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High-Throughput Sequencing of 5S-IGS Rdna in Fagus L. (Fagaceae) Reveals Complex Evolutionary Patterns and Hybrid Origin of Modern Species
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433057; this version posted February 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 a CC-BY-NC 4.0 International license. Cardoni, Piredda et al. High-Throughput Sequencing of Fagus 5S-IGS rDNA High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species Simone Cardoni1, Roberta Piredda2, Thomas Denk3, Guido W. Grimm4, Aristotelis C. Papageorgiou5, Ernst-Detlef Schulze6, Anna Scoppola1, Parvin Salehi Shanjani7, Yoshihisa Suyama8, Nobuhiro Tomaru9, James R.P. Worth10, Marco Cosimo Simeone1* Affiliations 1Department of Agricultural and Forestry Science (DAFNE), Università degli studi della Tuscia, 01100 Viterbo, Italy 2Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy 3Swedish Museum of Natural History, Stockholm, 10405 Sweden 4Unaffiliated, Orléans, France, ORCID ID: 0000-0003-0674-3553 5Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece 6Max-Planck Institute for Biogeochemistry, 07701 Jena, Germany 7Natural Resources Gene Bank, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization, Tehran, Iran 8Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi 989-6711 Japan 9Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, 464- 8601, Japan 10Ecological Genetics Laboratory, Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, 305-8687 Japan * Corresponding author Marco Cosimo Simeone; [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433057; this version posted February 27, 2021. -
Improvement and Silviculture of Beech Proceedings from the 7Th
Improvement and Silviculture of Beech Proceedings from the 7th International Beech Symposium IUFRO Research Group 1.10.00 10-20 May 2004, Tehran, Iran Editors: Khosro Sagheb-Talebi, Palle Madsen and Kazuhiko Terazawa Research Institute of Forests and Rangelands, Iran University of Tehran, Faculty of Natural Resources, Iran Forest, Range and Watershed Organization, Iran Danish Centre for Forest, Landscape and Planning, Denmark Hokkaido Forestry Research Institute, Japan Improvement and Silviculture of Beech Proceedings from the 7th International Beech Symposium IUFRO Research Group 1.10.00 10-20 May 2004, Tehran, Iran Editors: Khosro Sagheb-Talebi, Palle Madsen and Kazuhiko Terazawa Published by Research Insitute of Forests and Rangelands (RIFR), Iran Scientific committee: • Amani Manuchehr (Iran) • Assareh Mohammad Hassan (Iran) • Kerr Garry (England) • Lüpke Burghard von (Germany) • Madsen Palle (Denmark) • Marvie-Mohadjer Mohammad Reza (Iran) • Mosandle Reinhard (Germany) • Sagheb-Talebi Khosro (Iran) • Salehi Parviz (Iran) • Schütz Jean-Philippe (Switzerland) • Seifollahian Majid (Iran) • Teissier du Cros Eric (France) • Terazawa Kazuhiko (Japan) • Zahedi Amiri Ghavomedin (Iran) * Akhavan Reza (Secretary) Executive committee: • Boujari Jamshid • Ebrahimi Rastaghi Morteza • Etemad Vahid • Khodaie Mahammad Bagher • Pourtahmasi Kambiz • Rahimiyan Mohammed Sadegh • Sagheb-Talebi Khosro • Yazdani Shahbaz * Hassani Majid (Secretary) 2 Welcome address Forests in Iran, Constraints and Strategies By definition, Iran is categorized a country with low forest cover. Only 7.6% of its land is covered by forest ecosystems. Despite of this the vital role of these ecosystems can not be ignored, dependence of daily life of local population, recreational affects, soil and water conservation, and more important, its facilitation for sustaining high biodiversity of the country already have been recognized. -
The Complete Chloroplast Genome of Fagus Crenata (Subgenus Fagus) and Comparison with F
The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana) James R. P. Worth1, Luxian Liu2, Fu-Jin Wei1 and Nobuhiro Tomaru3 1 Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan 2 Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, China 3 Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan ABSTRACT This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus. Subjects Biodiversity, Evolutionary Studies, Genetics, Plant Science Keywords Beech, Chloroplast SSRs, Fagaceae phylogeny, Fagus crenata, Whole chloroplast Submitted 9 January 2019 genome, Chloroplast microsatellites Accepted 24 April 2019 Published 7 June 2019 INTRODUCTION Corresponding author James R. -
The Complete Chloroplast Genome of [I]Fagus Crenata
A peer-reviewed version of this preprint was published in PeerJ on 7 June 2019. View the peer-reviewed version (peerj.com/articles/7026), which is the preferred citable publication unless you specifically need to cite this preprint. Worth JRP, Liu L, Wei F, Tomaru N. 2019. The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana) PeerJ 7:e7026 https://doi.org/10.7717/peerj.7026 The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana) James Worth Corresp., 1 , Luxian Liu 2 , Nobuhiro Tomaru 3 1 Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan 2 Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, China 3 Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan, Japan Corresponding Author: James Worth Email address: [email protected] This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed between them and differing by 311 single nucleotide polymorphisms. The six most variable regions between the two genomes were the psbK-psbI, trnG-psbfM, trnV, rpl32, ndhD-psaC and ndhI-ndh regions. These highly variable chloroplast regions and the identification of 42 variable chloroplast SSRs found to be shared between the two species will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus. -
Supplementary Material
Xiang et al., Page S1 Supporting Information Fig. S1. Examples of the diversity of diaspore shapes in Fagales. Fig. S2. Cladogram of Fagales obtained from the 5-marker data set. Fig. S3. Chronogram of Fagales obtained from analysis of the 5-marker data set in BEAST. Fig. S4. Time scale of major fagalean divergence events during the past 105 Ma. Fig. S5. Confidence intervals of expected clade diversity (log scale) according to age of stem group. Fig. S6. Evolution of diaspores types in Fagales with BiSSE model. Fig. S7. Evolution of diaspores types in Fagales with Mk1 model. Fig. S8. Evolution of dispersal modes in Fagales with MuSSE model. Fig. S9. Evolution of dispersal modes in Fagales with Mk1 model. Fig. S10. Reconstruction of pollination syndromes in Fagales with BiSSE model. Fig. S11. Reconstruction of pollination syndromes in Fagales with Mk1 model. Fig. S12. Reconstruction of habitat shifts in Fagales with MuSSE model. Fig. S13. Reconstruction of habitat shifts in Fagales with Mk1 model. Fig. S14. Stratigraphy of fossil fagalean genera. Table S1 Genera of Fagales indicating the number of recognized and sampled species, nut sizes, habits, pollination modes, and geographic distributions. Table S2 List of taxa included in this study, sources of plant material, and GenBank accession numbers. Table S3 Primers used for amplification and sequencing in this study. Table S4 Fossil age constraints utilized in this study of Fagales diversification. Table S5 Fossil fruits reviewed in this study. Xiang et al., Page S2 Table S6 Statistics from the analyses of the various data sets. Table S7 Estimated ages for all families and genera of Fagales using BEAST. -
Living Collections Prioritization at Public Gardens
LIVING COLLECTIONS PRIORITIZATION AT PUBLIC GARDENS by Anna V. Bower A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Master of Science in Plant and Soil Sciences Summer 2017 © 2017 Anna V. Bower All Rights Reserved LIVING COLLECTIONS PRIORITIZATION AT PUBLIC GARDENS by Anna V. Bower Approved: __________________________________________________________ John J. Frett, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Robert E. Lyons, Ph.D. Chair of the Department of Plant and Soil Sciences Approved: __________________________________________________________ Mark W. Rieger, Ph.D. Dean of the College of Agriculture and Natural Resources Approved: __________________________________________________________ Ann L. Ardis, Ph.D. Senior Vice Provost for Graduate and Professional Education ACKNOWLEDGEMENTS I would like to express my thanks to all who contributed to this thesis. To my committee members, Dr. John Frett, Dr. Susan Barton, and Mrs. Kristina Aguilar, thank you for your constructive comments and suggestions. To the public garden professionals who contributed to the surveys and participated in case study interviews, thank you for your support of graduate student research and enthusiasm for the subject matter. To the staff at the University of Delaware Botanic Gardens, thank you for the opportunity to be selected as your curatorial graduate student. It was a pleasure to work with you for the past two years. Finally, to my friends and family, I am sincerely grateful for the opportunities you have provided me and your support during my time in graduate school. iii TABLE OF CONTENTS LIST OF TABLES ..................................................................................................... -
Phylogeny & Morphology of Fagus & Fagaceae
Phylogeny & Morphology of Fagus & Fagaceae Paul Goetghebeur, Ghent University APG III (2009) (Angiosperm Phylogeny Group) Eudicots Rosids Fabids Fagales Rosids (APG III 2009) : Rhizobium & Frankia alni Rule of the inverse : Frankia nodules on Alnus Symbiosis with 1 F 3 O / 8 F / 25 G Fagales pp with actinorhiza F F (Stevens 2001 onwards) F Fagaceae (+ Nothofagaceae) area worldwide (Jenkins 1993) Area of Fagus (N) and Nothofagus (S) 1-2 1-2 4-6 2-3 (Jenkins 1993) Fagus sylvatica area (Bradshaw et al. 2010) Fagales the “Calimero” pattern F 1 genus sister group of 32 genera F (Stevens 2001 onwards) F Cyme, the basic pattern False catkins = raceme of cymes, + cupula ! (Graf 1975) Nothofagus vs Fagaceae chromosome number 2n = 26 2n = 24 pollen morphology 5- or 8-colpate 3-colporate stipule morphology basal swelling thin scale Nothofagaceae Nothofagus pumilio Nothofagus moorei Nothofagus dombeyi Nothofagus B&B (El Chaltén, Argentina) Fagoideae (= Fagus) vs Quercoideae Germination phanerocotylar cryptocotylar (exc. Trigonobalanus) Staminate inflor. capitate catkin-like Cupules solitary grouped into catkins Fagus seedling = phanerocotylar Fagus seedling Fagus seedling Fagus seedling Fagus grandifolia, staminate flower & inflorescence (Wood 1974) Fagus grandifolia, pistillate inflorescences (Wood 1974) Fagus grandifolia, mature cupule & fruits (Wood 1974) Phylogeny of Fagus (after Denk et al. 2005) subgenus Fagus subgenus Englerianae Fagus subgenus Fagus - single-stemmed high-branching trees - lenticels small, inconspicuous - “buds sessile” (Denk -
Biogeographical Study of Japanese Beech Forests Under Diffe- Rent Climatic Conditions
©Reinhold-Tüxen-Gesellschaft (http://www.reinhold-tuexen-gesellschaft.de/) Ber. d. Reinh.-Tüxen-Ges. 20, 179-194. Hannover 2008 Biogeographical study of Japanese beech forests under diffe- rent climatic conditions - Yukito Nakamura, Tokyo - Abstract The Fagetea crenatae are endemic in the Japanese Archipelago and compromise two con- trasting alliances on the Japan Sea side and the Pacific side. Here we show that this distribu- tion pattern is not just caused by the actual environmental differentiation but also results from its synchorological vegetation history. The European Fagetalia sylvaticae are diverse due to continental glaciations. It shares species with the Vaccinio-Piceetea, Rhamno-Prunetea and Galio-Urticetea. The Japanese Saso-Fagetalia crenatae has its own forest species and is clear- ly distinct from other classes. The long south-north chain of the Japanese Islands functioned as a bridge facilitating migration and isolation of forest species during the glacial age. The Sasamorpho-Fagion crenatae on the Pacific side is vicarious to continental China and Taiwan. By contrast, the Saso kurilensis-Fagion crenatae on the Japan Sea side is characterized by newly evolved species of the Camellietea japonicae, which adapted to the heavy-snow climate which became established in the interglacial period of the Pleistocene. 1. Introduction Fagus is one of the most important canopy trees in the temperate forests of the Northern Hemisphere. There are about 10 species found in regions with mild, humid, oceanic climates (Fig. 1). Along the eastern coast of North America Fagus grandifolia forests belong to the Querceto-Fagetea grandifoliae Knapp 1957 ex Okuda 1994 (KNAPP 1957, 1965, OKUDA 1994). -
Fagaceae) Species
Journal of Asia-Pacific Biodiversity 7 (2014) 378e387 HOSTED BY Contents lists available at ScienceDirect Journal of Asia-Pacific Biodiversity journal homepage: http://www.elsevier.com/locate/japb Original article Leaf cuticle micromorphology of Fagus L. (Fagaceae) species Seong Ho Cho 1,2, Keum Seon Jeong 1, Sun-Hye Kim 1, Jae-Hong Pak 1,* 1 Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Korea 2 Natural History Museum, Kyungpook National University, Gunwi, Korea article info abstract Article history: Cuticle micromorphology of all eight species of Fagus and an outgroup were examined in the present Received 12 July 2014 study. The genus Trigonobalanus was selected as the outgroup. Thirteen characteristics of the inner Received in revised form surface and five of the outer surface of the cuticle were described. Some characteristics, such as the 7 October 2014 subsidiary cell shape, size of stomata, arrangement of subsidiary cell, shape of anticlinal and periclinal Accepted 7 October 2014 cell walls, texture of periclinal cell wall, development epicuticular wax, and presence of papillae, were Available online 12 November 2014 considered important for infrageneric classification. The topology was obtained from the analysis using two major lineages: (1) Fagus engleriana þ Fagus japonica þ Fagus longipetiolata and (2) Fagus Keywords: þ þ þ þ fi Cuticles sylvatica Fagus crenata Fagus lucida Fagus hayatae Fagus grandifolia. The rst clade supported a Fagaceae bootstrap value of 98% and the second clade a bootstrap value of 97%. Based on the cuticle morphology, Fagus our results support the previous study, by revealing F. engleriana, F. japonica, and F.