DOCSLIB.ORG

Genome Survey Sequencing of Dioscorea Zingiberensis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genome Survey Sequencing of Dioscorea Zingiberensis Genome Genome Survey Sequencing of Dioscorea zingiberensis Journal: Genome Manuscript ID gen-2018-0011.R2 Manuscript Type: Article Date Submitted by the Author: 22-May-2018 Complete List of Authors: Zhou, Wen; Shaanxi Normal University, Life Science School Li, Bin; Shaanxi Normal University, Life Science School Li, Lin; Shaanxi Normal University, Life Science School Ma, wen; Shaanxi Normal University, Life Science School Liu, Yuanchu;Draft Shaanxi Normal University, Life Science School Feng, Shuchao; Shaanxi Normal University, Life Science School Wang, Zhezhi; Shaanxi Normal University, Life Science School Keyword: Dioscorea zingiberensis, Genome survey sequencing, Genome analysis Is the invited manuscript for consideration in a Special N/A Issue? : https://mc06.manuscriptcentral.com/genome-pubs Page 1 of 34 Genome 1 Genome survey sequencing of Dioscorea zingiberensis 2 3 Wen Zhou+; Bin Li+; Lin Li; Wen Ma; Yuanchu Liu; Shuchao Feng; Zhezhi Wang* 4 5 1 Key Laboratory of the Ministry of Education for Medicinal Resources and Natural 6 Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China 7 2 National Engineering Laboratory for Resource Development of Endangered Chinese Crude 8 Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China 9 10 + These authors contributed equally to Draftthis work. 11 12 *Correspondence: Prof. Zhe-Zhi WANG; [email protected]; Tel.: +86-29-85310260 1 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 2 of 34 13 Abstract 14 Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal 15 sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. 16 Despite its large economic value, genomic information of this Dioscorea genus is currently 17 unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by 18 next-generation sequencing technology together with a genome size investigation inferred by flow 19 cytometry. The whole genome survey of D. zingiberensis generated 31.48 Gb of sequence data 20 with approximately 78.70× coverage. The estimated genome size is 800 Mb, with a high level of 21 heterozygosity based on K-mer analysis. These reads were assembled into 334,288 contigs with a 22 N50 length of 1,079 bp, which were furtherDraft assembled into 92,163 scaffolds with a total length of 23 173.46 Mb. A total of 4935 genes, 81 tRNAs, 69 rRNAs, and 661 miRNAs were predicted by the 24 genome analysis, and 263,484 repeated sequences were obtains with 419,372 simple sequence 25 repeats (SSRs). Among these SSRs, the mononucleotide repeat type was the most abundant (up to 26 54.60% of the total SSRs), followed by the dinucleotide (29.60%), trinucleotide (11.37%), 27 tetranucleotide (3.53%), pentanucleotide (0.65%), and hexanucleotide (0.25%) nucleotide repeat 28 types. The 1C-value of D. zingiberensis was calibrated against Salvia miltiorrhiza and calculated 29 as 0.87 pg (851 Mb) by flow cytometry, which was very close to the result of the genome survey. 30 This is the first report of genome-wide characterization within this taxon. 31 Key Words: Dioscorea zingiberensis, Genome survey sequencing, Genome analysis 2 https://mc06.manuscriptcentral.com/genome-pubs Page 3 of 34 Genome 32 Introduction 33 D. zingiberensis is an important and widely used medicinal herb in Traditional Chinese Medicine 34 (TCM). It has been applied for the treatment of various diseases, such as cough, anthrax, 35 rheumatoid arthritis, and sprains as well as cardiac diseases (Li et al. 2010a; Qin et al. 2009). 36 Plentiful diosgenin, a type of steroidal saponin extracted from the rhizomes of D. zingiberensis, is 37 an important steroidal precursor used in the pharmaceutical industry. In the medical industry, 38 diosgenin is widely used as the starting material for the synthesis of many steroidal drugs (e.g., 39 antioxidants, antiinflammatories, androgen, oestrogen, and contraceptives) due to the similarity in 40 their skeletons (Bertrand et al. 2009; Wang et al. 2007). More importantly, steroidal sapogenins 41 are attractive to many synthetic and medicinalDraft chemists aiming to harness their anticancer activity 42 (Minato et al. 2013). As the demand of the global market increases at 8% annually, steroid 43 hormones such as sexual hormones, cortical hormones, and protein anabolic hormones call for a 44 matching supply of the precursor to be produced (Bai et al. 2015). 45 At present, the extraction process of diosgenin from D. zingiberensis usually generates plenty of 46 high-acid and high-strength wastewater, which cannot be ignored as a great threat to the 47 environment. In consideration of this, microorganism bioengineering is an effective method for 48 producing diosgenin. However, genetic studies on D. zingiberensis remain underdeveloped 49 compared with many other herbs, such as Salvia miltiorrhiza (Wenping et al. 2011), Dendrobium 50 officinale (Liang et al. 2015), and Ganoderma lucidum (Chen et al. 2012), which might be due to 51 the insufficient genetic or genomic resources available for D. zingiberensis. 52 In recent years, great advances in genome survey sequencing technology and bioinformatics have 53 opened a new avenue to characterize the genetic background of organisms, e.g., Myricarubra (Jiao 3 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 4 of 34 54 et al. 2012), Gracilariopsis lemaneiformis (Zhou et al. 2013), Fagopyrum tartaricum (Hou et al. 55 2016), and others. Compared with the conventional methods for gene cloning and sequencing, the 56 new generation sequencing technology affords a quick, easy, and fullscale method of 57 investigation. To investigate and provide a genomic resource for further research (e.g., structural 58 and functional genomics studies, molecular cloning, comparative and evolutionary studies) on this 59 species, we conducted a genome survey of D. zingiberensis using NGS technology. This study 60 could pave the way for accelerating the progress of gene discovery and better utilization of the 61 existing genomic information in the future. 62 Materials and methods 63 Plant materials Draft 64 D. zingiberensis was collected from Xunyang County, Shaanxi Province, China. Voucher 65 specimens were prepared and identified by Prof. Tian Xianhua (College of Life Sciences, Shaanxi 66 Normal University, Xi’an, P. R. China) and then deposited at the Key Laboratory of Ministry of 67 Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal 68 University. Young leaves were collected and frozen in liquid nitrogen and stored at –80°C prior to 69 genomic DNA extraction using the Plant Genomic DNA Kit (Tiangen biotech, Beijing, China) 70 following the manufacturer’s instructions. The extracts were electrophoresed on 1% agarose to 71 confirm the DNA quality and quantity. The concentrations of nucleic acids and proteins were 72 measured spectrophotometrically at 260 nm on a BioPhotometer (Eppendorf, Germany). 73 Genome size estimation by flow cytometry 82 Salvia miltiorrhiza, (1C = 0.66 pg DNA, (Zhang et al. 2015)) served as an internal reference 83 standard. One to two young leaves per plant, equivalent to 300-500 mg, were excised and placed 4 https://mc06.manuscriptcentral.com/genome-pubs Page 5 of 34 Genome 84 into a 100 mm Petri dish. To this, 1.5 mL of LB01 buffer (Dpooležel et al. 1989) was added, and 85 the two types of tissue were chopped simultaneously with a razor for 30 s (~60 chops per sample) 86 to release the nuclei. The resulting homogenate was filtered through a 48 µm nylon filter into a 1.5 87 mL tube. Then, the nuclear suspension was stained with 10 µL of PI (10 mg/mL), and 10 µL of 88 RnaseA (10 mg/mL) was added immediately to prevent the staining of a double-standard RNA. 89 The samples were incubated on ice for 10 minutes. Then, the aqueous suspension of intact nuclei 90 from the samples and the internal reference DNA standard were analysed on a NovoCyte machine 91 (ACEA Biosciences, Inc.) with Novoexpress software (Version 1.2.4.1602). A green argon laser at 92 a wavelength of 488 nm was used as the light source, and the flow of at least 10000 nuclei was 93 measured in the sample. Draft 94 Genome sequencing and sequence assembly 95 Two paired-end libraries with an insert size of 220 base pairs (bp) were constructed from 96 fragmented random genomic DNA following the manufacturer’s instructions (Illumina, Beijing, 97 China). Sequence data were generated by Beijing Biomarker Technologies Co., Ltd. (Beijing, 98 China) using an Illumina HiSeq 2500 sequencing platform. The short tips and low quality 99 sequences of the raw genome survey sequence data were filtered to obtain high quality reads, 100 which were subsequently used for assembly with SOAP de novo software (Li et al. 2010b). All 101 sequencing reads were deposited in the Short Read Archive (SRA) database 102 (http://www.ncbi.nlm.nih.gov/sra/), and they are retrievable under the accession number 103 SRX3235157. 104 Genome size estimation by k-mer analysis 105 In shotgun genome sequencing, short reads are assumed to be randomly generated, so any k-mers 5 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 6 of 34 106 in the reads also occur randomly. Their depth of coverage follows the Poisson distribution (Li and 107 Waterman 2003), and the mean k-mer depth should be equal to the peak value of the k-mer depth 108 distribution. Two paired-end libraries with insert sizes of approximately 220 bp and 500 bp were 109 sequenced on one lane of the Illumina HiSeq 2500 system with the paired-end 150 bp. The 110 high-quality Illumina sequences generated from these two genomic libraries were applied to k-mer 111 counting using SOAPec (v2.01) in the SOAP de novo software package. Then, based on the K-mer 112 analysis, information on the peak depth and the number of 17-mers was obtained.
Load more

Recommended publications
  • Plant Production--Root Vegetables--Yams Yams
    AU.ENCI FOR INTERNATIONAL DEVILOPME4T FOR AID USE ONLY WASHINGTON. 0 C 20823 A. PRIMARYBIBLIOGRAPHIC INPUT SHEET I. SUBJECT Bbliography Z-AFOO-1587-0000 CL ASSI- 8 SECONDARY FICATIDN Food production and nutrition--Plant production--Root vegetables--Yams 2. TITLE AND SUBTITLE A bibliography of yams and the genus Dioscorea 3. AUTHOR(S) Lawani,S.M.; 0dubanjo,M.0. 4. DOCUMENT DATE IS. NUMBER OF PAGES 6. ARC NUMBER 1976 J 199p. ARC 7. REFERENCE ORGANIZATION NAME AND ADDRESS IITA 8. SUPPLEMENTARY NOTES (Sponaoring Ordanization, Publlahera, Availability) (No annotations) 9. ABSTRACT This bibliography on yams bring together the scattered literature on the genus Dioscorea from the early nineteenth century through 1975. The 1,562 entries in this bibliography are grouped into 36 subject categories, and arranged within each category alphabetically by author. Some entries, particularly those whose titles are not sufficiently informative, are annotated. The major section titles in the book are as follows: general and reference works; history and eography; social and cultural importance; production and economics; botany including taxonomy, genetics, and breeding); yam growing (including fertilizers and plant nutrition); pests and diseases; storage; processing; chemical composition, nutritive value, and utilization; toxic and pharmacologically active constituents; author index; and subject index. Most entries are in English, with a few in French, Spanish, or German. 10. CONTROL NUMBER I1. PRICE OF DOCUMENT PN-AAC-745 IT. DrSCRIPTORS 13. PROJECT NUMBER Sweet potatoes Yams 14. CONTRACT NUMBER AID/ta-G-1251 GTS 15. TYPE OF DOCUMENT AID 590-1 44-741 A BIBLIOGRAPHY OF YAMS AND THE GENUS DIOSCOREA by S.
    [Show full text]
  • 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.
    [Show full text]
  • Diversification Into Novel Habitats in the Africa Clade of Dioscorea (Dioscoreaceae): Erect Habit and Elephant’S Foot Tubers Olivier Maurin1,2, A
    Maurin et al. BMC Evolutionary Biology (2016) 16:238 DOI 10.1186/s12862-016-0812-z RESEARCHARTICLE Open Access Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephant’s foot tubers Olivier Maurin1,2, A. Muthama Muasya3*, Pilar Catalan4,5, Eugene Z. Shongwe1, Juan Viruel 6,7, Paul Wilkin 2 and Michelle van der Bank1 Abstract Background: Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or “elephant’sfoot” structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal. Results: The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet.
    [Show full text]
  • Dioscorea Spp.): Implication for Conservation and Agricultural Practices
    RESEARCH ARTICLE Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices Marie Florence Sandrine Ngo Ngwe1,3*, Denis Ndoumou Omokolo1, Simon Joly2 1 Laboratory of Plant Physiology, Higher Teacher’s Training College, University of Yaoundé 1, P. O. Box 47, Yaounde, Cameroon, 2 Institut de recherche en biologie végétale, Montreal Botanical Garden and Université de Montréal, 4101 Sherbrooke East, Montréal, QC, H1X 2B2, Canada, 3 Institute of Agricultural Research for Development-CEREFEN, BP 167, Meyomessala, Cameroon * [email protected] Abstract Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming prac- tices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to OPEN ACCESS properly address the genetic diversity of yam and manage its germplasm. As a first step Citation: Ngo Ngwe MFS, Omokolo DN, Joly S toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic (2015) Evolution and Phylogenetic Diversity of Yam diversity (PD) approach that has the advantage to investigate phylogenetic relationships Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices. PLoS ONE and test hypotheses of species monophyly while alleviating to the problem of ploidy varia- 10(12): e0145364. doi:10.1371/journal.pone.0145364 tion within and among species. The Bayesian phylogenetic analysis of 62 accessions from Editor: Genlou Sun, Saint Mary's University, 7 species from three regions of Cameroon showed that most Dioscorea sections were CANADA monophyletic, but species within sections were generally non-monophyletic.
    [Show full text]
  • UPCOMING EVENTS! and Center for Plant Diversity
    DAVIS BOTANICAL SOCIETY LASTHENIA LASTHENIA, the Newsletter of the Davis Botanical Society, is published in collaboration with the staff of the UC Davis Botanical Conservatory UPCOMING EVENTS! and Center for Plant Diversity. Editor: Kate Mawdsley Issue Contributors: E. Dean, E. San- doval, T. Barry, J. Clary, N. Williams, D. Sat. April 7 Jasper Ridge field trip Burge, S. Sumrall Design: Susan Gloystein Sat. April 21 Picnic Day Herbarium and Conserva- Layout: Ellen Dean tory open houses DBS OFFICERS, 2017-2018 President: Neal Williams Sun. April 29 Arboretum/Conservatory Plant Sale President-elect: Jeffrey Clary Membership Vice President: Thurs. May 3 Spring Meeting and Speaker, Judy Tom Starbuck, Johanna Kwan, & Kate Mawdsley Jernstedt will speak on “Stalking the wild Secretary: Chris Walden Welwitschia” Treasurer: Robert Rhode Past President: Judy Jernstedt Sat. July 14 Bliss State Park field trip Members at Large: Cherilyn Burton, Brenda Grewell Student Member at Large: Ross Brennan Ex officio: Dan Potter, Ernesto Sandoval, Ellen Dean UC Davis Mail ID: BTNY BTNY ID: Mail Davis UC Davis, CA 95616 95616 CA Davis, University of California California of University One Shields Avenue Avenue Shields One Plant Sciences Mail Stop #7 Stop Mail Sciences Plant Center for Plant Diversity Diversity Plant for Center 8 No. 49 Winter 2018 LASTHENIA NEWSLETTER OF THE DAVIS BOTANICAL SOCIETY STEBBINS COLD CANYON RESERVE POST-FIRE: IS RECOVERY IN THE WORKS? A year and a half ago (Lasthenia number Stebbins Cold Canyon Reserve and 46), we published an article by Marcel the surrounding landscape went up in Rejmanek on the effects of the Wragg flames in July of 2015.
    [Show full text]
  • A Plastid Gene Phylogeny of the Yam Genus, Dioscorea: Roots, Fruits and Madagascar
    Systematic Botany (2005), 30(4): pp. 736–749 ᭧ Copyright 2005 by the American Society of Plant Taxonomists A Plastid Gene Phylogeny of the Yam Genus, Dioscorea: Roots, Fruits and Madagascar PAUL WILKIN,1,6 PETER SCHOLS,2 MARK W. C HASE,1 KONGKANDA CHAYAMARIT,3 CAROL A. FURNESS,1 SUZY HUYSMANS,2 FRANCK RAKOTONASOLO,4 ERIK SMETS,2 and CHIRDSAK THAPYAI5 1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, U.K.; 2Laboratory of Plant Systematics, Institute of Botany and Microbiology, K.U.Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; 3Forest Herbarium, 61 Phahonyothin Rd., Chatuchak, Bangkok 10900 Thailand; 4Parc Botanique et Zoologique de Tsimbazaza, BP 4096, Antananarivo, Madagascar; 5Biology Department, Faculty of Science, Naresuan University, Muang District, Phitsanulok 65000, Thailand 6Author for correspondence ([email protected]) Communicating Editor: Alan W. Meerow ABSTRACT. Following recent phylogenetic studies of the families and genera of Dioscoreales, the identification of mono- phyletic infrageneric taxa in the pantropical genus Dioscorea is a priority. A phylogenetic analysis based on sequence data from the plastid genes rbcL and matK is presented, using 67 species of Dioscorea and covering all the main Old World and selected New World lineages. The analysis used 14 outgroup taxa, including Trichopus Gaertn., Tacca J.R. & G. Forster, Stenomeris Planch., Burmannia L. and Thismia Griff. The main findings are: a) that a clade of rhizomatous taxa is sister to the rest of Dioscorea; b) the main Old World groups (such as the right-twining D. sect. Enantiophyllum) are monophyletic and c) there are two distinct lineages among the endemic Malagasy taxa.
    [Show full text]
  • Greenhouse Guide 2014
    Student Name______________________Student Number___________________ Biol 441, 20 points BOTANY GREENHOUSE SELF TOUR This is a self-guided tour of the greenhouses, with a focus on angiosperms. As you go through the various rooms and look at the plants, read the information carefully and answer the questions in each section. Due on or before the last lab period. ROOM 2. LYCOPHYTES: Homosporous lycopods: Huperzia Huperzia are characterized by their equal dichotomizing branching patterns in their shoots, strobili, and roots. The epiphytic tropical species have stomata situated exclusively on the adaxial surface of the leaf (unlike many other plants which have the majority of their stomata situated on the abaxial surface of the leaf). This stomatal arrangement is an adaptation for curtailing water loss, since these tropical epiphytic Huperzia have leaves borne on pendant branches, their abaxial surface is exposed to the sun while the adaxial surface is in the shade Epiphytic Huperzia can achieve very large sizes (with some such as H. goebellii producing hanging branches over 20 ft long!). These plants don’t bear strobili on stalks but the sporangia are typically aggregated towards the branch tips. Some species appear to show adaptations for growing in drier climates: H. goebellii has a thick waxy cuticle that gives it its chalky blue color. Heterosporous lycopods: Selaginella and Isoetes Selaginella is a huge genus containing several hundred species. This is a particularly ancient genus of vascular plants, with fossils of plants almost indistinguishable from modern species occurring in coal swamp deposits from the mid Carboniferous (over 300 million years ago!) Selaginella have no true roots, but instead have highly specialized stilt-like branching systems called “rhizophores.” In addition, Selaginella have independently evolved vessels similar to those in Angiosperms and perhaps most surprisingly two species have also evolved true megaphyllous leaves with reticulate venation very similar to the leaves of angiosperms.
    [Show full text]
  • Dioscorea, Dioscoreaceae
    Journal of Biogeography (J. Biogeogr.) (2016) 43, 750–762 – ORIGINAL Late Cretaceous Early Eocene origin of ARTICLE yams (Dioscorea, Dioscoreaceae) in the Laurasian Palaearctic and their subsequent Oligocene–Miocene diversification Juan Viruel1,2, Jose Gabriel Segarra-Moragues3, Lauren Raz4,Felix Forest5, Paul Wilkin5, Isabel Sanmartın6 and Pilar Catalan2,7* 1Departamento Biologıa Vegetal y Ecologıa, ABSTRACT Facultad de Biologıa, Universidad de Sevilla, Aim Dioscorea (Dioscoreaceae) is a predominantly pantropical genus (< 600 Sevilla 41012, Spain, 2Departamento de species) that includes the third most important tropical tuber crop and species Ciencias Agrarias y del Medio Natural, Escuela Politecnica Superior-Huesca, of pharmacological value. Fossil records from both the Northern and Southern Universidad de Zaragoza, 22071 Huesca, Hemispheres were used to test hypotheses about the origin of the genus Dios- Spain, 3Departamento de Biologıa Vegetal, corea, and to examine potential macroevolutionary processes that led to its Facultad de Ciencias Biologicas, Universitat current distribution. de Valencia, E-46100 Valencia, Spain, Location Pantropical distribution. 4Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogota, Colombia, Methods Divergence times were estimated using the most comprehensive 5Royal Botanic Gardens, Kew, Richmond, phylogeny of the group published to date based on plastid sequences and fossil Surrey, TW9 3AB, UK, 6Real Jardın Botanico calibrations, applying a relaxed-clock model approach. Ancestral areas and (RJB-CSIC), 28014 Madrid, Spain, 7Institute range shifts were reconstructed using time-stratified likelihood-based models, of Biology, Tomsk State University, Tomsk reflecting past continental connectivity and biogeographical models incorporat- 634050, Russia ing the spatial range of fossils. Results Fossil-informed biogeographical analysis supported colonization of the Nearctic by ancient yam lineages from the western Palaearctic and subsequent migration to the South.
    [Show full text]
  • Succulent Plants
    This guide covers the main succulent species, other than cacti, Sajeva Maurizio and Groves , Madeleine Catherine Rutherford Plants Succulent regulated by the Convention on International Trade in Endangered Succulent Plants Species (CITES). It provides information on the implementation of the Convention for these species with details on their A guide to CITES-listed species distribution, uses, traded parts and derivatives, and scientific names. It is written for the non-expert and additional sections cover identification, guidance on CITES documentation and key resources. ISBN 9781999896201 Catherine Rutherford Madeleine Groves 7819999 896201 Maurizio Sajeva Succulent Plants A guide to CITES-listed species Catherine Rutherford Madeleine Groves Maurizio Sajeva © Rutherford Groves Publishing, London 2018 The authors have asserted their rights to be identified as the authors of this work in accordance with the Copyright, Designs and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form, or by any means, electronic, mechanical, photocopying, recording or otherwise, without written permission of the publisher unless in accordance with the provisions of the Copyright Designs and Patents Act 1988. Great care has been taken to maintain the accuracy of the information contained in this work. However, neither the publisher, the editors nor the authors can be held responsible for any consequences arising from use of the information contained herein. First published in 2018 by Rutherford Groves Publishing London, UK ISBN 978-1-9998962-0-1 Design and page layout: Trockenbrot Published with the support of the Swedish Environmental Protection Agency Printed in the UK by Blissetts The paper used for this publication is FSC certified Contents Introduction .....................................
    [Show full text]
  • Metabolite Profiling of Dioscorea (Yam) Species Reveals Underutilised Biodiversity and Renewable Sources for High-Value Compounds
    www.nature.com/scientificreports OPEN Metabolite profiling ofDioscorea (yam) species reveals underutilised biodiversity and renewable sources Received: 09 March 2016 Accepted: 15 June 2016 for high-value compounds Published: 07 July 2016 Elliott J. Price1,2, Paul Wilkin2, Viswambharan Sarasan2 & Paul D. Fraser1 Yams (Dioscorea spp.) are a multispecies crop with production in over 50 countries generating ~50 MT of edible tubers annually. The long-term storage potential of these tubers is vital for food security in developing countries. Furthermore, many species are important sources of pharmaceutical precursors. Despite these attributes as staple food crops and sources of high-value chemicals, Dioscorea spp. remain largely neglected in comparison to other staple tuber crops of tropical agricultural systems such as cassava (Manihot esculenta) and sweet potato (Ipomoea batatas). To date, studies have focussed on the tubers or rhizomes of Dioscorea, neglecting the foliage as waste. In the present study metabolite profiling procedures, using GC-MS approaches, have been established to assess biochemical diversity across species. The robustness of the procedures was shown using material from the phylogenetic clades. The resultant data allowed separation of the genotypes into clades, species and morphological traits with a putative geographical origin. Additionally, we show the potential of foliage material as a renewable source of high-value compounds. Dioscorea (yam) species comprise a genus of 613 tuberous climbing plants1. Of these, seven to ten are cultivated on a large scale2,3 and two (D. alata, D. cayennensis Lam. subsp. cayennensis and D. cayenennsis Lam. subsp. rotundata (Poir.) J. Miège [referred to D. rotundata throughout]) are of primary importance as a staple crop, predominately in Western Africa4, for over 100 million people5.
    [Show full text]
  • Newsletter of the Central Oklahoma Cactus and Succulent Society
    THE OFFSET Echinocereus reichenbachii subsp baileyi JULY 2015 in the Wichita Mountains NWR, Oklahoma. Mount Scott in the background. Photo by Webpage https://sites.google.com/site/cocssok/ Michael Douglas NEWSLETTER OF THE CENTRAL OKLAHOMA CACTUS AND SUCCULENT SOCIETY OFFICERS IN THIS ISSUE President: Niki Furrh [email protected] 405-722-1718 Vice–President, newsletter editor and Web master: Rosario Douglas [email protected] Club News pp 2-7 405-447-7617 Cactus and Succulent Treasurer: Peggy Anglin [email protected] Happenings in the region pp 8 405-840-4583 Librarian: Tony Furrh [email protected] Succulent Plants pp 9 405-722-1718 Article of the month pp10-13 Secretary: Robert Millison What is blooming pp 14 [email protected] The Botanical corner pp 15 CSSA Affiliate: Joyce Hochtritt [email protected] 405-737-1831 Meeting: Third Thursday of the month at 7 pm. At the Will Rogers Garden Center at 3400 NW 36th in Oklahoma City (except for the month of our 1 Show&Sale, picnic and Christmas party). THE OFFSET July 2015 issue CLUB NEWS Summer is now in full swing and we are still getting plenty of rain. Got another 4 inches in our backyard for the days of July 2nd and 3rd and another 1.75 inches were added In the last two days. This month we have a program about our trip to the Canary Islands last Spring. In August we are having our annual “build your own dish garden workshop”. If you have any friends that may be interested let them know since registration is required.
    [Show full text]
  • Inventory No. 160
    Inventory No. 160 UNITED STATES DEPARTMENT OF AGRICULTURE Washington, D. C, September 1957 I? PUNT MATERIAL INTRODUCED JANUARY 1 TO DECEMBER 31, 1952 (NOS. 198915 TO 204340) CONTENTS Inventory ;> Index of common scientific names 20o This inventory, No. 160, lists the plant material (Nos. 198915 to 204340) received by the Plant Introduction Section, Crops re- search Division, Agricultural Research Service, during the period from January 1 to December 31, 1952. It is a historical record of plant material introduced for Department and other specialists, and is not to be considered as a list of plant material for distribution. This unit prior to 1954 was known as the Division of Plant Explora- tion and Introduction, Bureau of Plant Industry, Soils, and Agricul- tural Engineering, Agricultural Research Administration, United States Department of Agriculture. PAUL G. RUSSELL, Botanist. Plant Industry Station, Belts ville, Md. d 415896—57- INVENTORY 198915 to 198919. ORYZA SATIVA L. Poaceae. Rice. From Brazil. Seeds presented by the Departmento da Produeao, Campinas, Sao Paulo. Received Jan. 3, 1042. 198915. IAC-1. 198918. Dourado Agulha. 198916. IAC-3. 198919. Ignape Agulha. 198917. IAC-1. 198920. TRIFOLIUM REPENS L. Fabaceae. White clover. From England. Seeds presented by the Ministry of Agriculture and Fisheries, London. Received Jan. 4, lt)f>2. Certified Kersey. Originally from Witnesham, Suffolk. A vigorous, produc- tive strain. 198921 and 198922. SACCHARUM. Poacae, Sugarcane. From the Canal Zone. Seeds presented by Jack L. Bean, Pedro Miguel. Re- ceived Jan. 4, 1952. 198921. 1-51 198922. 2-»J. 198923 to 198926. From the Union of South Africa. Seeds presented by Mildred Wilman, Kim- berley, Cape Province.
    [Show full text]