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Morphological and Molecular Barcode Analysis of the Medicinal Tree Mimusops Coriacea (A.DC.) Miq
Morphological and molecular barcode analysis of the medicinal tree Mimusops coriacea (A.DC.) Miq. collected in Ecuador Katherine Bustamante1, Efrén Santos-Ordóñez2,3, Migdalia Miranda4, Ricardo Pacheco2, Yamilet Gutiérrez5 and Ramón Scull5 1 Facultad de Ciencias Químicas, Ciudadela Universitaria “Salvador Allende,” Universidad de Guayaquil, Guayaquil, Ecuador 2 Centro de Investigaciones Biotecnológicas del Ecuador, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador 3 Facultad de Ciencias de la Vida, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador 4 Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador 5 Instituto de Farmacia y Alimentos, Universidad de La Habana, Ciudad Habana, Cuba ABSTRACT Background: Mimusops coriacea (A.DC.) Miq., (Sapotaceae), originated from Africa, were introduced to coastal areas in Ecuador where it is not extensively used as a traditional medicine to treat various human diseases. Different therapeutically uses of the species include: analgesic, antimicrobial, hypoglycemic, inflammation and pain relieve associated with bone and articulation-related diseases. Furthermore, Mimusops coriacea could be used as anti-oxidant agent. However, botanical, chemical or molecular barcode information related to this much used species is not available from Ecuador. In this study, morphological characterization was performed from leaves, stem and seeds. Furthermore, genetic characterization was performed using molecular barcodes for rbcL, matk, ITS1 and ITS2 using DNA extracted from leaves. Methods: Macro-morphological description was performed on fresh leaves, stem Submitted 25 March 2019 and seeds. For anatomical evaluation, tissues were embedded in paraffin and Accepted 29 August 2019 transversal dissections were done following incubation with sodium hypochlorite Published 11 October 2019 and safranin for coloration and fixated later in glycerinated gelatin. -
Accounting for Variation of Substitution Rates Through Time in Bayesian Phylogeny Reconstruction of Sapotoideae (Sapotaceae)
Molecular Phylogenetics and Evolution 39 (2006) 706–721 www.elsevier.com/locate/ympev Accounting for variation of substitution rates through time in Bayesian phylogeny reconstruction of Sapotoideae (Sapotaceae) Jenny E.E. Smedmark ¤, Ulf Swenson, Arne A. Anderberg Department of Phanerogamic Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden Received 9 September 2005; revised 4 January 2006; accepted 12 January 2006 Available online 21 February 2006 Abstract We used Bayesian phylogenetic analysis of 5 kb of chloroplast DNA data from 68 Sapotaceae species to clarify phylogenetic relation- ships within Sapotoideae, one of the two major clades within Sapotaceae. Variation in substitution rates through time was shown to be a very important aspect of molecular evolution for this data set. Relative rates tests indicated that changes in overall rate have taken place in several lineages during the history of the group and Bayes factors strongly supported a covarion model, which allows the rate of a site to vary over time, over commonly used models that only allow rates to vary across sites. Rate variation over time was actually found to be a more important model component than rate variation across sites. The covarion model was originally developed for coding gene sequences and has so far only been tested for this type of data. The fact that it performed so well with the present data set, consisting mainly of data from noncoding spacer regions, suggests that it deserves a wider consideration in model based phylogenetic inference. Repeatability of phylogenetic results was very diYcult to obtain with the more parameter rich models, and analyses with identical settings often supported diVerent topologies. -
New Genetic Markers for Sapotaceae Phylogenomics: More Than 600 Nuclear Genes Applicable from Family to Population Levels
Molecular Phylogenetics and Evolution 160 (2021) 107123 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels Camille Christe a,b,*,1, Carlos G. Boluda a,b,1, Darina Koubínova´ a,c, Laurent Gautier a,b, Yamama Naciri a,b a Conservatoire et Jardin botaniques, 1292 Chamb´esy, Geneva, Switzerland b Laboratoire de botanique syst´ematique et de biodiversit´e de l’Universit´e de Gen`eve, Department of Botany and Plant Biology, 1292 Chamb´esy, Geneva, Switzerland c Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel,^ Rue Emile-Argand 11, 2000 Neuchatel,^ Switzerland ARTICLE INFO ABSTRACT Keywords: Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Conservation Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here Gene capture we identified531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae STR using target capture and NGS. The probes were designed using two genome skimming samples from Capur Phylogenetics odendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara Population genetics Species tree zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously Tropical trees published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. -
Taxonomic Revision of the Genus Manilkara ( Sapotaceae) in Madagascar
E D I N B U R G H J O U R N A L O F B O T A N Y 65 (3): 433–446 (2008) 433 Ó Trustees of the Royal Botanic Garden Edinburgh (2008) doi:10.1017/S096042860800485X TAXONOMIC REVISION OF THE GENUS MANILKARA ( SAPOTACEAE) IN MADAGASCAR V. PLANA1 &L.GAUTIER2 A revision of the five Madagascan species of the genus Manilkara (Sapotaceae)is presented, including a key, descriptions, diagnostic characters, ecological notes and a distribution map. Of the seven species originally described by Aubre´ville, Manilkara tampoloensis is placed in synonymy with M. boivinii, and M. sohihy is removed from the genus and placed within the existing Labramia boivinii (Pierre) Aubre´v. Keywords. Madagascar, Manilkara, Sapotaceae, taxonomic revision. Introduction The genus Manilkara Adans., probably best known for American species such as M. zapota (sapodilla) and M. chicle (chicle), is a pantropical genus comprising c.82 species (Govaerts et al., 2001). Of these, approximately one third are found in Africa (Plana, in prep.) and Madagascar. Although the Madagascan species of Manilkara share some characteristics with mainland African species, none are found in Africa. Afro-Madagascan species can be divided, according to their gross morphology, into three broad biogeographic regions: Madagascar, East and South Africa, and Central and West Africa. Malagasy species share characteristics with species in both regions, where they are commonly constituents of evergreen forest. Manilkara is one of six genera constituting the subtribe Manilkarinae H.J.Lam (tribe Mimusopeae Hartog) (Pennington, 1991) which also includes Labramia A.DC., Faucherea Lecomte, Northia Hook.f., Labourdonnaisia Bojer and Letestua Lecomte. -
DNA Barcoding Identifies Cryptic Animal Tool Materials
DNA barcoding identifies cryptic animal tool materials Matthew Steele, Linda Neaves, Barbara Klump, James St Clair, Joana Fernandes, Vanessa Hequet, Phil Shaw, Peter Hollingsworth, Christian Rutz To cite this version: Matthew Steele, Linda Neaves, Barbara Klump, James St Clair, Joana Fernandes, et al.. DNA barcoding identifies cryptic animal tool materials. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2021, 118 (29), pp.e2020699118. hal-03285541 HAL Id: hal-03285541 https://hal.inrae.fr/hal-03285541 Submitted on 13 Jul 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License DNA barcoding identifies cryptic animal tool materials BRIEF REPORT Matthew P. Steelea,1, Linda E. Neavesb,c,1, Barbara C. Klumpa,2, James J. H. St Claira, Joana R. S. M. Fernandesa, Vanessa Hequetd, Phil Shawa, Peter M. Hollingsworthb, and Christian Rutza,3 aCentre for Biological Diversity, School of Biology, University of St Andrews, St Andrews KY16 9TH, United Kingdom; bRoyal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom; cThe Fenner School of Environment and Society, The Australian National University, Canberra, ACT 2600, Australia; and dInstitut de Recherche pour le Développement, Centre de Nouméa, 98848 Nouméa, New Caledonia, France Edited by Scott V. -
Complete Chloroplast Genome of Argania Spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae
plants Article Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae Slimane Khayi 1,* , Fatima Gaboun 1, Stacy Pirro 2, Tatiana Tatusova 3, Abdelhamid El Mousadik 4 , Hassan Ghazal 5 and Rachid Mentag 1,* 1 CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco; [email protected] 2 Iridian Genomes, Inc., Bethesda, MD 20817, USA; [email protected] 3 National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20817, USA; [email protected] 4 Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir 80000, Morocco; [email protected] 5 National Center for Scientific and Technological Research (CNRST), Rabat 10102, Morocco; [email protected] * Correspondence: [email protected] (R.M.); [email protected] (S.K.); Tel.: +212-661-558-622 (R.M.); +212-664-141-380 (S.K.) Received: 18 May 2020; Accepted: 25 June 2020; Published: 13 October 2020 Abstract: Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. -
Patterns of Diversification Amongst Tropical Regions
ORIGINAL RESEARCH ARTICLE published: 03 December 2014 doi: 10.3389/fgene.2014.00362 Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae Kate E. Armstrong 1,2,3*, Graham N. Stone 2, James A. Nicholls 2, Eugenio Valderrama 2,3, Arne A. Anderberg 4, Jenny Smedmark 5, Laurent Gautier 6, Yamama Naciri 6, Richard Milne 7 and James E. Richardson 3,8 1 The New York Botanical Garden, Bronx, NY, USA 2 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland 3 Royal Botanic Garden Edinburgh, Edinburgh, Scotland 4 Naturhistoriska Riksmuseet, Stockholm, Sweden 5 University Museum of Bergen, Bergen, Norway 6 Conservatoire et Jardin botaniques, Genève, Switzerland 7 Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, Scotland 8 Laboratorio de Botánica y Sistemática, Universidad de los Andes, Bogotá DC, Colombia Edited by: Species diversity is unequally distributed across the globe, with the greatest concentration Marshall Abrams, University of occurring in the tropics. Even within the tropics, there are significant differences in the Alabama at Birmingham, USA numbers of taxa found in each continental region. Manilkara is a pantropical genus of Reviewed by: trees in the Sapotaceae comprising c. 78 species. Its distribution allows for biogeographic Marcial Escudero, Doñana Biological Station - Consejo Superior de investigation and testing of whether rates of diversification differ amongst tropical Investigaciones Científicas, Spain regions. The age and geographical origin of Manilkara are inferred to determine whether Ze-Long Nie, Chinese Academy of Gondwanan break-up, boreotropical migration or long distance dispersal have shaped Sciences, China its current disjunct distribution. Diversification rates through time are also analyzed to *Correspondence: determine whether the timing and tempo of speciation on each continent coincides with Kate E. -
University of Florida Thesis Or Dissertation Formatting
SIDEROXYLON SECTION FRIGORICOLA (SAPOTACEAE): A CLADE ENDEMIC TO TEMPERATE NORTH AMERICA By PAUL THOMAS COROGIN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2015 © 2015 Paul Thomas Corogin To Ananda Devi, my wife and soulmate, whose presence beside me gives me strength ACKNOWLEDGMENTS I thank the following herbaria for loans of specimens: A, AUA, FLAS, FNPS, FSU, FTG, GA, GH, LSU, MISS, OKL, TENN, UNA, US, USCH, and USF. I thank the following people without whose help this study could not have succeeded: Kent Perkins of the University of Florida Herbarium (FLAS) for his generous assistance with processing specimen loans; Brett Jestrow of Fairchild Tropical Garden (FTG) and Jennifer Stafford of the National Park Service herbarium (FNPS) for facilitating my examination of south Florida herbarium specimens; Jimi Sadle, Mark Whitten, Bob Simons, Wendy Poag, Lisa Kruse, and Dee Mincey, for assisting with field work; Karen Kelley, electron microscopy manager, and Kim Backer-Kelley, lab technician, of the ICBR Electron Microscopy Core lab at the University of Florida, for their kindness and expertise, and Kurt Neubig for his guidance and insights with the molecular work. And I thank my supervisory committee: Drs. Norris Williams, Pamela Soltis, Nigel Smith, and my advisor, Dr. Walter S. Judd, who gives so generously of his time to inspire in his students something of his passion for scholarship and botanical field expertise. I have indeed studied and learned from one of the best there is. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS................................................................................................ -
Towards an Account of Sapotaceae for Flora Malesiana
Gardens’ Bulletin Singapore 63(1 & 2): 145–153. 2011 145 Towards an account of Sapotaceae for Flora Malesiana Peter Wilkie Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, U.K. [email protected] ABSTRACT. An overview of the pan-tropical family Sapotaceae is provided with particular focus on the Malesian region. Past and current taxonomic and phylogenetic research is summarised and publications relating to the production of a Flora Malesiana Sapotaceae account highlighted. Challenges to delivering a Flora Malesiana account are identified and some potential solutions suggested. Keywords. Flora Malesiana, Sapotaceae, systematics, taxonomy Introduction Sapotaceae is a pantropical family of trees and shrubs and is composed of about 50 genera and 1000 species. In Malesia there are an estimated 15 genera and 300 species. The family is ecologically important with representatives of the family common in the forests of Malesia. They occur from beach forests at sea level to mossy montane forests at over 4000 m altitude. The family is economically important and produces the important heavy hardwood timber, Bitis (mainly Madhuca utilis (Ridl.) H.J.Lam, Palaquium ridleyi King & Gamble and Palaquium stellatum King & Gamble) and the light to medium hardwood, Nyatoh, from many other species (Ng 1972). The family also produces edible fruit with Manilkara zapota (L.) P.Royen (sapodilla plum, ciku), and Chrysophyllum cainito L. (star apple), introduced from Central America, the most widely cultivated. The latex produced from Palaquium gutta (Hook.) Burck (Gutta Percha) has been used in the insulation of cables, golf balls and in root fillings in dentistry (Burkill 1966, Boer & Ella 2000). -
Typifications in Neotropical Sapotaceae
PhytoKeys 170: 45–69 (2020) A peer-reviewed open-access journal doi: 10.3897/phytokeys.170.54718 RESEARCH ARTICLE https://phytokeys.pensoft.net Launched to accelerate biodiversity research Typifications in neotropical Sapotaceae Anderson Alves-Araújo1,2, Quélita dos Santos Moraes2, Renara Nichio-Amaral1, Victor Santos Miranda1 1 Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo-UFES, Rodovia BR 101 Norte, Km 60, São Mateus-ES, Brazil 2 Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Feira de Santana-BA, Brazil Corresponding author: Anderson Alves-Araujo ([email protected]) Academic editor: G. Shimizu | Received 25 May 2020 | Accepted 28 November 2020 | Published 21 December 2020 Citation: Alves-Araújo A, dos Santos Moraes Q, Nichio-Amaral R, Miranda VS (2020) Typifications in neotropical Sapotaceae. PhytoKeys 170: 45–69. https://doi.org/10.3897/phytokeys.170.54718 Abstract Sapotaceae is historically known as having a tricky and challenging taxonomy due to tangled morphologic heterogeneity. Consequently, this resulted in a large number of described genera and binomials. After Pennington’s Flora Neotropica work, several of those nomenclature issues were resolved. Nevertheless, many binomials remain unsolved and up for typification. Thus, following the International Code of Nomenclature for Algae, Fungi and Plants, we propose 74 new lectotype designations, four of these are second-step typifications. Keywords Ericales, historical botany, lectotypification, nomenclature Introduction Sapotaceae has 65–70 genera with around 1,250 species and is an important plant component from tropical regions in the world (Swenson et al. 2020). It is an economi- cally interesting family by providing latex-derived products such as gutta-percha and chewing gum, valuable and durable timber and edible fruits (Pennington 1990, 1991). -
Details/Summary/ 197892/0]
2017 LanguaL proposals from Australian NUTTAB2010 The Australian NUTTAB2010 data set includes 484 indigenous foods, which presents is a particular challenge for LanguaL indexing, as most of these plants and animals are absent from facet B of the thesaurus. 1. ANIMAL USED AS FOOD SOURCE Proposals for new animal food sources in facet B are pretty straightforward. ANIMAL USED AS FOOD SOURCE> ANIMAL (MAMMAL) [B1134] BT proposed AI synonyms NUTTAB2010 proposed descriptor ANIMAL POSSUM Phalangeriformes, or possums, any of a number brushtail Trichosurus (MAMMAL) of arboreal marsupial species native to possum, arnhemensis, [B1134] Australia, New Guinea, and Sulawesi: trichosuru northern - Phalangeridae (possums and cuscuses), a s, brushtail family of mammals native to Australia and New pseudoch possum, flesh Guinea containing most of the species referred eirus, cooked; to as "possums" in Australia phalanger Northern - Common brushtail possum (Trichosurus idae Brushtail vulpecula), a common possum in Australian Possum urban areas, invasive in New Zealand [15A20119] - Common ringtail possum (Pseudocheirus Trichosurus peregrinus), also common in Australian urban arnhemensis, areas, absent from New Zealand northern [https://en.wikipedia.org/wiki/Possum] brushtail possum, kidney cooked; Northern Brushtail Possum [15A20120] Trichosurus arnhemensis, northern brushtail possum, liver cooked; Northern Brushtail Possum [15A20121] MARINE SEA COW <SCINAM>Sirenia Illiger, 1811 [ITIS 180676] sirenia, Dugong MAMMAL sirens [B1122] Sirenia, commonly referred to -
2020 Phang.Pdf (8.127Mb)
An account of Madhuca (Sapotaceae) for the Flora of Singapore including a comparison of virtual and in-herbarium taxonomic methods Thesis submitted in partial fulfilment for the MSc in the Biodiversity and Taxonomy of Plants. Aireen Phang August 2020 1 CONTENTS Abstract …………………………………………………………………………………….… 2 Acknowledgements ………………………………………………………………………...… 3 List of Tables ………………………………………………………………………………… 4 List of Figures ………………………………………………………………………….…….. 5 List of Appendices …………………………………………………………………………… 6 1. INTRODUCTION ……………………………………………………………………….. 7 1.1 Aims of the Project ……………..………………………………………….…………….. 7 1.2 Introduction to Madhuca ………………………………………………….……………... 7 1.3 Taxonomic History of Madhuca …………………………………………….………….. 11 1.4 Molecular Advances in Sapotaceae Classification ……………………………………... 16 2. MATERIALS & METHODS ………………………………………………………….. 23 2.1 Taxonomic Investigation ……..…………………………………………………………. 23 2.1.1 Sources of Information ……………………………………………………… 23 2.1.2 Digital Specimen Images ……………………………………………………… 24 2.1.3 In-herbarium Analysis ..………….………………….………………………... 25 2.2 Species Concept ………………………………………………………………………... 26 2.3 Morphological Character Assessment ……………….…………………………………. 26 2.4 Taxonomic Treatment …………………………………………………………………... 29 2.5 National Red List Assessments ………………………………………………………….. 30 3. RESULTS ……………………………………………………………………………….. 32 3.1 Taxonomy .……………………………………………………………………………… 32 3.1.1 Digital Specimen Images ……………………………………………………… 34 3.1.2 In-herbarium Analysis ………………………………………………………... 37 3.2 Morphological Character Assessment