Darwin As a Plant Scientist: a Southern Hemisphere Perspective
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Stable and Widespread Structural Heteroplasmy in Chloroplast Genomes Revealed by a New Long-Read Quantification Method
bioRxiv preprint doi: https://doi.org/10.1101/692798; this version posted July 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Classification: Biological Sciences, Evolution Title: Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method Weiwen Wang a, Robert Lanfear a a Research School of Biology, Australian National University, Canberra, ACT, Australia, 2601 Corresponding Author: Weiwen Wang, [email protected] Robert Lanfear, [email protected], +61 2 6125 2536 Keywords: Single copy inversion, flip-flop recombination, chloroplast genome structural heteroplasmy 1 bioRxiv preprint doi: https://doi.org/10.1101/692798; this version posted July 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. 1 Abstract 2 The chloroplast genome usually has a quadripartite structure consisting of a large 3 single copy region and a small single copy region separated by two long inverted 4 repeats. It has been known for some time that a single cell may contain at least two 5 structural haplotypes of this structure, which differ in the relative orientation of the 6 single copy regions. However, the methods required to detect and measure the 7 abundance of the structural haplotypes are labour-intensive, and this phenomenon 8 remains understudied. -
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 -
Alphabetical Lists of the Vascular Plant Families with Their Phylogenetic
Colligo 2 (1) : 3-10 BOTANIQUE Alphabetical lists of the vascular plant families with their phylogenetic classification numbers Listes alphabétiques des familles de plantes vasculaires avec leurs numéros de classement phylogénétique FRÉDÉRIC DANET* *Mairie de Lyon, Espaces verts, Jardin botanique, Herbier, 69205 Lyon cedex 01, France - [email protected] Citation : Danet F., 2019. Alphabetical lists of the vascular plant families with their phylogenetic classification numbers. Colligo, 2(1) : 3- 10. https://perma.cc/2WFD-A2A7 KEY-WORDS Angiosperms family arrangement Summary: This paper provides, for herbarium cura- Gymnosperms Classification tors, the alphabetical lists of the recognized families Pteridophytes APG system in pteridophytes, gymnosperms and angiosperms Ferns PPG system with their phylogenetic classification numbers. Lycophytes phylogeny Herbarium MOTS-CLÉS Angiospermes rangement des familles Résumé : Cet article produit, pour les conservateurs Gymnospermes Classification d’herbier, les listes alphabétiques des familles recon- Ptéridophytes système APG nues pour les ptéridophytes, les gymnospermes et Fougères système PPG les angiospermes avec leurs numéros de classement Lycophytes phylogénie phylogénétique. Herbier Introduction These alphabetical lists have been established for the systems of A.-L de Jussieu, A.-P. de Can- The organization of herbarium collections con- dolle, Bentham & Hooker, etc. that are still used sists in arranging the specimens logically to in the management of historical herbaria find and reclassify them easily in the appro- whose original classification is voluntarily pre- priate storage units. In the vascular plant col- served. lections, commonly used methods are systema- Recent classification systems based on molecu- tic classification, alphabetical classification, or lar phylogenies have developed, and herbaria combinations of both. -
Polyploidy and the Evolutionary History of Cotton
POLYPLOIDY AND THE EVOLUTIONARY HISTORY OF COTTON Jonathan F. Wendel1 and Richard C. Cronn2 1Department of Botany, Iowa State University, Ames, Iowa 50011, USA 2Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, Oregon 97331, USA I. Introduction II. Taxonomic, Cytogenetic, and Phylogenetic Framework A. Origin and Diversification of the Gossypieae, the Cotton Tribe B. Emergence and Diversification of the Genus Gossypium C. Chromosomal Evolution and the Origin of the Polyploids D. Phylogenetic Relationships and the Temporal Scale of Divergence III. Speciation Mechanisms A. A Fondness for Trans-oceanic Voyages B. A Propensity for Interspecific Gene Exchange IV. Origin of the Allopolyploids A. Time of Formation B. Parentage of the Allopolyploids V. Polyploid Evolution A. Repeated Cycles of Genome Duplication B. Chromosomal Stabilization C. Increased Recombination in Polyploid Gossypium D. A Diverse Array of Genic and Genomic Interactions E. Differential Evolution of Cohabiting Genomes VI. Ecological Consequences of Polyploidization VII. Polyploidy and Fiber VIII. Concluding Remarks References The cotton genus (Gossypium ) includes approximately 50 species distributed in arid to semi-arid regions of the tropic and subtropics. Included are four species that have independently been domesticated for their fiber, two each in Africa–Asia and the Americas. Gossypium species exhibit extraordinary morphological variation, ranging from herbaceous perennials to small trees with a diverse array of reproductive and vegetative -
Phytochemical Profile and Antioxidant Activity of the Aerial Part Extracts from Matthiola Incana Subsp
DOI: 10.1002/cbdv.202100167 FULL PAPER Phytochemical Profile and Antioxidant Activity of the Aerial Part Extracts from Matthiola incana subsp. rupestris and subsp. pulchella (Brassicaceae) Endemic to Sicily Natalizia Miceli,*a Emilia Cavò,a, b Vivienne Spadaro,c Francesco Maria Raimondo,d Salvatore Ragusa,e Francesco Cacciola,f Yassine Oulad El Majdoub,a Katia Arena,a Luigi Mondello,a, g, h, i Concetta Condurso,j Fabrizio Cincotta,j and Maria Fernanda Tavianoa a Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Palatucci, 98168 Messina, Italy, e-mail: [email protected] b Foundation ‘Prof. Antonio Imbesi’, University of Messina, Piazza Pugliatti 1, 98122 Messina, Italy, c Department STEBICEF/Section of Botany, Anthropology and Zoology, University of Palermo, Via Archirafi 38, 90123 Palermo, Italy, d PLANTA/Research, Documentation and Training Center, Via Serraglio Vecchio 28, 90123 Palermo, Italy, e Department of Health Sciences, University ‘Magna Graecia’ of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy, f Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Via Consolare Valeria, 98125 Messina, Italy, g Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Palatucci, 98168 Messina, Italy, h BeSep s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Palatucci, 98168 Messina, Italy, i Department of Sciences and Technologies for Human and Environment, University Campus Bio-Medico of Rome, via Àlvaro del Portillo 21, 00128 Rome, Italy, j Department of Veterinary Sciences, University of Messina, Viale Palatucci, 98168 Messina, Italy. -
The First Geological Map of Patagonia
Revista de la Asociación Geológica Argentina 64 (1): 55 - 59 (2009) 55 THE FIRST GEOLOGICAL MAP OF PATAGONIA Eduardo O. ZAPPETTINI and José MENDÍA Servicio Geológico Minero Argentino (SEGEMAR) - Av. Julio A. Roca 651 (1322) Buenos Aires Emails: [email protected], [email protected] ABSTRACT This contribution analyses the first geological map of Patagonia drawn by Darwin around 1840, and colour-painted by Darwin himself. It had remained unpublished and only a small version in black and white had been printed before. The different units mapped by Darwin are analysed from a modern perspective, and his ability to show a synthesis of the complex geological structure of Patagonia is stressed. Keywords: Geological map, Patagonia, Patagonian Shingle, Darwin geologist. RESUMEN: El primer mapa geológico de la Patagonia. La presente contribución analiza el primer mapa geológico de la Patagonia reali- zado por Darwin cerca de 1840, pintado en colores por el mismo Darwin, que ha permanecido inédito y del que sólo se cono- cía una versión de tamaño reducido en blanco y negro. Se analizan las diferentes unidades mapeadas por Darwin desde una perspectiva actual, destacándose su habilidad para mostrar en esa síntesis la compleja estructura de la Patagonia. Palabras clave: Mapa geológico, Patagonia, Rodados Patagónicos, Darwin geólogo. DARWIN AND THE VOYAGE OF HMS BEAGLE At the time Charles Darwin set sail on board HMS Beagle on a journey that was to last two years and ended up lasting five, he was not more than an amateur naturalist that had quitted his medical courses and after that abandoned his in- tention of applying for a position in the Church of England, just to embrace the study of natural history. -
GENOME EVOLUTION in MONOCOTS a Dissertation
GENOME EVOLUTION IN MONOCOTS A Dissertation Presented to The Faculty of the Graduate School At the University of Missouri In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy By Kate L. Hertweck Dr. J. Chris Pires, Dissertation Advisor JULY 2011 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled GENOME EVOLUTION IN MONOCOTS Presented by Kate L. Hertweck A candidate for the degree of Doctor of Philosophy And hereby certify that, in their opinion, it is worthy of acceptance. Dr. J. Chris Pires Dr. Lori Eggert Dr. Candace Galen Dr. Rose‐Marie Muzika ACKNOWLEDGEMENTS I am indebted to many people for their assistance during the course of my graduate education. I would not have derived such a keen understanding of the learning process without the tutelage of Dr. Sandi Abell. Members of the Pires lab provided prolific support in improving lab techniques, computational analysis, greenhouse maintenance, and writing support. Team Monocot, including Dr. Mike Kinney, Dr. Roxi Steele, and Erica Wheeler were particularly helpful, but other lab members working on Brassicaceae (Dr. Zhiyong Xiong, Dr. Maqsood Rehman, Pat Edger, Tatiana Arias, Dustin Mayfield) all provided vital support as well. I am also grateful for the support of a high school student, Cady Anderson, and an undergraduate, Tori Docktor, for their assistance in laboratory procedures. Many people, scientist and otherwise, helped with field collections: Dr. Travis Columbus, Hester Bell, Doug and Judy McGoon, Julie Ketner, Katy Klymus, and William Alexander. Many thanks to Barb Sonderman for taking care of my greenhouse collection of many odd plants brought back from the field. -
Berberine: Botanical Occurrence, Traditional Uses, Extraction Methods, and Relevance in Cardiovascular, Metabolic, Hepatic, and Renal Disorders
REVIEW published: 21 August 2018 doi: 10.3389/fphar.2018.00557 Berberine: Botanical Occurrence, Traditional Uses, Extraction Methods, and Relevance in Cardiovascular, Metabolic, Hepatic, and Renal Disorders Maria A. Neag 1, Andrei Mocan 2*, Javier Echeverría 3, Raluca M. Pop 1, Corina I. Bocsan 1, Gianina Cri¸san 2 and Anca D. Buzoianu 1 1 Department of Pharmacology, Toxicology and Clinical Pharmacology, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania, 2 Department of Pharmaceutical Botany, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania, 3 Department of Environmental Sciences, Universidad de Santiago de Chile, Santiago de Chile, Chile Edited by: Berberine-containing plants have been traditionally used in different parts of the world for Anna Karolina Kiss, the treatment of inflammatory disorders, skin diseases, wound healing, reducing fevers, Medical University of Warsaw, Poland affections of eyes, treatment of tumors, digestive and respiratory diseases, and microbial Reviewed by: Pinarosa Avato, pathologies. The physico-chemical properties of berberine contribute to the high diversity Università degli Studi di Bari Aldo of extraction and detection methods. Considering its particularities this review describes Moro, Italy various methods mentioned in the literature so far with reference to the most important Sylwia Zielinska, Wroclaw Medical University, Poland factors influencing berberine extraction. Further, the common separation and detection *Correspondence: methods like thin layer chromatography, high performance liquid chromatography, and Andrei Mocan mass spectrometry are discussed in order to give a complex overview of the existing [email protected] methods. Additionally, many clinical and experimental studies suggest that berberine Specialty section: has several pharmacological properties, such as immunomodulatory, antioxidative, This article was submitted to cardioprotective, hepatoprotective, and renoprotective effects. -
1 Charles Darwin's Notebooks from the Voyage of the `Beagle`. Transcribed, Edited and Introduced by Gordon Chancellor and John
Charles Darwin’s Notebooks from the Voyage of the `Beagle`. Transcribed, edited and introduced by Gordon Chancellor and John van Wythe. xxxiii + 615 pp. Cambridge, UK: Cambridge University Press. 2009. $ 150 (cloth). Until now, it has not been possible to read in book form the immediate notes that Darwin himself had written during his 1832-1836 voyage of H.M.S. Beagle. Darwin’s Beagle records comprised five different kinds: field notebooks, personal diary, geological and zoological diaries, and specimen catalogues. Unlike the many other documents that Darwin created during the voyage, the field notebooks are not confined to any one subject. They contain notes and observations on geology, zoology, botany, ecology, weather notes, barometer and thermometer readings, ethnography, archaeology, and linguistics as well as maps, drawings, financial records, shopping lists, reading notes, and personal entries. The editors described the notebooks as the most difficult and complex of all of Darwin’s manuscripts. They were for the most part written in pencil which was often faint or smeared. They were generally not written while sitting at a desk but held in one hand, on mule or horseback or on the deck of the Beagle. Furthermore the lines were very short and much was not written in complete sentences. Added to this, they were full of Darwin’s chaotic spelling of foreign names so the handwriting was sometimes very difficult to decipher. Alternative readings were often possible. Darwin did not number the pages of the notebooks, and often wrote in them at different times from opposite ends. Most of the notebook space was devoted to geological descriptions and drawings, a reflection of Darwin’s interest in the works of Charles Lyell and his previous fieldwork with Adam Sedgwick. -
Berberidaceae) Endemic to China
Phytotaxa 204 (2): 147–152 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ PHYTOTAXA Copyright © 2015 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.204.2.5 Taxonomic notes on three species of Epimedium (Berberidaceae) endemic to China YAN-JUN ZHANG, HAI-SHAN DANG, JIAN-QIANG LI* & YING WANG * Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China * Authors for correspondence: E-mails: [email protected]; [email protected] Abstract Three species of Epimedium (Berberidaceae), E. reticulatum, E. shuichengense and E. truncatum, are controversial based on flower characteristics. In this paper, the descriptions of their flower characters of these three species are revised based on our extensive studies in herbaria and observations in the field and cultivation. E. reticulatum is transferred from ser. Brachycerae to ser. Campanulatae, and E. shuichengense is recognized as a member of ser. Davidianae. The holotype and isotypes of E. reticulatum represent two species, E. reticulatum and E. membranaceum, and the type material of E. truncatum has been lost. Here we lectotypy E. reticulatum and neotypify E. truncatum. Key words: Epimedium, flower characters, revision, lectotype, neotype Introduction Epimedium Linnaeus (1753: 117) is the largest herbaceous genus of Berberidaceae, with about 58 species distributed disjunctly and very unevenly in temperate hilly or montane regions from Algeria in North Africa to Japan in Asia (Stearn 2002; Ying et al. 2011). China is the diversity center of Epimedium, and possesses about 48 species of the genus which are all endemics except Epimedium koreanum Nakai (1936: 63). -
Jan Dvorak (As Quickly Written Down by a Person with Poor Hearing…Me)
1/22/2018 The Impact of Polyploidy on Genome Evolution in Poales and Other Monocots “I don’t have to emphasize that gene duplications are the fabric of evolution in plants.” -Jan Dvorak (as quickly written down by a person with poor hearing…me) Michael R. McKain The University of Alabama @mrmckain @mrmckain Poales Diversity Grass genomes: the choose your own adventure of genome evolution • ~22,800 species • ~11,088 species in Poaceae • Transposons (McClintock, Wessler) • GC content bias (Carels and Bernardi 2000) • Three WGD events 0 0 4 0 0 • rho (Peterson et al. 2004) 3 y c n 0 e 0 u 2 q e r F • 0 sigma (Tang et al. 2010) 0 1 • tau (Tang et al. 2010, Jiao et al. 2014) 0 %GC Givnish et al. 2010 @mrmckain Schnable et al., 2009 Zeroing in on WGD placement Banana genome Pineapple genome How has ancient polyploidy altered the genomic landscape in grasses and other Poales? D’Hont et al. 2012 Ming, VanBuren et al. 2015 Recovered sigma after grass divergence from commelinids Recovered sigma after grass+pineapple divergence from commelinids @mrmckain @mrmckain 1 1/22/2018 Phylotranscriptomic approach Coalescence-based Phylogeny of 234 Single-copy genes • Sampling 27 transcriptomes and 7 genomes • Phylogeny consistent with previous • Representation for all families (except Thurniaceae) in nuclear gene results Poales • Conflicting topology with • RNA from young leaf or apical meristem, a combination of chloroplast genome tree: Moncot Tree of Life and 1KP • Ecdeiocolea/Joinvillea sister instead of • General steps: a grade • Trinity assembly • Typha -
Ontogenetic Studies on the Determination of the Apical Meristem In
Ontogenetic studies on the determination of the apical meristem in racemose inflorescences D i s s e r t a t i o n Zur Erlangung des Grades Doktor der Naturwissenschaften Am Fachbereich Biologie Der Johannes Gutenberg-Universität Mainz Kester Bull-Hereñu geb. am 19.07.1979 in Santiago Mainz, 2010 CONTENTS SUMMARY OF THE THESIS............................................................................................ 1 ZUSAMMENFASSUNG.................................................................................................. 2 1 GENERAL INTRODUCTION......................................................................................... 3 1.1 Historical treatment of the terminal flower production in inflorescences....... 3 1.2 Structural understanding of the TF................................................................... 4 1.3 Parallel evolution of the character states referring the TF............................... 5 1.4 Matter of the thesis.......................................................................................... 6 2 DEVELOPMENTAL CONDITIONS FOR TERMINAL FLOWER PRODUCTION IN APIOID UMBELLETS...................................................................................................... 7 2.1 Introduction...................................................................................................... 7 2.2 Materials and Methods..................................................................................... 9 2.2.1 Plant material....................................................................................