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An Integrated Orchid Functional Genomics Database
Orchidstra: An Integrated Orchid Functional Genomics Database Special Focus Issue Chun-lin Su1,3, Ya-Ting Chao1,3, Shao-Hua Yen1, Chun-Yi Chen1, Wan-Chieh Chen1, Yao-Chien Alex Chang2 and Ming-Che Shih1,* 1Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan 2Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, Taiwan. 3These authors contributed equally to this work. *Corresponding author: E-mail: [email protected]; Fax, +886-2-26515693. (Received November 9, 2012; Accepted January 5, 2013) A specialized orchid database, named Orchidstra (URL: Abbreviations: BLAST, basic local alignment search tool; – Databases http://orchidstra.abrc.sinica.edu.tw), has been constructed CAM, crassulacean acid metabolism; EIF5A, eukaryotic trans- to collect, annotate and share genomic information for lation initiation factor 5A; EST, expressed sequence tag; GO, orchid functional genomics studies. The Orchidaceae is a Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and large family of Angiosperms that exhibits extraordinary bio- Genomes; miRNA, microRNA; NGS, next-generation sequen- diversity in terms of both the number of species and their cing; SRA, sequence read archive; TSA, transcriptome distribution worldwide. Orchids exhibit many unique biolo- shotgun assembly. gical features; however, investigation of these traits is cur- rently constrained due to the limited availability of genomic information. Transcriptome information for five orchid spe- Introduction cies and one commercial hybrid has been included in the Orchidaceae, the orchid family, diverged from the Liliaceae Orchidstra database. Altogether, these comprise >380,000 and Amaryllidaceae, is the largest family of Angiosperms, with non-redundant orchid transcript sequences, of which >800 genera and >25,000 species. -
Dendrobium Kingianum Bidwill Ex Lindl
Volume 24: 203–232 ELOPEA Publication date: 19 May 2021 T dx.doi.org/10.7751/telopea14806 Journal of Plant Systematics plantnet.rbgsyd.nsw.gov.au/Telopea • escholarship.usyd.edu.au/journals/index.php/TEL • ISSN 0312-9764 (Print) • ISSN 2200-4025 (Online) A review of Dendrobium kingianum Bidwill ex Lindl. (Orchidaceae) with morphological and molecular- phylogenetic analyses Peter B. Adams1,2, Sheryl D. Lawson2, and Matthew A.M. Renner 3 1The University of Melbourne, School of BioSciences, Parkville 3010, Victoria 2National Herbarium of Victoria, Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne 3004, Victoria 3National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney 2000, New South Wales Author for correspondence: [email protected] Abstract Populations of Dendrobium kingianum Bidwill ex Lindl. from near Newcastle, New South Wales to southern and central west Queensland and encompassing all regions of the distribution were studied using field observations, morphometric analysis and nrITS sequences. A total of 281 individuals were used to construct regional descriptions of D. kingianum and 139 individuals were measured for 19 morphological characters, and similarities and differences among specimens summarised using multivariate statistical methods. Patterns of morphological variation within D. kingianum are consistent with a single variable species that expresses clinal variation, with short-growing plants in the south and taller plants in the northern part of the distribution. The nrITS gene tree suggests two subgroups within D. kingianum subsp. kingianum, one comprising northern, the other southern individuals, which may overlap in the vicinity of Dorrigo, New South Wales. The disjunct D. kingianum subsp. carnarvonense Peter B. -
Australia Lacks Stem Succulents but Is It Depauperate in Plants With
Available online at www.sciencedirect.com ScienceDirect Australia lacks stem succulents but is it depauperate in plants with crassulacean acid metabolism (CAM)? 1,2 3 3 Joseph AM Holtum , Lillian P Hancock , Erika J Edwards , 4 5 6 Michael D Crisp , Darren M Crayn , Rowan Sage and 2 Klaus Winter In the flora of Australia, the driest vegetated continent, [1,2,3]. Crassulacean acid metabolism (CAM), a water- crassulacean acid metabolism (CAM), the most water-use use efficient form of photosynthesis typically associated efficient form of photosynthesis, is documented in only 0.6% of with leaf and stem succulence, also appears poorly repre- native species. Most are epiphytes and only seven terrestrial. sented in Australia. If 6% of vascular plants worldwide However, much of Australia is unsurveyed, and carbon isotope exhibit CAM [4], Australia should host 1300 CAM signature, commonly used to assess photosynthetic pathway species [5]. At present CAM has been documented in diversity, does not distinguish between plants with low-levels of only 120 named species (Table 1). Most are epiphytes, a CAM and C3 plants. We provide the first census of CAM for the mere seven are terrestrial. Australian flora and suggest that the real frequency of CAM in the flora is double that currently known, with the number of Ellenberg [2] suggested that rainfall in arid Australia is too terrestrial CAM species probably 10-fold greater. Still unpredictable to support the massive water-storing suc- unresolved is the question why the large stem-succulent life — culent life-form found amongst cacti, agaves and form is absent from the native Australian flora even though euphorbs. -
BIODIVERSITY CONSERVATION on the TIWI ISLANDS, NORTHERN TERRITORY: Part 1. Environments and Plants
BIODIVERSITY CONSERVATION ON THE TIWI ISLANDS, NORTHERN TERRITORY: Part 1. Environments and plants Report prepared by John Woinarski, Kym Brennan, Ian Cowie, Raelee Kerrigan and Craig Hempel. Darwin, August 2003 Cover photo: Tall forests dominated by Darwin stringybark Eucalyptus tetrodonta, Darwin woollybutt E. miniata and Melville Island Bloodwood Corymbia nesophila are the principal landscape element across the Tiwi islands (photo: Craig Hempel). i SUMMARY The Tiwi Islands comprise two of Australia’s largest offshore islands - Bathurst (with an area of 1693 km 2) and Melville (5788 km 2) Islands. These are Aboriginal lands lying about 20 km to the north of Darwin, Northern Territory. The islands are of generally low relief with relatively simple geological patterning. They have the highest rainfall in the Northern Territory (to about 2000 mm annual average rainfall in the far north-west of Melville and north of Bathurst). The human population of about 2000 people lives mainly in the three towns of Nguiu, Milakapati and Pirlangimpi. Tall forests dominated by Eucalyptus miniata, E. tetrodonta, and Corymbia nesophila cover about 75% of the island area. These include the best developed eucalypt forests in the Northern Territory. The Tiwi Islands also include nearly 1300 rainforest patches, with floristic composition in many of these patches distinct from that of the Northern Territory mainland. Although the total extent of rainforest on the Tiwi Islands is small (around 160 km 2 ), at an NT level this makes up an unusually high proportion of the landscape and comprises between 6 and 15% of the total NT rainforest extent. The Tiwi Islands also include nearly 200 km 2 of “treeless plains”, a vegetation type largely restricted to these islands. -
Molecularphylogeneticsof Phalaenopsis(Orchidaceae)
The JapaneseSocietyJapanese Society for Plant Systematics ISSN 1346-7565 Acta Phytotax. GeoboL 56 (2): 14]-161 (200S)・ Molecular Phylogenetics of Phalaenopsis (Orchidaceae)and allied Genera: Re-evaluation of Generic Concepts TOMOHISA YUKAWAi, KOICHI KITA2, TAKASHI HANDA2, TOPIK HIDAYAT3 and MOTOMHTo3 i71sukuba 21hstitute Botanical Garcien, Nlational Scienee Mtiseum, Amakuho, Tyuketba, 305-OO05. Jopan; of 3Graduate Agricultnre andforestn)). Uhivensity qf'Tgukuba, fennodai, 71yukuba, 305-857Z Japan; Schoot ofArts and Seience, Uhivensity of7bdy,o, Kbmaba, 7bkyo, J53-8902, JZu)an, Molecular phylogenetic analyscs were performed using data sets derived from DNA sequences ofthe plastid genome (matK and trnK introns) and the nuelear genome (rDNA ITS) in an examination ofrela- tionships of all sections ofPhataenqpsis and closely related gcnera. The fo11owing insights were pro- vided: (1) The genera Lesliea and IVbthodoritis are nested within Phalaenopsis, (2) Phalaenopsis subgenus Aphyilae and section EsmeJ'aldd, often treated as thc independent genera Kirrgidium and Doritis respectively, are also nested within Phalaenqpsis. (3) Two subgenera of Phalaenqpsis, namely, Phalaenopsis and 1larishianae, are not monophyletic. (4) Phalaenopsis sections Deliciosae, SZautqglottis, Amboinenses and Zehrinae are not monophyletic. (5) lnconsistencies bctween the plastid and nuclear lineages indicate a hybrid origin ofPhalaenopsis minus and Phalaenopsis phitmpinensis. (6) In light of these findings, and to accommodate phylogenetic integrity and stability in nomenclature, we adopt a broadly defincd Doritis characterized by the possession of fbur pollinia, an explicit character state. Key words: Doritis,introgression, ITS, mati(l moleculag Orchidaceae, Ahalaenopsis, phylogcnctics, tttnK Phakzenopsis Blume is an orchid genus to which 62 tion ofthe genus has been thoroughly reviewed by species are currently assigned (Christenson 2001). -
Nuclear DNA Contents of Phalaenopsis Sp. and Doritis Pulcherrima
J. AMER. SOC. HORT. SCI. 126(2):195–199. 2001. Nuclear DNA Contents of Phalaenopsis sp. and Doritis pulcherrima Sandy Lin and Hsiao-Ching Lee Department of Life Science, National Tsing Hua University, Hsinchu, 30043, Taiwan, Republic of China Wen-Huei Chen Department of Horticulture, Taiwan Sugar Research Institute, Tainan, 701, Taiwan, Republic of China Chi-Chang Chen and Yen-Yu Kao Department of Botany, National Taiwan University, Taipei, 10764, Taiwan, Republic of China Yan-Ming Fu and Yao-Huang Chen Department of Horticulture, Taiwan Sugar Research Institute, Tainan, 701, Taiwan, Republic of China Tsai-Yun Lin1 Department of Life Science, National Tsing Hua University, Hsinchu, 30043, Taiwan, Republic of China ADDITIONAL INDEX WORDS. Orchidaceae, endoreduplication, flow cytometry, genome size ABSTRACT. Nuclear DNA contents were estimated by flow cytometry in 18 Phalaenopsis Blume species and Doritis pulcherrima Lindl. DNA amounts differed 6.07-fold, from 2.74 pg/diploid nuclear DNA content (2C) in P. sanderiana Rchb.f. to 16.61 pg/2C in P. parishii Rchb.f. Nuclear DNA contents of P. aphrodite Rchb.f. clones, W01-38 (2n = 2x = 38), W01-41 (2n = 3x = 57), and W01-22 (2n = 4x = 76), displayed a linear relationship with their chromosome numbers, indicating the accuracy of flow cytometry. Our results also suggest that the 2C-values of the Phalaenopsis sp. correlate with their chromosome sizes. The comparative analyses of DNA contents may provide information to molecular geneticists and systematists for genome analysis in Phalaenopsis. Endoreduplication was found in various tissues of P. equestris at different levels. The highest degree of endoreduplication in P. -
Growing Dendrobium Orchids in Hawaii
Growing dendrobium orchids in Hawaii GROWING DENDROBIUM ORCHIDS IN HAWAII Production and Pest Management Guide Edited by Ken Leonhardt and Kelvin Sewake Published by the College of Tropical Agriculture and Human Resources (CTAHR) and issued in furtherance of Cooperative Extension work, Acts of May 8 and June 30, 1914, in cooperation with the U.S. Department of Agriculture. Charles W. Laughlin, Director and Dean, Cooperative Extension Service, CTAHR, University of Hawaii at Manoa, Honolulu, Hawaii 96822. An Equal Opportunity / Affirmative Action Institution providing programs and services to the people of Hawaii without regard to race, sex, age, religion, color, national origin, ancestry, disability, marital status, arrest and court record, sexual orientation, or veteran status. 1 Growing dendrobium orchids in Hawaii Edited by Ken Leonhardt and Kelvin Sewake The authors and their affiliations Kent Fleming, extension economist, Department of Horticulture, College of Tropical Agriculture and Human Resources (CTAHR), University of Hawaii at Manoa John Halloran, extension economist, Department of Horticulture, CTAHR Arnold Hara, specialist in entomology, Department of Entomology, CTAHR Trent Hata, research associate, Department of Entomology, CTAHR Ken Leonhardt, specialist in horticulture, Department of Horticulture, CTAHR Edwin Mersino, county extension agent, CTAHR Kelvin Sewake, county extension agent, CTAHR Janice Uchida, plant pathologist, Department of Plant Pathology, CTAHR Acknowledgments The authors thank the following people for -
PC25 Doc. 32.2
Original language: English PC25 Doc. 32.2 CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD FAUNA AND FLORA ___________________ Twenty-fifth meeting of the Plants Committee Online, 2-4, 21 and 23 June 2021 Species specific matters Maintenance of the Appendices Orchids checklists APPENDIX-II ORCHID CHECKLIST 1. This document has been submitted by the Scientific Authority for Flora of the United Kingdom of Great Britain and Northern Ireland.* 2. The context of this document pertains to PC24 Com. 8 (Rev. by Sec.). The UK Scientific Authority and the United Nations Environment Programme – World Conservation Monitoring Centre (UNEP-WCMC) were to prepare a checklist for Orchidaceae, presenting Appendix I and Appendix II species separately. a) This was to be undertaken by generating an output for Orchidaceae from the World Checklist of Selected Plant Families. The output includes accepted names, synonyms and country-level distribution information. b) The dataset for Orchidaceae was provided by The World Checklist of Selected Plant Families. The World Checklist of Selected Plant Families has become an international collaborative programme with more than 150 contributors from 22 countries. The main goal of the World Checklist of Selected Plant Families is to provide high quality peer reviewed baseline data on all accepted taxa included in each family. c) To make the review of proposed changes manageable, a comparison was undertaken between the World Checklist of Selected Plant Families output and the current CITES nomenclature standard references for Orchidaceae. 3. The Appendix I Orchid Checklist was adopted at the 18th CITES Conference of the Parties (Switzerland, 2019). This checklist and the proposed checklist were compiled using the same methodology. -
Detection of Somaclonal Variation by Random Amplified Polymorphic DNA Analysis During Micropropagation of Phalaenopsis Bellina (Rchb.F.) Christenson
African Journal of Biotechnology Vol. 9(40), pp. 6632-6639, 4 October, 2010 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB10.714 ISSN 1684–5315 ©2010 Academic Journals Full Length Research Paper Detection of somaclonal variation by random amplified polymorphic DNA analysis during micropropagation of Phalaenopsis bellina (Rchb.f.) Christenson Khoddamzadeh A. A1, Sinniah U. R1*, Kadir M. A2, Kadzimin S. B1, Mahmood M 3 and Sreeramanan S 4 1Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43300, Serdang, Malaysia. 2Department of Agrotechnology, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43300, Serdang, Malaysia. 3Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43300, Serdang, Malaysia. 4School of Biological Sciences, Universiti Sains Malaysia (USM), Minden Heights, 11800, Georgetown, Penang, Malaysia. Accepted 23 August, 2010 Phalaenopsis bellina (Rchb.f.) Christenson orchid species are known for their beautiful flower shape, graceful inflorescence and fragrance. Protocorm-like bodies (PLBs) of P. bellina were induced from leaf segments. The PLBs were then subjected to proliferation using ½ strength Murashige and Skoog (MS) media with two subcultures at three months intervals. Twelve decamer random amplified polymorphic DNA (RAPD) primers were used to study somaclonal variation among the mother plant, the initially induced PLBs and proliferated PLBs after 3 and 6 months in culture. Eight out of twelve primers produced 172 bands with 18 polymorphic bands in all the treatments. The amplified products varied between 125 to 8000 bp. Among the primers used, P 16 produced the highest number of bands (29), while primer OPU 10 produced the lowest number (15). -
Society for Growing Australian Plants, Cairns Branch
Society for Growing Australian Plants, Cairns Branch Newsletter 148 April 2015 In this issue… MARCH 2015 EXCURSION REPORT – REDDEN ISLAND1 REDDEN ISLAND SPECIES LIST ............................ 4 ANTON VAN DER SCHANS IN SINGAPORE ................. 4 GARDENS ’ ‘WALKING ENCYCLOPAEDIA ’ ................ 4 INTERVIEW ....................... 5 WHAT’S ON? .................... 7 CAIRNS SGAP ................ 7 TABLELANDS SGAP .......... 7 TOWNSVILLE SGAP .......... 7 OTHER EVENTS ............... 7 MARCH 2015 EXCURSION REPORT – REDDEN ISLAND Don Lawie Redden Island is formed by Redden Creek to the north, a mangrove swamp to the west, Trinity Bay to the east and the main channel of the Barron River to the south. The beachside community of Machan’s Beach adjoins Redden Creek and the Cairns CBD is just a few kilometres south. We have inspected the Island several times over the years and it is always of interest to note any changes. The area is low lying and dynamic, being part of the large Barron delta system with its potential of flood generated change. Indeed, as we walked along the river bank there was evidence of erosion from the strong currents resulting from heavy cyclonic rain during the previous few days. March is A.G.M. month and we had a larger than usual attendance of members vying to be elected to the Executive! Long term member Liz invited us to meet at her place and we enjoyed the idyllic ambience of a beach-side house built in the way that one can only dream of. Open areas, cool breezes, sweeping ocean views and extensive gardens built around existing trees augmented by appropriate plants native to the area. -
Orchids Diversity on Six Forest Types in Wasur National Park, Merauke, Papua, Indonesia
ASIAN JOURNAL OF FORESTRY Volume 5, Number 2, December 2021 E-ISSN: 2580-2844 Pages: 101-110 DOI: 10.13057/asianjfor/r050206 Orchids diversity on six forest types in Wasur National Park, Merauke, Papua, Indonesia NOVITYASARI KUSUMASTUTI♥, SURATMAN, ARI PITOYO Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret. Jl. Ir. Sutami 36A Surakarta 57 126, Central Java, Indonesia. Tel./fax.: +62-271-663375, email: [email protected] Manuscript received: 24 June 2021. Revision accepted: 19 August 2021. Abstract. Kusumastuti NK, Suratman, Pitoyo A. 2021. Orchids diversity on six forest types in Wasur National Park, Merauke, Papua, Indonesia. Asian J For 5: 101-110. Orchidaceae is one of the two largest families of flowering plants. Wasur National Park is the habitat of many orchid species and one of the in-situ conservation areas in Papua that is very suitable for orchids. This research aimed to determine the orchid species in Seksi Pengelolaan Taman Nasional Wilayah III (SPTN III) Wasur, Wasur National Park, Merauke District, Papua Province, Indonesia and to determine the distribution of orchid species in six different types of forest. This research was conducted using the exploratory method. A total of 25 orchid species belonging to 11 genera have been identified from SPTN III Wasur. Monsoon forest is the type of forest with the highest number of orchid species, with 15 orchid species. It is followed by savanna with ten species, Melaleuca forest with ten species, woodland forest with nine species, riparian forest with six species, and Melaleuca-Eucalyptus forest with 5 species. Dendrobium smillieae and Dendrobium rigidum are the most widely distributed epiphytic orchid species, and occur in almost all forest types. -
World Journal of Advanced Research and Reviews
World Journal of Advanced Research and Reviews, 2020, 05(02), 167–176 World Journal of Advanced Research and Reviews e-ISSN: 2581-3250, CODEN (USA): GBPSC2 Journal homepage: https://www.wjarr.com (RESEARCH ARTICLE) Biodiversity mapping of Dendrobium Sw. section Spathulata Lindl. in the Ramsar Site of Wasur National Park of Indonesia New Guinea Arobaya Agustina Yohana Setyarini 1, 2, *, Heipon Agape 1, Sinery Anton Silas 3 and Wakum Abner 4 1 Laboratorium Konservasi dan Lingkungan Hidup, Fahutan UNIPA, Jl. Gunung Salju Amban, 98314, Manokwari, West Papua Province, Indonesia. 2 Biodiversity Research Center in University of Papua, Manokwari, West Papua, Indonesia. 3 Research Center for Environmental Science at University of Papua, Manokwari, West Papua, Indonesia. 4 Ranger and Officer of Wasur National Park in Merauke, Papua Province, Indonesia. Publication history: Received on 02 February 2020; revised on 15 February 2020; accepted on 17 February 2020 Article DOI: https://doi.org/10.30574/wjarr.2020.5.2.0032 Abstract Wasur National Park is a vast area of tropical lowland forest, swamp forest, savannah and wetland in the far south- east corner of Papua-Indonesia. It is bordered by the sea to the south and PNG to the east. It lies within the Trans-Fly region of New Guinea and both the habitat and birds have much in common with northern Australia only 200 km to the south. The site is very seasonal, with both a pronounced wet and dry season. This park displays a tremendous biodiversity of flora and fauna. One prime example of flowering plants is Orchids species. Most orchids in this park resembles to the Australian plants as it share similar vegetation types of heath forest and savanna woodland.