VOLUME 5 Biology and Taxonomy
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Dendrocalamus Sinicus)
RESEARCH ARTICLE Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus) Kai Cui1, Haiying Wang1, Shengxi Liao1*, Qi Tang2,LiLi1, Yongzhong Cui1, Yuan He1 1 Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s Republic of China, 2 Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultral University, Changsha, 410128, People’s Republic of China a11111 * [email protected] Abstract Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized OPEN ACCESS for multi-functional applications including furniture, construction, and industrial paper pulp. Citation: Cui K, Wang H, Liao S, Tang Q, Li L, Cui Y, To comprehensively elucidate the molecular processes involved in its culm elongation, et al. (2016) Transcriptome Sequencing and Analysis Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus). PLoS ONE 11(6): were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A e0157362. doi:10.1371/journal.pone.0157362 total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were Editor: Binying Fu, Institute of Crop Sciences, annotated in the NCBI non-redundant protein database and 35,262 were annotated in the CHINA Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to Received: December 5, 2015 gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. -
Perennials for Winter Gardens Perennials for Winter Gardens
TheThe AmericanAmerican GARDENERGARDENER® TheThe MagazineMagazine ofof thethe AAmericanmerican HorticulturalHorticultural SocietySociety November / December 2010 Perennials for Winter Gardens Edible Landscaping for Small Spaces A New Perspective on Garden Cleanup Outstanding Conifers contents Volume 89, Number 6 . November / December 2010 FEATURES DEPARTMENTS 5 NOTES FROM RIVER FARM 6 MEMBERS’ FORUM 8 NEWS FROM THE AHS Boston’s garden contest grows to record size, 2011 AHS President’s Council trip planned for Houston, Gala highlights, rave reviews for Armitage webinar in October, author of article for The American Gardener receives garden-writing award, new butterfly-themed children’s garden installed at River Farm. 12 2010 AMERICA IN BLOOM AWARD WINNERS Twelve cities are recognized for their community beautification efforts. 42 ONE ON ONE WITH… David Karp: Fruit detective. page 26 44 HOMEGROWN HARVEST The pleasures of popcorn. EDIBLE LANDSCAPING FOR SMALL SPACES 46 GARDENER’S NOTEBOOK 14 Replacing pavement with plants in San BY ROSALIND CREASY Francisco, soil bacterium may boost cognitive With some know-how, you can grow all sorts of vegetables, fruits, function, study finds fewer plant species on and herbs in small spaces. earth now than before, a fungus-and-virus combination may cause honeybee colony collapse disorder, USDA funds school garden CAREFREE MOSS BY CAROLE OTTESEN 20 program, Park Seed sold, Rudbeckia Denver Looking for an attractive substitute for grass in a shady spot? Try Daisy™ wins grand prize in American moss; it’ll grow on you. Garden Award Contest. 50 GREEN GARAGE® OUTSTANDING CONIFERS BY RITA PELCZAR 26 A miscellany of useful garden helpers. This group of trees and shrubs is beautiful year round, but shines brightest in winter. -
The Evolution and Utility of Ribosomal ITS Sequences in Bambusinae and Related Species: Divergence, Pseudogenes, and Implications for Phylogeny
c Indian Academy of Sciences RESEARCH ARTICLE The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny HUI-XING SONG, SU-PING GAO, MING-YAN JIANG, GUANG-LI LIU, XIAO-FANG YU and QI-BING CHEN∗ School of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People’s Republic of China Abstract Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evo- lution. Concerted evolution leads to intragenomic uniformity of repeats even between loci on nonhomologous chromosomes. However, a number of studies have shown that the ITS polymorphism within individuals is quite common. The molecu- lar systematics of Bambusinae and related species were recently assessed by different teams using independently generated ITS sequences, and the results disagreed in some remarkable features. Here we compared the ITS sequences of the mem- bers of Bambusa s. l., the genera Dendrocalamus, Dinochloa, Gigantochloa, Guadua, Melocalamus, Monocladus, Oxytenan- thera, Thyrsostachys, Pleioblastus, Pseudosasa and Schizostachyum. We have reanalysed the ITS sequences used by different research teams to reveal the underlying patterns of their different results. After excluding the sequences suspected to repre- sent paralogous loci, a phylogenetic analysis of the subtribe Bambusinae species were performed using maximum parsimony and maximum-likelihood methods. The implications of the findings are discussed. The risk of incorporating ITS paralogues in plant evolutionary studies that can distort the phylogenetic signal should caution molecular systematists. [Song H.-X., Gao S.-P., Jiang M.-Y., Liu G.-L., Yu X.-F. -
SELECTED BAMBOO LITERATURE Ades, G. 1999. Important Discovery
SELECTED BAMBOO LITERATURE Ades, G. 1999. Important discovery of lesser bamboo bat roosting site in Hong Kong. Porcupine! 19: 22. Brailovsky, H. 1988. Hemiptera—Heteroptera de Mexico. XXXIX. Descripción de una tribu nueva, un género Nuevo y una especie nueva de coreidos recolectados en bamboo (Bambusa sp.) (Coreidae-Coreinae). Anal. Inst. Biol. UNAM 58, ser. Zool. 1: 155-164. Bystriakova, N., V. Kapos & I. Lysenko. 2004. Bamboo biodiversity: Africa, Madgascar and the Americas. UNEP-WCMC/INBAR, Biodiversity Series 19. UK: Swaingrove Imaging. http://www.ourplanet.com/wcmc/19.html Bystriakova, N., V. Kapos, C. Stapleton & I. Lysenko. 2003. Bamboo biodiversity: information for planning conservation and management in the Asia-Pacific region. UNEP- WCMC/INBAR, Biodiversity Series 14. UK: Swaingrove Imaging. http://www.ourplanet.com/wcmc/14.html Clark, L.G. 2001. Bambusoideae. Pp. 21-49 in Flora Fanerogâmica do Estado de São Paulo, Volume I, Poaceae, H. Longhi-Wagner, ed. São Paulo: Editora Hucitec. [Includes collaboration with X. Londoño (Eremocaulon, Guadua), H. Longhi-Wagner and R.P. de Oliveira (Olyra, Parodiolyra), T. Sendulsky (Merostachys).] Clark, L.G. 2004. Two new species of Aulonemia and Chusquea (Poaceae: Bambusoideae) from Brazil. Revista Brasileira de Botânica 27: 31-36. Clark, L.G., G. Davidse & R.P. Ellis. 1989. Natural hybridization in bamboos: Evidence from Chusquea sect. Swallenochloa (Poaceae: Bambusoideae). National Geographic Research 5: 459-476. Clark, L.G., S. Dransfield, J. Triplett & J.G. Sánchez-Ken. In press. Phylogenetic relationships among the one-flowered genera of Bambuseae (Poaceae: Bambusoideae). In J. T. Columbus et al. (eds.). Monocots: Comparative biology and evolution. 2 vols. -
Biological Report 30 May 1995 National Biological Service
Biological Report 30 May 1995 National Biological Service The National Biological Service publishes five technical report series. Manuscripts are accepted from Service employees or contractors, students and faculty associated with cooperative research units, and other persons whose work is sponsored by the Service. Manuscripts are received with the understanding that they are unpublished. Manuscripts receive anonymous peer review. The final decision to publish lies with the editor. Editorial Staff Series Descrhtions WAGING EDITOR Biological Report ISSN 0895-1926 Paul A. Opler -Technical papers about applied research of limited scope. Subjects include new information arising from comprehensive studies, surveys and inventories, effects of land use on fish ASSISTANT BRANCH LEADER and wildlife, diseases of fish and wildlife, and developments Paul A. Vohs in technology. Proceedings of technical conferences and symposia may be published in this series. SCIENTIFIC EDITORS Fish and Wildlife Leaflet ISSN 0899461X Elizabeth D. Rockwell Summaries of technical information for readers of non- James R. Zuboy technical or semitechnical material. Subjects include topics of current interest, results of inventories and surveys, management techniques, and descriptions of imported fish TECHNICAL EDITORS and wildlife and their diseases. Jerry D. Cox Fish and Wildlife Research ISSN 1040-2411 Deborah K. Harris Papers on experimental research, theoretical presentations, and interpretive literature reviews. VISUAL INFORMATION SPECIALIST North American Fauna ISSN 0078-1304 Monographs of long-term or basic research on faunal and Constance M. Lemos floral life histories, distributions, population dynamics, and taxonomy and on community ecology. EDITORIAL ASSISTANT Resource Publication ISSN 0163-4801 Martha W. Nichols Semitechnical and nonexperimental technical topics including surveys; data, status, and historical reports; handbooks; checklists; manuals; annotated bibliographies; EDITORIAL CLERK and workshop papers. -
Proposed Sampling of Woody Bamboos and Outgroups (Oryzeae, Olyreae, Streptogyneae) for the Bamboo Phylogeny Project
Proposed sampling of woody bamboos and outgroups (Oryzeae, Olyreae, Streptogyneae) for the Bamboo Phylogeny Project. * = monotypic genus; # = DNA at ISU or Fairchild; & = silica gel dried leaf material at ISU; C = in cultivation in the U.S.; ¸ = sequenced or scored; - = to be sequenced or scored; p = partially complete; e = expected from ongoing projects (symbols in green = E. Widjaja in Indonesia; symbols in red = Li De-Zhu in China; symbols in blue = Trevor Hodkinson in Ireland). Type species for a genus in boldface. Total number of taxa for sequencing: 160 (6 OG + 30 NT Clade + 90 P + 34 N) Total number of taxa for AFLPs (46 NT clade + 2 OG): 48 (-32 sequenced = 16 additional) Total number of taxa in study: 176 (for two rounds) Taxon rbcL ndhF rpl16 trnL- morph intron trnF # of taxa already sequenced or scored 18 31 51 39 49 # of taxa to be sequenced or scored 142 129 109 121 127 ORYZEAE Oryza sativa ¸ ¸ ¸ ¸ ¸ STREPTOGYNEAE Streptogyna americana # ¸ ¸ ¸ - ¸ Streptogyna crinita (Africa, S India, Sri Lanka) - p - - - OLYREAE Buergersiochloa bambusoides # (PNG) - ¸ ¸ - ¸ Pariana radiciflora # & - ¸ ¸ ¸ ¸ Sucrea maculata # & - ¸ ¸ - ¸ BAMBUSEAE (81-98 g, 1,290 spp) NORTH TEMPERATE CLADE Subtribe Arundinariinae (13-22 g, 287 spp) Acidosasa chinensis # (China) - - - - - Acidosasa purpurea # - - - - - Ampelocalamus patellaris # - - - - - Ampelocalamus scandens #C # - ¸ ¸ ¸ p Arundinaria gigantea #&C ## ? ¸ ¸ ¸ ¸ Bashania faberi C? (China) - - - - - Bashania fargesii #&C # - ¸ - ¸ p Borinda macclureana (China, Tibet) # - - - ¸ - Borinda frigida -
Genome-Wide RAD Sequencing Data Provide Unprecedented Resolution
www.nature.com/scientificreports OPEN Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of Received: 1 February 2017 Accepted: 23 August 2017 temperate bamboos (Poaceae: Published: xx xx xxxx Bambusoideae) Xueqin Wang 1,2, Xiaying Ye1,3,4, Lei Zhao1,3,4, Dezhu Li1,5, Zhenhua Guo1 & Huifu Zhuang6 The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution. The Phyllostachys, Shibataea, and Arundinaria clades defned from plastid phylogeny, were not supported as monophyletic group. However, the RAD-seq phylogeny largely agreed with the morphology-based taxonomy, with two clades having leptomorph rhizomes strongly supported as monophyletic group. We also explored two approaches, BWA-GATK (a mapping system) and Stacks (a grouping system), for diferences in SNP calling and phylogeny inference. For the same level of missing data, the BWA-GATK pipeline produced much more SNPs in comparison with Stacks. Phylogenetic analyses of the largest data matrices from both pipelines, using concatenation and coalescent methods provided similar tree topologies, despite the presence of missing data. Our study demonstrates the utility of RAD-seq data for elucidating phylogenetic relationships between genera and higher taxonomic levels in this important but phylogenetically challenging group. Te temperate bamboos (tribe Arundinarieae, Bambusoideae, Poaceae) are a clade of diverse taxa containing 32 genera and about 600 species1–4. -
VOLUME 5 Biology and Taxonomy
VOLUME 5 Biology and Taxonomy Table of Contents Preface 1 Cyanogenic Glycosides in Bamboo Plants Grown in Manipur, India................................................................ 2 The First Report of Flowering and Fruiting Phenomenon of Melocanna baccifera in Nepal........................ 13 Species Relationships in Dendrocalamus Inferred from AFLP Fingerprints .................................................. 27 Flowering gene expression in the life history of two mass-flowered bamboos, Phyllostachys meyeri and Shibataea chinensis (Poaceae: Bambusoideae)............................................................................... 41 Relationships between Phuphanochloa (Bambuseae, Bambusoideae, Poaceae) and its related genera ......... 55 Evaluation of the Polymorphic of Microsatellites Markers in Guadua angustifolia (Poaceae: Bambusoideae) ......................................................................................................................................... 64 Occurrence of filamentous fungi on Brazilian giant bamboo............................................................................. 80 Consideration of the flowering periodicity of Melocanna baccifera through past records and recent flowering with a 48-year interval........................................................................................................... 90 Gregarious flowering of Melocanna baccifera around north east India Extraction of the flowering event by using satellite image data ...................................................................................................... -
Poaceae, Bambusoideae) in a New Genus from Laos’ Karst Areas, with a Unique Adaptation to Seasonal Drought
A peer-reviewed open-access journal PhytoKeys 156: 125–137 (2020) The first succulent bamboo 125 doi: 10.3897/phytokeys.156.51636 RESEARCH ARTICLE http://phytokeys.pensoft.net Launched to accelerate biodiversity research Discovery of the first succulent bamboo (Poaceae, Bambusoideae) in a new genus from Laos’ karst areas, with a unique adaptation to seasonal drought Thomas Haevermans1, Dulce Mantuano1, 4, Meng-Yuan Zhou2, Vichith Lamxay3, Agathe Haevermans1, Patrick Blanc5, De-Zhu Li2 1 Institut de Systématique Évolution Biodiversité (ISYEB), Muséum national d’histoire naturelle, Centre natio- nal de la recherche scientifique, École Pratique des Hautes Études, Université des Antilles, Sorbonne Université. 45 rue Buffon, CP 50, 75005 Paris, France 2 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China 3 Faculty of Natural Sciences, National University of Laos, Vientiane Capital, Lao PDR 4 Plant Ecophysiology Lab, Institute of Biology, Universidade Federal do Rio de Janeiro, Brazil 5 Centre national de la recherche scientifique (CNRS), 3 rue Michel-Ange, Paris, France Corresponding author: Thomas Haevermans ([email protected]) Academic editor: Maria Vorontsova | Received 1 March 2020 | Accepted 26 June 2020 | Published 21 August 2020 Citation: Haevermans T, Mantuano D, Zhou M-Y, Lamxay V, Haevermans A, Blanc P, Li, D-Z (2020) Discovery of the first succulent bamboo (Poaceae, Bambusoideae) in a new genus from Laos’ karst areas, with a unique adaptation to seasonal drought. PhytoKeys 156: 125–137. https://doi.org/10.3897/phytokeys.156.51636 Abstract Lush jungle flagship species, woody bamboos (Poaceae–Bambusoideae) are famed for their synchronous flowering as well as the extensive “bamboo forests” some species can form in tropical or temperate environ- ments. -
Addis Ababa University Addis Ababa Ethiopia July, 2020
Phylogenetic Relationships among Indigenous and Introduced Bamboo Species and Genetic Diversity Study of Ethiopian Lowland Bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] Using cpDNA Genes ( matK , ndhF and rps16 ) and ISSR Markers Oumer Abdie Oumer Addis Ababa University Addis Ababa Ethiopia July, 2020 Phylogenetic Relationships among Indigenous and Introduced Bamboo Species and Genetic Diversity Study of Ethiopian Lowland Bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] Using cpDNA Genes ( matK , ndhF and rps16 ) and ISSR Markers Oumer Abdie Oumer A Dissertation Submitted to Department of Microbial, Cellular and Molecular Biology in Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology (Applied Genetics) Addis Ababa University Addis Ababa Ethiopia July, 2020 DECLARATION I declare that this Dissertation entitled “Phylogenetic Relationships among Indigenous and Introduced Bamboo Species and Genetic Diversity Study of Ethiopian Lowland Bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] Using cpDNA Genes ( matK , ndhF and rps16 ) and ISSR Markers” submitted for the Degree of Doctor of Philosophy (PhD) in Biology (Applied Genetics) to the School of Graduate Studies, Addis Ababa University, is my original work and its composition has never been submitted elsewhere for any other award. All sources of materials used for the Dissertation have been duly acknowledged. Name: Oumer Abdie Signature: . Date: 20- July-2020 . i ACKNOWLEDGMENT .( ْٱﻟ َﺤ ْﻤﺪ ُ ِ ﱠ @ ِ َ ﺭ ِّ ﺏ ْٱﻟ َٰﻌ َﻠ ِﻤ َﻴﻦ ) First and for most, I would like to thank the Almighty I am highly indebted to eIpress my deepest and genuine appreciation and than.s to my supervisors0 the late Dr. Jifle Dagne, Dr. Tileye Feyissa and Dr. -
Poaceae: Bambusoideae) Reveals Ten Major Lineages and Low Rate of Molecular Divergence
Molecular Phylogenetics and Evolution 56 (2010) 821–839 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence Chun-Xia Zeng a,b,c,1, Yu-Xiao Zhang a,b,c,1, Jimmy K. Triplett d, Jun-Bo Yang a,c, De-Zhu Li a,c,* a Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, PR China b Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China c Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming, Yunnan 650204, PR China d Department of Biology, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA article info abstract Article history: The temperate bamboos (tribe Arundinarieae) are notorious for being taxonomically extremely difficult. Received 30 December 2009 China contains some of the world’s greatest diversity of the tribe Arundinarieae, with most genera and Revised 31 March 2010 species endemic. Previous investigation into phylogenetic relationships of the temperate bamboos Accepted 31 March 2010 revealed several major clades, but emphasis on the species-level relationships among taxa in North Available online 8 April 2010 America and Japan. To further elucidate relationships among the temperate bamboos, a very broad sam- pling of Chinese representatives was examined. We produced 9463 bp of sequences from eight non-cod- Keywords: ing chloroplast regions for 146 species in 26 genera and 5 outgroups. -
Hainan-BR-2.Pdf
Bot. Rev. (2010) 76:346–376 DOI 10.1007/s12229-010-9055-7 Seed Plant Endemism on Hainan Island: A Framework for Conservation Actions Javier Francisco-Ortega1,2 & Zhong-Sheng Wang3,12 & Fa-Guo Wang4 & Fu-Wu Xing4 & Hong Liu2,5 & Han Xu6 & Wei-Xiang Xu3 & Yi-Bo Luo7 & Xi-Qiang Song8 & Stephan Gale9 & David E. Boufford10 & Mike Maunder1,2,11 & Shu-Qing An3,12 1 Department of Biological Sciences, Florida International University, Miami FL33199, USA 2 Center for Tropical Plant Conservation, Fairchild Tropical Botanic Garden, Coral Gables, Miami, FL 33156, USA 3 Laboratory of Forest Ecology and Global Change, School of Life Science, Nanjing University, Nanjing 210093, People’s Republic of China 4 South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People’s Republic of China 5 Department of Earth and Environment, Florida International University, Miami FL33199, USA 6 Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, People’s Republic of China 7 Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, People’s Republic of China 8 Key Laboratory of Tropical Horticultural Plant Resources and Genetic Improvement, Hainan University, Haikou 570228, People’s Republic of China 9 Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong SAR, People’s Republic of China 10 Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA 11 Al Ain Wildlife Park and Resort, PO Box 1204, Al Ain, Abu Dhabi, United Arab Emirates 12 Authors for Correspondence; e-mail: [email protected]; [email protected] Published online: 20 May 2010 # The New York Botanical Garden 2010 Abstract Hainan, the second largest island of China, has the most extensive and best preserved tropical forests of this country.