Coptis Teeta: a Potential Endemic and Endangered Medicinal Plant Of
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Coptis Trifolia Conservation Assessment
CONSERVATION ASSESSMENT for Coptis trifolia (L.) Salisb. Originally issued as Management Recommendations December 1998 Marty Stein Reconfigured-January 2005 Tracy L. Fuentes USDA Forest Service Region 6 and USDI Bureau of Land Management, Oregon and Washington CONSERVATION ASSESSMENT FOR COPTIS TRIFOLIA Table of Contents Page List of Tables ................................................................................................................................. 2 List of Figures ................................................................................................................................ 2 Summary........................................................................................................................................ 4 I. NATURAL HISTORY............................................................................................................. 6 A. Taxonomy and Nomenclature.......................................................................................... 6 B. Species Description ........................................................................................................... 6 1. Morphology ................................................................................................................... 6 2. Reproductive Biology.................................................................................................... 7 3. Ecological Roles ............................................................................................................. 7 C. Range and Sites -
The First Comprehensive Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Classification
RESEARCH ARTICLE The First Comprehensive Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Classification Kun-Li Xiang1,2, Sheng-Dan Wu3, Sheng-Xian Yu1, Yang Liu4, Florian Jabbour5, Andrey S. Erst6,7, Liang Zhao8, Wei Wang1*, Zhi-Duan Chen1 1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, 2 University of Chinese Academy of Sciences, Beijing, 100049, China, 3 College of Life Sciences, Shanxi Normal University, Linfen, 041004, China, 4 Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269–3043, United States of America, 5 Muséum national d’Histoire naturelle, Institut de Systématique, Evolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, Paris, 75005, France, 6 Central Siberian Botanical Garden of the Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia, 7 Laboratory of Systematics and Phylogeny of Plants, National Research Tomsk State University, prospekt Lenina 36, Tomsk, 634050, Russia, 8 College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China * [email protected] OPEN ACCESS Citation: Xiang K-L, Wu S-D, Yu S-X, Liu Y, Jabbour F, Erst AS, et al. (2016) The First Comprehensive Abstract Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Coptis (Ranunculaceae) contains 15 species and is one of the pharmaceutically most Classification. PLoS ONE 11(4): e0153127. important plant genera in eastern Asia. Understanding of the evolution of morphological doi:10.1371/journal.pone.0153127 characters and phylogenetic relationships within the genus is very limited. -
CONSERVATION ASSESSMENT for Coptis Aspleniifolia Salisb
CONSERVATION ASSESSMENT for Coptis aspleniifolia Salisb. Originally issued as Management Recommendations December 1998 R.D. Lesher and J.A. Henderson Reconfigured-November 2004 Tracy L. Fuentes USDA Forest Service Region 6 and USDI Bureau of Land Management, Oregon and Washington CONSERVATION ASSESSMENT FOR COPTIS ASPLENIIFOLIA Table of Contents List of Tables ................................................................................................................................. 3 List of Figures ................................................................................................................................ 3 SUMMARY…………………………………………………………………………………...….5 I. NATURAL HISTORY ......................................................................................................... 6 A. Taxonomy and Nomenclature……………………………………………………….……6 B. Species Description ............................................................................................................. 6 1. Morphology………...…………………………………………………………………6 2. Reproductive Biology…………………………………………………………………6 3. Ecological Roles……………………………………………………………………….7 C. Range and Sites……………………………………………………………………………7 D. Habitat Characteristics and Species Abundance ............................................................. 8 II. CURRENT SPECIES SITUATION .................................................................................... 9 A. Status History ..................................................................................................................... -
The Complete Chloroplast Genome of Coptis Teeta (Ranunculaceae), An
Research Article iMedPub Journals Biochemistry & Molecular Biology Journal 2018 www.imedpub.com Vol.4 No.3:19 ISSN 2471-8084 DOI: 10.21767/2471-8084.100068 The Complete Chloroplast Genome of Coptis teeta (Ranunculaceae), An Endangered Plant Species Endemic to the Eastern Himalaya Ya-Fang Gao1, Xiao-Li Liu1, Guo-Dong Li1*, Zi-Gang Qian1*, Yong-Hong Zhang2 and Ying-Ying Liu1,3 1Faculty of Traditional Chinese Pharmacy, Yunnan University of Traditional Chinese Medicine, Kunming, P.R. China 2School of Life Sciences, Yunnan Normal University, Kunming, P.R. China 3Yunnan Institute for Food and Drug, Kunming, P.R. China *Corresponding author: Guo-Dong Li and Zi-Gang Qian Faculty of Traditional Chinese Pharmacy, Yunnan University of Traditional Chinese Medicine, Kunming-650500, P.R. China. E-mail: [email protected] ; [email protected] Received Date: August 23, 2018; Accepted Date: September 06, 2018; Published Date: September 10, 2018 Citation: Gao YF, Liu XL, Li GD, Qian ZG, Zhang YH, et al. (2018) The Complete Chloroplast Genome of Coptis teeta (Ranunculaceae), An Endangered Plant Species Endemic to the Eastern Himalaya. Biochem Mol Biol J Vol. 4: No.3:19. (Yunlian in Chinese), is important Chinese herbology since the period of Sheng-Nong (3000 B.C.) [1]. It has excellent Abstract pharmacological activity and was used to treat various diseases such as diarrhea, disorder of glucose metabolism, Coptis teeta is an endemic and endangered medicinal hypertension, cardiovascular and cerebral vessel diseases [3]. plant from the Eastern Himalaya. It has been categorized The previous study revealed that the species have highly by the International Union for Conservation of Nature specific microsite requirements that cannot be met in other (IUCN) as Endangered (EN). -
Special Forest Products
United States Department of Agriculture SPECIAL FOREST PRODUCTS Forest Service Species Information Guide Pacific Northwest Research Station for the Pacific Northwest General Technical Report PNW-GTR-513 Nan C. Vance, Melissa Borsting, David Pilz, and September 2001 Jim Freed Authors Nan C. Vance is a principle plant physiologist, and David Pilz is a botanist, For- estry Sciences Laboratory, 3200 SW Jefferson Way, Corvallis, OR 97331; Melissa Borsting is a graduate student, College of Forest Resources, University of Wash- ington, Box 352100, Seattle, WA 98195; and Jim Freed is an extension special forest products specialist, Washington State University, PO Box 4703, Olympia, WA 98504. Disclaimer This publication reports research and management information involving mush- room and plant harvesting. It neither recommends the use and ingestion of mush- rooms and plants nor implies that using wild plants and mushrooms is without risks. CAUTION: Mushroom and wild plant consumption can pose a serious, even fatal, risk to humans. It is strongly recommended that you spend your first collecting season using field identification guides and collecting with an expert if you intend to collect wild plants or mushrooms to eat. Abstract Vance, Nan C.; Borsting, Melissa; Pilz, David; Freed, Jim. 2001. Special forest products: species information guide for the Pacific Northwest. Gen. Tech. Rep. PNW-GTR-513. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 169 p. This guide is a collection of information about economically important vascular and nonvascular plants and fungi found in the Pacific Northwest that furnish special forest products. Many of these plants and fungi are also found in Alaska, northern Idaho, and western Montana. -
Phylogenetic Relationships Among Early-Diverging Eudicots Based on Four Genes: Were the Eudicots Ancestrally Woody?
MOLECULAR PHYLOGENETICS AND EVOLUTION Molecular Phylogenetics and Evolution 31 (2004) 16–30 www.elsevier.com/locate/ympev Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody? Sangtae Kim,a,* Douglas E. Soltis,b,* Pamela S. Soltis,c Michael J. Zanis,d and Youngbae Suhe a Department of Botany, University of Florida, Gainesville, FL 32611, USA b Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA c Florida Museum of Natural History and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA d School of Biological Sciences, Washington State University, Pullman, WA 99164, USA e Natural Products Research Institute, Seoul National University, Seoul 110-460, Republic of Korea Received 24 October 2002; revised 23 July 2003 Abstract Based on analyses of combined data sets of three genes (18S rDNA, rbcL, and atpB), phylogenetic relationships among the early- diverging eudicot lineages (Ranunculales, Proteales, Trochodendraceae, Sabiaceae, and Buxaceae) remain unclear, as are relationships within Ranunculales, especially the placement of Eupteleaceae. To clarify relationships among these early-diverging eudicot lineages, we added entire sequences of 26S rDNA to the existing three-gene data set. In the combined analyses of four genes based on parsimony, ML, and Bayesian analysis, Ranunculales are strongly supported as a clade and are sister to other eudicots. Proteales appear as sister to the remaining eudicots, which are weakly (59%) supported as a clade. Relationships among Trocho- dendraceae, Buxaceae (including Didymeles), Sabiaceae, and Proteales remain unclear. Within Ranunculales, Eupteleaceae are sister to all other Ranunculales, with bootstrap support of 70% in parsimony analysis and with posterior probability of 1.00 in Bayesian analysis. -
The First Comprehensive Phylogeny of Coptis
The First Comprehensive Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Classification Kun-Li Xiang, Sheng-Dan Wu, Sheng-Xian Yu, Yang Liu, Florian Jabbour, Andrey S. Erst, Liang Zhao, Wei Wang, Zhi-Duan Chen To cite this version: Kun-Li Xiang, Sheng-Dan Wu, Sheng-Xian Yu, Yang Liu, Florian Jabbour, et al.. The First Com- prehensive Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Classification. PLoS ONE, Public Library of Science, 2016, 11 (4), pp.e0153127. 10.1371/jour- nal.pone.0153127. hal-01310776 HAL Id: hal-01310776 https://hal.sorbonne-universite.fr/hal-01310776 Submitted on 3 May 2016 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 RESEARCH ARTICLE The First Comprehensive Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Classification Kun-Li Xiang1,2, Sheng-Dan Wu3, Sheng-Xian Yu1, Yang Liu4, Florian Jabbour5, Andrey S. Erst6,7, Liang Zhao8, Wei Wang1*, Zhi-Duan -
Analysis of the Coptis Chinensis Genome Reveals the Diversification
ARTICLE https://doi.org/10.1038/s41467-021-23611-0 OPEN Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids ✉ Yifei Liu 1,9 , Bo Wang2,9, Shaohua Shu3,9, Zheng Li4,9, Chi Song5, Di Liu1, Yan Niu5, Jinxin Liu3, Jingjing Zhang1, Heping Liu3, Zhigang Hu1, Bisheng Huang1, Xiuyu Liu6, Wei Liu1, Liping Jiang1, Mohammad Murtaza Alami3, Yuxin Zhou2, Yutao Ma3, Xiangxiang He5, Yicheng Yang5, Tianyuan Zhang5, ✉ ✉ ✉ Hui Hu7, Michael S. Barker 4, Shilin Chen8 , Xuekui Wang3 & Jing Nie2 1234567890():,; Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine- type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model gen- ome for genetic and applied studies of Ranunculales. 1 College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China. 2 Hubei Institute for Drug Control, Wuhan, China. -
Flowering Dicots Before I Worked on This Project, I Had No Idea How to Apply GIS to Basic Ecological Concepts
Galbreath Wildlands Preserve Galbreath Special Status Species Assessment – Flowering Dicots Before I worked on this project, I had no idea how to apply GIS to basic ecological concepts. – Christoph Schopfer, Geography Major Project Summary A team of students and Center staff mapped potential habitat for 110 special status plants and animals on the Galbreath Wildlands Preserve. We identified special status species with potential to occur in the Galbreath Preserve using existing agency databases and publications. These included fungi, bryophytes, plants, invertebrates, amphibians, reptiles, birds and mammals. For each species, we collected biological information, undertook GIS-based habitat suitability analysis, and assessed the likelihood of occurrence within preserve boundaries. The project created professional experience for Biology and Geography undergraduates and graduate students who worked on an interdisciplinary team to develop assessment techniques and methods. See Methods (PDF) and Species List (PDF) for additional information. Project Lead: Claudia Luke Dates: 2010-2011 Funding: Robert and Sue Johnson Family Students: Neal Ramus (Business), Emily Harvey (Biology), Kandis Gilmore (Biology), Linden Schneider (Biology), Christoph Schopfer (Geography), James Sherwood (Geography) Flowering Dicots These results are part of a larger assessment of all special status species with potential to occur at the Galbreath Wildlands Preserve. Assessments were conducted as planning exercise and do not constitute evidence of occurrence. SSU Center for Environmental Inquiry sonoma.edu/cei Page 1 of 150 Asteraceae Hemizonia congesta ssp. congesta, Pale Yellow Hayfield Tarplant: HECO Text, HECO Map Lasthenia burkei, Burke's Goldfields: LABU Text, LABU Map Layia septentrionalis, Colusa Layia: LASE Text, LASE Map Packera bolanderi var. bolanderi, Seacoast Ragwort: PABO Text, PABO Map Tracyina rostrata, Beaked Tracyina: TRRO Text, TRRO Map Boraginaceae Cryptantha clevelandii var. -
Structural Variation of the Complete Chloroplast Genome And
www.nature.com/scientificreports OPEN Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae) Jian He1,5, Min Yao1,5, Ru-Dan Lyu1,5, Le-Le Lin1, Hui-Jie Liu4, Lin-Ying Pei2, Shuang-Xi Yan3, Lei Xie1* & Jin Cheng1 Two complete chloroplast genome sequences of Asteropyrum, as well as those of 25 other species from Ranunculaceae, were assembled using both Illumina and Sanger sequencing methods to address the structural variation of the cp genome and the controversial systematic position of the genus. Synteny and plastome structure were compared across the family. The cp genomes of the only two subspecies of Asteropyrum were found to be diferentiated with marked sequence variation and diferent inverted repeat-single copy (IR-SC) borders. The plastomes of both subspecies contains 112 genes. However, the IR region of subspecies peltatum carries 27 genes, whereas that of subspecies cavaleriei has only 25 genes. Gene inversions, transpositions, and IR expansion-contraction were very commonly detected in Ranunculaceae. The plastome of Asteropyrum has the longest IR regions in the family, but has no gene inversions or transpositions. Non-coding regions of the cp genome were not ideal markers for inferring the generic relationships of the family, but they may be applied to interpret species relationship within the genus. Plastid phylogenomic analysis using complete cp genome with Bayesian method and partitioned modeling obtained a fully resolved phylogenetic framework for Ranunculaceae. Asteropyrum was detected to be sister to Caltha, and diverged early from subfamily Ranunculoideae. In recent years, the use of whole chloroplast (cp) genome data for plant phylogenetic reconstruction has been greatly improved our understanding of evolutionary relationships of angiosperms at a wide range of taxonomic levels1–4. -
Complete Chloroplast Genome Sequence of Coptis Chinensis Franch
Hindawi BioMed Research International Volume 2017, Article ID 8201836, 7 pages https://doi.org/10.1155/2017/8201836 Research Article Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History Yang He,1 Hongtao Xiao,2 Cao Deng,3 Gang Fan,1 Shishang Qin,3 and Cheng Peng1 1 College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China 2Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China 3Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 610000, China Correspondence should be addressed to Cheng Peng; [email protected] Received 10 February 2017; Accepted 23 May 2017; Published 18 June 2017 Academic Editor: Isabel Portugal Copyright © 2017 Yang He et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two26,758bplonginvertedrepeatsseparatedthegenomeintoatypicalquadripartitestructure.TheC. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. -
Phylogeny and Classification of Ranunculales: Evidence from Four
ARTICLE IN PRESS Perspectives in Plant Ecology, Evolution and Systematics Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 81–110 www.elsevier.de/ppees Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data Wei Wanga, An-Ming Lua, Yi Renb, Mary E. Endressc, Zhi-Duan Chena,Ã aState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China bKey Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an 710062, PR China cInstitute of Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland Received 30 June 2008; received in revised form 21 November 2008; accepted 5 January 2009 Abstract Previous phylogenetic analyses of Ranunculales, which have mostly been focused on an individual family and were based on molecular data alone, have recovered three main clades within the order. However, support for relationships among these three clades was weak. Earlier hypotheses were often hampered by limited taxon sampling; to date less than one-tenth of the genera in the order have been sampled. In this study, we used a greatly enlarged taxon sampling (105 species, representing 99 genera of all seven families in the order). Our study is, furthermore, the first to employ morphology (65 characters) in combination with sequence data from four genomic regions, including plastid rbcL, matK and trnL-F, and nuclear ribosomal 26S rDNA to reconstruct phylogenetic relationships within Ranunculales. Maximum parsimony and Bayesian inference were performed on the individual and combined data sets.