORIENTADOR: Dr. CIRO CESAR ZANINI BRANCO Comissão Examinadora: Prof. Dr. Ciro Cesar Zanini Branco Departamento de Ciências Biológicas – Unesp/ Assis Prof. Dr. Carlos Eduardo de Mattos Bicudo Seção de Ecologia – Instituto de Botânica de São Paulo Prof. Dr. Orlando Necchi Júnior Departamento de Zoologia e Botânica/ IBILCE – UNESP/ São José do Rio Preto Profa. Dra. Ina de Souza Nogueira Departamento de Biologia – Universidade Federal de Goiás Profa. Dra. Célia Leite Sant´Anna Seção de Ficologia – Instituto de Botânica de São Paulo RIO CLARO 2011 AGRADECIMENTOS Muitas pessoas contribuíram com o desenvolvimento desse trabalho e com a minha formação pessoal e gostaria de deixar a todos meu reconhecimento e um sincero agradecimento. Porém, algumas pessoas/instituições foram fundamentais nestes quatro anos de doutorado, sendo imprescindível agradecê-las nominalmente: Aos meus pais, Euclinir e Lidia, por terem sempre acreditado em mim e por me incentivarem a continuar na área que escolhi. Agradeço imensamente pela melhor herança que uma pessoa pode receber que é o exemplo de humildade e dignidade que vocês têm. -
Freshwater Algae in Britain and Ireland - Bibliography
Freshwater algae in Britain and Ireland - Bibliography Floras, monographs, articles with records and environmental information, together with papers dealing with taxonomic/nomenclatural changes since 2003 (previous update of ‘Coded List’) as well as those helpful for identification purposes. Theses are listed only where available online and include unpublished information. Useful websites are listed at the end of the bibliography. Further links to relevant information (catalogues, websites, photocatalogues) can be found on the site managed by the British Phycological Society (http://www.brphycsoc.org/links.lasso). Abbas A, Godward MBE (1964) Cytology in relation to taxonomy in Chaetophorales. Journal of the Linnean Society, Botany 58: 499–597. Abbott J, Emsley F, Hick T, Stubbins J, Turner WB, West W (1886) Contributions to a fauna and flora of West Yorkshire: algae (exclusive of Diatomaceae). Transactions of the Leeds Naturalists' Club and Scientific Association 1: 69–78, pl.1. Acton E (1909) Coccomyxa subellipsoidea, a new member of the Palmellaceae. Annals of Botany 23: 537–573. Acton E (1916a) On the structure and origin of Cladophora-balls. New Phytologist 15: 1–10. Acton E (1916b) On a new penetrating alga. New Phytologist 15: 97–102. Acton E (1916c) Studies on the nuclear division in desmids. 1. Hyalotheca dissiliens (Smith) Bréb. Annals of Botany 30: 379–382. Adams J (1908) A synopsis of Irish algae, freshwater and marine. Proceedings of the Royal Irish Academy 27B: 11–60. Ahmadjian V (1967) A guide to the algae occurring as lichen symbionts: isolation, culture, cultural physiology and identification. Phycologia 6: 127–166 Allanson BR (1973) The fine structure of the periphyton of Chara sp. -
An Unrecognized Ancient Lineage of Green Plants Persists in Deep Marine Waters
FAU Institutional Repository http://purl.fcla.edu/fau/fauir This paper was submitted by the faculty of FAU’s Harbor Branch Oceanographic Institute. Notice: ©2010 Phycological Society of America. This manuscript is an author version with the final publication available at http://www.wiley.com/WileyCDA/ and may be cited as: Zechman, F. W., Verbruggen, H., Leliaert, F., Ashworth, M., Buchheim, M. A., Fawley, M. W., Spalding, H., Pueschel, C. M., Buchheim, J. A., Verghese, B., & Hanisak, M. D. (2010). An unrecognized ancient lineage of green plants persists in deep marine waters. Journal of Phycology, 46(6), 1288‐1295. (Suppl. material). doi:10.1111/j.1529‐8817.2010.00900.x J. Phycol. 46, 1288–1295 (2010) Ó 2010 Phycological Society of America DOI: 10.1111/j.1529-8817.2010.00900.x AN UNRECOGNIZED ANCIENT LINEAGE OF GREEN PLANTS PERSISTS IN DEEP MARINE WATERS1 Frederick W. Zechman2,3 Department of Biology, California State University Fresno, 2555 East San Ramon Ave, Fresno, California 93740, USA Heroen Verbruggen,3 Frederik Leliaert Phycology Research Group, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium Matt Ashworth University Station MS A6700, 311 Biological Laboratories, University of Texas at Austin, Austin, Texas 78712, USA Mark A. Buchheim Department of Biological Science, University of Tulsa, Tulsa, Oklahoma 74104, USA Marvin W. Fawley School of Mathematical and Natural Sciences, University of Arkansas at Monticello, Monticello, Arkansas 71656, USA Department of Biological Sciences, North Dakota State University, Fargo, North Dakota 58105, USA Heather Spalding Botany Department, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA Curt M. Pueschel Department of Biological Sciences, State University of New York at Binghamton, Binghamton, New York 13901, USA Julie A. -
Downloaded from Genbank on That Full Plastid Genomes Are Not Sufficient to Reject Al- February 28, 2012
Ruhfel et al. BMC Evolutionary Biology 2014, 14:23 http://www.biomedcentral.com/1471-2148/14/23 RESEARCH ARTICLE Open Access From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes Brad R Ruhfel1*, Matthew A Gitzendanner2,3,4, Pamela S Soltis3,4, Douglas E Soltis2,3,4 and J Gordon Burleigh2,4 Abstract Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. Results: We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. -
Especies De Algas De Ríos De Nuevo León, México: Nuevos Registros Para El Estado
Núm. 46: 1-25 Julio 2018 ISSN electrónico: 2395-9525 Polibotánica ISSN electrónico: 2395-9525 [email protected] Instituto Politécnico Nacional México http:www.polibotanica.mx ESPECIES DE ALGAS DE RÍOS DE NUEVO LEÓN, MÉXICO: NUEVOS REGISTROS PARA EL ESTADO ALGAE SPECIES FROM NUEVO LEON, MEXICO: NEW RECORDS FOR THE STATE Aguirre-Cavazos, D.E.; S. Moreno-Limón, y S.M. Salcedo-Martínez ESPECIES DE ALGAS DE RÍOS DE NUEVO LEÓN, MÉXICO: NUEVOS REGISTROS PARA EL ESTADO. ALGAE SPECIES FROM NUEVO LEON, MEXICO: NEW RECORDS FOR THE STATE. Núm. 46: 1-25 México. Julio 2018 Instituto Politécnico Nacional DOI: 10.18387/polibotanica.46.1 1 Núm. 46: 1-25 Julio 2018 ISSN electrónico: 2395-9525 ESPECIES DE ALGAS DE RÍOS DE NUEVO LEÓN, MÉXICO: NUEVOS REGISTROS PARA EL ESTADO ALGAE SPECIES FROM NUEVO LEON, MEXICO: NEW RECORDS FOR THE STATE D.E. Aguirre-Cavazos Herbario, Facultad de Ciencias Biológicas, Aguirre-Cavazos, D.E.; S. Moreno-Limón, y Universidad Autónoma de Nuevo León. S.M. Salcedo Martínez S. Moreno-Limón Laboratorio de Fisiología Vegetal, Facultad de Ciencias Biológicas, ESPECIES DE ALGAS DE RÍOS DE NUEVO LEÓN, Universidad Autónoma de Nuevo León. MÉXICO: NUEVOS REGISTROS PARA EL S.M. Salcedo-Martínez/ [email protected] ESTADO Herbario, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León. ALGAE SPECIES FROM NUEVO LEON, MEXICO: NEW RECORDS FOR THE STATE RESUMEN: El conocimiento de las algas continentales de México es aún deficiente. Los registros taxonómicos suman actualmente 3 256 especies, pero muchos de ellos carecen de una descripción, una ilustración o de ambas, además de información ecológica o de su potencial económico. -
Tesis Doctoral
Universidad Nacional del Sur Tesis de Doctor en Biología LAGUNAS SOMERAS COMO ECOSISTEMAS CENTINELAS DE LA VARIABILIDAD CLIMÁTICA: RESPUESTA DE LAS COMUNIDADES FITOPLANCTÓNICAS Josefina Zunino Bahía Blanca Argentina 2018 Universidad Nacional del Sur Tesis de Doctor en Biología LAGUNAS SOMERAS COMO ECOSISTEMAS CENTINELAS DE LA VARIABILIDAD CLIMÁTICA: RESPUESTA DE LAS COMUNIDADES FITOPLANCTÓNICAS JOSEFINA ZUNINO BAHÍA BLANCA ARGENTINA 2018 PREFACIO Esta Tesis se presenta como parte de los requisitos para optar al grado Académico de Doctor en Biología de la Universidad Nacional del Sur y no ha sido presentada previamente para la obtención de otro título en esta Universidad u otra. La misma contiene los resultados obtenidos en investigaciones llevadas a cabo Instituto Argentino de Oceanografía (IADO) perteneciente al Centro Científico Tecnológico Bahía Blanca (CCT-CONICET-BB), dependiente del Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), durante el período comprendido entre 1 de abril de 2014 y 1 de mayo de 2018, bajo la dirección de la Dra. María Cintia Piccolo (IADO-CONICET) y la Dra. Irina Izaguirre (UBA-CONICET). UNIVERSIDAD NACIONAL DEL SUR Secretaría General de Posgrado y Educación Continua La presente tesis ha sido aprobada el……/……/……., mereciendo la calificación de ……………….(…………………...) A Simón AGRADECIMIENTOS Quiero expresar mi agradecimiento a todas aquellas personas e instituciones que hicieron posible el desarrollo de esta Tesis Doctoral. En primer lugar a mi directora, la Dra. M. Cintia Piccolo por su tenacidad y dedicación para lograr la mejor versión profesional de mí y por su apoyo en todo momento. A mi codirectora la Dra. Irina Izaguirre por los aportes brindados y su gran predisposición. -
Especies De Algas De Ríos De Nuevo León, México: Nuevos Registros Para El Estado Polibotánica, Núm
Polibotánica ISSN: 1405-2768 Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas Aguirre-Cavazos, D.E.; Moreno-Limón, S.; Salcedo-Martínez, S.M. Especies de algas de ríos de Nuevo León, México: nuevos registros para el estado Polibotánica, núm. 46, 2018, pp. 1-25 Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas DOI: https://doi.org/10.18387/polibotanica.46.1 Disponible en: https://www.redalyc.org/articulo.oa?id=62158254001 Cómo citar el artículo Número completo Sistema de Información Científica Redalyc Más información del artículo Red de Revistas Científicas de América Latina y el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto Núm. 46: 1-25 Julio 2018 ISSN electrónico: 2395-9525 Polibotánica ISSN electrónico: 2395-9525 [email protected] Instituto Politécnico Nacional México http:www.polibotanica.mx ESPECIES DE ALGAS DE RÍOS DE NUEVO LEÓN, MÉXICO: NUEVOS REGISTROS PARA EL ESTADO ALGAE SPECIES FROM NUEVO LEON, MEXICO: NEW RECORDS FOR THE STATE Aguirre-Cavazos, D.E.; S. Moreno-Limón, y S.M. Salcedo-Martínez ESPECIES DE ALGAS DE RÍOS DE NUEVO LEÓN, MÉXICO: NUEVOS REGISTROS PARA EL ESTADO. ALGAE SPECIES FROM NUEVO LEON, MEXICO: NEW RECORDS FOR THE STATE. Núm. 46: 1-25 México. Julio 2018 Instituto Politécnico Nacional DOI: 10.18387/polibotanica.46.1 1 Núm. 46: 1-25 Julio 2018 ISSN electrónico: 2395-9525 ESPECIES DE ALGAS DE RÍOS DE NUEVO LEÓN, MÉXICO: NUEVOS REGISTROS PARA EL ESTADO ALGAE SPECIES FROM NUEVO LEON, MEXICO: NEW RECORDS FOR THE STATE D.E.