DOCSLIB.ORG

The Pennsylvania State University the Graduate School

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Pennsylvania State University the Graduate School The Pennsylvania State University The Graduate School COMPUTATIONAL METHODS FOR COMPARATIVE GENOMICS OF NON- MODEL SPECIES A CASE STUDY IN THE PARASITIC PLANT FAMILY OROBANCHACEAE A Dissertation in Biology by Eric Kenneth Wafula Ó2019 Eric Kenneth Wafula Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2019 ii The dissertation of Eric Kenneth Wafula was reviewed and approved* by the following: Claude W. dePamphilis Professor of Biology Dissertation Advisor Naomi S. Altman Professor of Statistics Istvan Albert Research Professor of Bioinformatics Director of Online Graduate Certificate in Applied Bioinformatics James H. Marden Professor of Biology Associate Director Huck Institute of the Life Sciences Chair of Committee Stephen W. Schaeffer Professor of Biology Associate Department Head of Graduate Education *Signatures are on file in the Graduate School iii ABSTRACT The rapid development of sequencing technologies coupled with the continuous drop in the cost of sequencing has facilitated studies of genomes, transcriptomes, and metagenomes of a variety of organisms at unprecedented resolution. However, sequencing and accurately assembling the genomes of many non-model organisms, especially plants, remains cost-prohibitive because they are often large or complex, which pose challenges to current sequencing technologies and assembly algorithms. Therefore, many researchers are now relying on comparative genomic approaches that integrate data from genomes and transcriptomes to gain novel insights into evolutionary history, including the unique features of complex non-model organisms. The genomes of parasitic angiosperms are relatively understudied. Past genome-scale research has been focused primarily on understanding the mechanisms of plant parasitism as a means to control weedy species that parasitize crops. Research efforts to understand the evolutionary aspects of parasitic plants have been restricted to the plastome degradation associated with the reduction and loss of photosynthesis. In this dissertation, I present PlantTribes 2, a gene family analysis framework that utilizes objective classifications of complete protein sequences from genomes for comparative and evolutionary analyses of gene families and transcriptomes on a genome-scale. Utilizing PlantTribes 2, and the draft genome of Striga asiatica, including transcriptomes of sister lineages, I present evidence for an ancient polyploidy event shared by parasitic Orobanchaceae and closely related non-parasitic sister lineages. The observed gene family evolutionary dynamics in Striga reveal an association between whole genome duplication (WGD) and the evolutionary origins of parasitism in Orobanchaceae. Gene losses are overrepresented by iv older genes whose functions are complemented by the host, while gene gains often result from the WGD event specific to Orobanchaceae whose functions are associated with further adaptations to the parasitic lifestyle. The evolutionary transition from autotrophy to heterotrophy is associated with changes in gene functions common to non-parasitic plants. These findings will provide a focus for future studies into the mechanisms of plant parasitism and potential targets for parasite control. v TABLE OF CONTENTS LIST OF FIGURES ......................................................................................................... viii LIST OF TABLES .............................................................................................................. x ACKNOWLEDGEMENTS ............................................................................................... xi Chapter 1 Introduction and overview ................................................................................. 1 Introduction ..................................................................................................................... 1 Gene discovery ............................................................................................................... 2 Gene expression following character evolution .............................................................. 3 Phylogenetic analysis ...................................................................................................... 5 Gene and genome duplication ......................................................................................... 6 Parasitic plants ................................................................................................................ 8 Content of this dissertation ........................................................................................... 10 References ..................................................................................................................... 11 Chapter 2 PlantTribes 2: tools for comparative gene family analysis in plant genomics . 19 Abstract ......................................................................................................................... 19 Introduction ................................................................................................................... 20 Pipeline implementation ............................................................................................... 22 Gene family scaffolds ................................................................................................... 24 Analysis tools ................................................................................................................ 26 Assembly post-processing ........................................................................................ 26 Gene family classification ......................................................................................... 26 Gene family alignment estimation ............................................................................ 27 Gene family phylogenetic inference ......................................................................... 28 Estimation of genome duplications ........................................................................... 29 Pipeline test dataset ....................................................................................................... 30 Performance evaluation ................................................................................................ 32 vi Evaluation of gene family inference methods .......................................................... 32 Evaluation of sequence classifiers ............................................................................ 35 Evaluation of targeted gene family assembly ........................................................... 37 Conclusions ................................................................................................................... 39 Availability and requirements ....................................................................................... 40 References ..................................................................................................................... 41 Chapter 3 Ancient whole genome duplication events in the parasitic lineages of Orobanchaceae .................................................................................................................. 48 Abstract ......................................................................................................................... 48 Introduction ................................................................................................................... 48 Results and discussion .................................................................................................. 51 Gene annotation ........................................................................................................ 51 Genome cleaning .................................................................................................. 52 Annotation-specific repeat masking ..................................................................... 53 Gene prediction and quality assessment ............................................................... 54 Genome duplication history ...................................................................................... 57 Global gene family phylogenetic analysis ............................................................ 57 Duplicated gene divergence of phylogenetic syntelogs ........................................ 59 Genome structure analysis .................................................................................... 63 Conclusions ................................................................................................................... 73 Materials and methods .................................................................................................. 74 Genome assembly cleaning ....................................................................................... 74 Repeat library construction ....................................................................................... 75 RNA-Seq sequencing and transcriptome assembly .................................................. 75 Gene prediction and functional assignment .............................................................. 77 Gene family classification ......................................................................................... 79 Phylogenetic and gene collinearity analysis ............................................................. 80 Analysis of synonymous substitutions rates (Ks) ....................................................
Load more

Recommended publications
  • (Olea Europaea L.) Through Plastome Sequence Comparison Roberto Mariotti1, Nicolò GM Cultrera1, Concepcion Muñoz Díez2, Luciana Baldoni1*, Andrea Rubini1
    Mariotti et al. BMC Plant Biology 2010, 10:211 http://www.biomedcentral.com/1471-2229/10/211 RESEARCH ARTICLE Open Access Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison Roberto Mariotti1, Nicolò GM Cultrera1, Concepcion Muñoz Díez2, Luciana Baldoni1*, Andrea Rubini1 Abstract Background: The cultivated olive (Olea europaea L.) is the most agriculturally important species of the Oleaceae family. Although many studies have been performed on plastid polymorphisms to evaluate taxonomy, phylogeny and phylogeography of Olea subspecies, only few polymorphic regions discriminating among the agronomically and economically important olive cultivars have been identified. The objective of this study was to sequence the entire plastome of olive and analyze many potential polymorphic regions to develop new inter-cultivar genetic markers. Results: The complete plastid genome of the olive cultivar Frantoio was determined by direct sequence analysis using universal and novel PCR primers designed to amplify all overlapping regions. The chloroplast genome of the olive has an organisation and gene order that is conserved among numerous Angiosperm species and do not contain any of the inversions, gene duplications, insertions, inverted repeat expansions and gene/intron losses that have been found in the chloroplast genomes of the genera Jasminum and Menodora, from the same family as Olea. The annotated sequence was used to evaluate the content of coding genes, the extent, and distribution of repeated and long dispersed sequences and the nucleotide composition pattern. These analyses provided essential information for structural, functional and comparative genomic studies in olive plastids. Furthermore, the alignment of the olive plastome sequence to those of other varieties and species identified 30 new organellar polymorphisms within the cultivated olive.
    [Show full text]
  • The Genomic Impact of Mycoheterotrophy in Orchids
    fpls-12-632033 June 8, 2021 Time: 12:45 # 1 ORIGINAL RESEARCH published: 09 June 2021 doi: 10.3389/fpls.2021.632033 The Genomic Impact of Mycoheterotrophy in Orchids Marcin J ˛akalski1, Julita Minasiewicz1, José Caius2,3, Michał May1, Marc-André Selosse1,4† and Etienne Delannoy2,3*† 1 Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdansk,´ Gdansk,´ Poland, 2 Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, France, 3 Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Orsay, France, 4 Sorbonne Université, CNRS, EPHE, Muséum National d’Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, Paris, France Mycoheterotrophic plants have lost the ability to photosynthesize and obtain essential mineral and organic nutrients from associated soil fungi. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy Edited by: Susann Wicke, to mycoheterotrophy has occurred independently in many major lineages of land Humboldt University of Berlin, plants, most frequently in Orchidaceae. Yet the molecular mechanisms underlying this Germany shift are still poorly understood. A comparison of the transcriptomes of Epipogium Reviewed by: Maria D. Logacheva, aphyllum and Neottia nidus-avis, two completely mycoheterotrophic orchids, to other Skolkovo Institute of Science autotrophic and mycoheterotrophic orchids showed the unexpected retention of several and Technology, Russia genes associated with photosynthetic activities. In addition to these selected retentions, Sean W. Graham, University of British Columbia, the analysis of their expression profiles showed that many orthologs had inverted Canada underground/aboveground expression ratios compared to autotrophic species. Fatty Craig Barrett, West Virginia University, United States acid and amino acid biosynthesis as well as primary cell wall metabolism were among *Correspondence: the pathways most impacted by this expression reprogramming.
    [Show full text]
  • Outline of Angiosperm Phylogeny
    Outline of angiosperm phylogeny: orders, families, and representative genera with emphasis on Oregon native plants Priscilla Spears December 2013 The following listing gives an introduction to the phylogenetic classification of the flowering plants that has emerged in recent decades, and which is based on nucleic acid sequences as well as morphological and developmental data. This listing emphasizes temperate families of the Northern Hemisphere and is meant as an overview with examples of Oregon native plants. It includes many exotic genera that are grown in Oregon as ornamentals plus other plants of interest worldwide. The genera that are Oregon natives are printed in a blue font. Genera that are exotics are shown in black, however genera in blue may also contain non-native species. Names separated by a slash are alternatives or else the nomenclature is in flux. When several genera have the same common name, the names are separated by commas. The order of the family names is from the linear listing of families in the APG III report. For further information, see the references on the last page. Basal Angiosperms (ANITA grade) Amborellales Amborellaceae, sole family, the earliest branch of flowering plants, a shrub native to New Caledonia – Amborella Nymphaeales Hydatellaceae – aquatics from Australasia, previously classified as a grass Cabombaceae (water shield – Brasenia, fanwort – Cabomba) Nymphaeaceae (water lilies – Nymphaea; pond lilies – Nuphar) Austrobaileyales Schisandraceae (wild sarsaparilla, star vine – Schisandra; Japanese
    [Show full text]
  • Invasive Alien Plants an Ecological Appraisal for the Indian Subcontinent
    Invasive Alien Plants An Ecological Appraisal for the Indian Subcontinent EDITED BY I.R. BHATT, J.S. SINGH, S.P. SINGH, R.S. TRIPATHI AND R.K. KOHL! 019eas Invasive Alien Plants An Ecological Appraisal for the Indian Subcontinent FSC ...wesc.org MIX Paper from responsible sources `FSC C013604 CABI INVASIVE SPECIES SERIES Invasive species are plants, animals or microorganisms not native to an ecosystem, whose introduction has threatened biodiversity, food security, health or economic development. Many ecosystems are affected by invasive species and they pose one of the biggest threats to biodiversity worldwide. Globalization through increased trade, transport, travel and tour- ism will inevitably increase the intentional or accidental introduction of organisms to new environments, and it is widely predicted that climate change will further increase the threat posed by invasive species. To help control and mitigate the effects of invasive species, scien- tists need access to information that not only provides an overview of and background to the field, but also keeps them up to date with the latest research findings. This series addresses all topics relating to invasive species, including biosecurity surveil- lance, mapping and modelling, economics of invasive species and species interactions in plant invasions. Aimed at researchers, upper-level students and policy makers, titles in the series provide international coverage of topics related to invasive species, including both a synthesis of facts and discussions of future research perspectives and possible solutions. Titles Available 1.Invasive Alien Plants : An Ecological Appraisal for the Indian Subcontinent Edited by J.R. Bhatt, J.S. Singh, R.S. Tripathi, S.P.
    [Show full text]
  • Resolution of Deep Angiosperm Phylogeny Using Conserved Nuclear Genes and Estimates of Early Divergence Times
    ARTICLE Received 24 Mar 2014 | Accepted 11 Aug 2014 | Published 24 Sep 2014 DOI: 10.1038/ncomms5956 OPEN Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times Liping Zeng1, Qiang Zhang2, Renran Sun1, Hongzhi Kong3, Ning Zhang1,4 & Hong Ma1,5 Angiosperms are the most successful plants and support human livelihood and ecosystems. Angiosperm phylogeny is the foundation of studies of gene function and phenotypic evolution, divergence time estimation and biogeography. The relationship of the five divergent groups of the Mesangiospermae (B99.95% of extant angiosperms) remains uncertain, with multiple hypotheses reported in the literature. Here transcriptome data sets are obtained from 26 species lacking sequenced genomes, representing each of the five groups: eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae. Phylogenetic analyses using 59 carefully selected low-copy nuclear genes resulted in highly supported relationships: sisterhood of eudicots and a clade containing Chloranthaceae and Ceratophyllaceae, with magnoliids being the next sister group, followed by monocots. Our topology allows a re-examination of the evolutionary patterns of 110 morphological characters. The molecular clock estimates of Mesangiospermae diversification during the late to middle Jurassic correspond well to the origins of some insects, which may have been a factor facilitating early angiosperm radiation. 1 State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratoryof Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Yangpu District, Shanghai 200433, China. 2 Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin 541006, China.
    [Show full text]
  • Studies on the Trichomes of Some Oleaceae, Structure and Ontogeny
    STUDIES ON THE TRICHOMES OF SOME OLEACEAE, STRUCTURE AND ONTOGENY B~ J. A. INAMDAR (Department of Botany, Sardar Patel Univeraity, Vallabh Vidyanagar, Gujarat) Received August 22, 1967 (Communicated by Prof. V. Puff, r.A.sc.) ABSTRACT Some twelve types of tricho~aes are described for four species of Jasminum and Nyctanthes arbor-tristis L. They fall under two main categories, the eglandular and the glandular trichomes. The systematic position of Nyctanthes seems to be quite natural in the family Oleaceae. INTRODUCTION The family Oleaceae has received considerable attention of the botanists particularly with reference to the systcmatic position of Nyctanthes and the monotypic genus Dimetra. Airy SEaw (1952) transferred these gcnera to the Verbenaceae on morphological grounds. Stant (1952) has supported Airy Shaw on anatomical grounds. Johnson (1957) in a review of the family Oleaceae opined that Nyctanthes should be excluded from Oleaceae based on the cytological findings of Taylor (1945). On the other hand the embryo- logical data (Patel, 1963; Kapil, 1967) suggests that Nyctanthes should be retained in the Oleaceae. Several workers (De Bary, 1884; Cowan, 1950, Goodspeed, 1954; Carlquist, 1958, 1959a, 1959b, 1959c, 1961; Mathur, 1961 ; Ramayya, 1962 a, 1962b, 1963) have described the structure and development of trichomes and glands in several angisoperm families. The present investi- gation was carried out to find if the trichomes ~nd glands could be of any help in settling the doubtful systematic position of Oleaceous genera. The present paper deals with the study of eglandular and glandular (glands) trichomes on the vegetative organs of four species of Jasminum, viz., J.
    [Show full text]
  • Towards Resolving Lamiales Relationships
    Schäferhoff et al. BMC Evolutionary Biology 2010, 10:352 http://www.biomedcentral.com/1471-2148/10/352 RESEARCH ARTICLE Open Access Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences Bastian Schäferhoff1*, Andreas Fleischmann2, Eberhard Fischer3, Dirk C Albach4, Thomas Borsch5, Günther Heubl2, Kai F Müller1 Abstract Background: In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past. Results: Our analysis of the rapidly evolving trnK/matK, trnL-F and rps16 chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae) and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position. Conclusions: Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales.
    [Show full text]
  • Invisible Connections: Introduction to Parasitic Plants Dr
    Invisible Connections: Introduction to Parasitic Plants Dr. Vanessa Beauchamp Towson University What is a parasite? • An organism that lives in or on an organism of another species (its host) and benefits by deriving nutrients at the other's expense. Symbiosis https://www.superpharmacy.com.au/blog/parasites-protozoa-worms-ectoparasites Food acquisition in plants: Autotrophy Heterotrophs (“different feeding”) • True parasites: obtain carbon compounds from host plants through haustoria. • Myco-heterotrophs: obtain carbon compounds from host plants via Image Credit: Flickr User wackybadger, via CC mycorrhizal fungal connection. • Carnivorous plants (not parasitic): obtain nutrients (phosphorus, https://commons.wikimedia.org/wiki/File:Pin nitrogen) from trapped insects. k_indian_pipes.jpg http://www.welivealot.com/venus-flytrap- facts-for-kids/ Parasite vs. Epiphyte https://chatham.ces.ncsu.edu/2014/12/does-mistletoe-harm-trees-2/ By © Hans Hillewaert /, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=6289695 True Parasitic Plants • Gains all or part of its nutrition from another plant (the host). • Does not contribute to the benefit of the host and, in some cases, causing extreme damage to the host. • Specialized peg-like root (haustorium) to penetrate host plants. https://www.britannica.com/plant/parasitic-plant https://chatham.ces.ncsu.edu/2014/12/does-mistletoe-harm-trees-2/ Diversity of parasitic plants Eudicots • Parasitism has evolved independently at least 12 times within the plant kingdom. • Approximately 4,500 parasitic species in Monocots 28 families. • Found in eudicots and basal angiosperms • 1% of the dicot angiosperm species • No monocot angiosperm species Basal angiosperms Annu. Rev. Plant Biol. 2016.67:643-667 True Parasitic Plants https://www.alamy.com/parasitic-dodder-plant-cuscuta-showing-penetration-parasitic-haustor The defining structural feature of a parasitic plant is the haustorium.
    [Show full text]
  • Pollen and Stamen Mimicry: the Alpine Flora As a Case Study
    Arthropod-Plant Interactions DOI 10.1007/s11829-017-9525-5 ORIGINAL PAPER Pollen and stamen mimicry: the alpine flora as a case study 1 1 1 1 Klaus Lunau • Sabine Konzmann • Lena Winter • Vanessa Kamphausen • Zong-Xin Ren2 Received: 1 June 2016 / Accepted: 6 April 2017 Ó The Author(s) 2017. This article is an open access publication Abstract Many melittophilous flowers display yellow and Dichogamous and diclinous species display pollen- and UV-absorbing floral guides that resemble the most com- stamen-imitating structures more often than non-dichoga- mon colour of pollen and anthers. The yellow coloured mous and non-diclinous species, respectively. The visual anthers and pollen and the similarly coloured flower guides similarity between the androecium and other floral organs are described as key features of a pollen and stamen is attributed to mimicry, i.e. deception caused by the flower mimicry system. In this study, we investigated the entire visitor’s inability to discriminate between model and angiosperm flora of the Alps with regard to visually dis- mimic, sensory exploitation, and signal standardisation played pollen and floral guides. All species were checked among floral morphs, flowering phases, and co-flowering for the presence of pollen- and stamen-imitating structures species. We critically discuss deviant pollen and stamen using colour photographs. Most flowering plants of the mimicry concepts and evaluate the frequent evolution of Alps display yellow pollen and at least 28% of the species pollen-imitating structures in view of the conflicting use of display pollen- or stamen-imitating structures. The most pollen for pollination in flowering plants and provision of frequent types of pollen and stamen imitations were pollen for offspring in bees.
    [Show full text]
  • Aeginetia Indica L
    Bioscience Discovery, 9(4):498-500, Oct - 2018 © RUT Printer and Publisher Print & Online, Open Access, Research Journal Available on http://jbsd.in ISSN: 2229-3469 (Print); ISSN: 2231-024X (Online) Research Article Aeginetia indica L. and Conyza bonariensis (L.) Cronq. are new distributional records in Satpuda range of Khandesh region, Maharashtra Tanveer A. Khan1 and Javed V. Khan2 1Department of Botany, H. J. Thim College of Arts and Science, Mehrun, Jalgaon, Maharashtra, India. 2Department of Biotechnology, PGCSTR, Jalgaon, Maharashtra, India. Article Info Abstract Received: 21-09-2018, Satpuda range of Khandesh region with great diversity of plants. The present paper Revised: 06-10-2018, deals with addition of two new flowering plants records from different parts of the Accepted: 11-10-2018 Satpuda ranges of Khandesh region of Maharashtra are new distributional records for Keywords: the first time. These species are Aeginetia indica L. (Orobanchaceae) and Conyza New Records, Satpuda bonariensis (L.) Cronq. (Asteraceae) are reported for the first time for Satpuda ranges Ranges, Khandesh of Khandesh region of Maharashtra. The study provides a detailed taxonomic region. description, photographs and relevant information based on fresh collections. INTRODUCTION and 760 28' East longitude. Khandesh covers a total Vegetational and floristic studies have been area of 26,703.36 sq. km. The forest of the gained increased importance and relevance in recent Khandesh region is of dry deciduous type. The years in view of the present need for a thorough, up vegetation varies with the changes in altitude, to date assessment of the natural resources of our aspect and rainfall. While working on floristic of vast country.
    [Show full text]
  • Eucalyptus Parvula L.Johnson & K
    NSW SCIENTIFIC COMMITTEE Eucalyptus parvula L.Johnson & K. Hill (Myrtaceae) Review of Current Information in NSW June 2008 Current status: Eucalyptus parvula is currently listed as Vulnerable under the Commonwealth Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act). The NSW Scientific Committee recently determined that Eucalyptus parvula meets criteria for listing as Endangered in NSW under the Threatened Species Conservation Act 1995 (TSC Act), based on information contained in this report and other information available for the species. Species description: Eucalyptus parvula is described in Brooker et al. (2000) as follows: “Tree to 10 m tall. Bark smooth throughout or with some persistent rough, grey bark on lower trunk; smooth bark predominantly dark grey, at times with ribbons of decorticated bark in the upper branches. Juvenile stem rounded in cross-section; juvenile leaves opposite for many pairs, sessile, elliptical to ovate or lanceolate, 1.6-4cm long, 0.9-1.3cm wide, green. Crown characteristically retains large numbers of juvenile leaves, with some petiolate, lanceolate intermediate and adult leaves. Crown leaves opposite or alternate, petiole 0-0.3cm long, elliptical to lanceolate, 3-8cm long, 0.5- 1.5cm wide, base tapering to petiole, concolorous, dull, green, penniveined, moderately reticulate, intramarginal vein parallel to and just within margin, oil glands mostly island. Inflorescences axillary unbranched, peduncles 0.3-0.7cm long, 7-flowered; buds sessile, ovoid to clavate, smooth or slightly warty, scar present, operculum conical to rounded, stamens irregularly flexed or inflexed, anthers cuboid to globoid, versatile, slits separate, style short, stigma blunt, locules 3 or 4, the placentae each with 4 vertical ovule rows; flowers white.
    [Show full text]
  • Monitoring and Indicators of Forest Biodiversity in Europe – from Ideas to Operationality
    Monitoring and Indicators of Forest Biodiversity in Europe – From Ideas to Operationality Marco Marchetti (ed.) EFI Proceedings No. 51, 2004 European Forest Institute IUFRO Unit 8.07.01 European Environment Agency IUFRO Unit 4.02.05 IUFRO Unit 4.02.06 Joint Research Centre Ministero della Politiche Accademia Italiana di University of Florence (JRC) Agricole e Forestali – Scienze Forestali Corpo Forestale dello Stato EFI Proceedings No. 51, 2004 Monitoring and Indicators of Forest Biodiversity in Europe – From Ideas to Operationality Marco Marchetti (ed.) Publisher: European Forest Institute Series Editors: Risto Päivinen, Editor-in-Chief Minna Korhonen, Technical Editor Brita Pajari, Conference Manager Editorial Office: European Forest Institute Phone: +358 13 252 020 Torikatu 34 Fax. +358 13 124 393 FIN-80100 Joensuu, Finland Email: [email protected] WWW: http://www.efi.fi/ Cover illustration: Vallombrosa, Augustus J C Hare, 1900 Layout: Kuvaste Oy Printing: Gummerus Printing Saarijärvi, Finland 2005 Disclaimer: The papers in this book comprise the proceedings of the event mentioned on the back cover. They reflect the authors' opinions and do not necessarily correspond to those of the European Forest Institute. © European Forest Institute 2005 ISSN 1237-8801 (printed) ISBN 952-5453-04-9 (printed) ISSN 14587-0610 (online) ISBN 952-5453-05-7 (online) Contents Pinborg, U. Preface – Ideas on Emerging User Needs to Assess Forest Biodiversity ......... 7 Marchetti, M. Introduction ...................................................................................................... 9 Session 1: Emerging User Needs and Pressures on Forest Biodiversity De Heer et al. Biodiversity Trends and Threats in Europe – Can We Apply a Generic Biodiversity Indicator to Forests? ................................................................... 15 Linser, S. The MCPFE’s Work on Biodiversity .............................................................
    [Show full text]