Ganesan Orchids
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The Genomic Impact of Mycoheterotrophy in Orchids
fpls-12-632033 June 8, 2021 Time: 12:45 # 1 ORIGINAL RESEARCH published: 09 June 2021 doi: 10.3389/fpls.2021.632033 The Genomic Impact of Mycoheterotrophy in Orchids Marcin J ˛akalski1, Julita Minasiewicz1, José Caius2,3, Michał May1, Marc-André Selosse1,4† and Etienne Delannoy2,3*† 1 Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdansk,´ Gdansk,´ Poland, 2 Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, France, 3 Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Orsay, France, 4 Sorbonne Université, CNRS, EPHE, Muséum National d’Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, Paris, France Mycoheterotrophic plants have lost the ability to photosynthesize and obtain essential mineral and organic nutrients from associated soil fungi. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy Edited by: Susann Wicke, to mycoheterotrophy has occurred independently in many major lineages of land Humboldt University of Berlin, plants, most frequently in Orchidaceae. Yet the molecular mechanisms underlying this Germany shift are still poorly understood. A comparison of the transcriptomes of Epipogium Reviewed by: Maria D. Logacheva, aphyllum and Neottia nidus-avis, two completely mycoheterotrophic orchids, to other Skolkovo Institute of Science autotrophic and mycoheterotrophic orchids showed the unexpected retention of several and Technology, Russia genes associated with photosynthetic activities. In addition to these selected retentions, Sean W. Graham, University of British Columbia, the analysis of their expression profiles showed that many orthologs had inverted Canada underground/aboveground expression ratios compared to autotrophic species. Fatty Craig Barrett, West Virginia University, United States acid and amino acid biosynthesis as well as primary cell wall metabolism were among *Correspondence: the pathways most impacted by this expression reprogramming. -
The Diversity of Wild Orchids in the Southern Slope of Mount Merapi, Yogyakarta, Indonesia Eight Years After the 2010 Eruption
BIODIVERSITAS ISSN: 1412-033X Volume 21, Number 9, September 2020 E-ISSN: 2085-4722 Pages: 4457-4465 DOI: 10.13057/biodiv/d210964 The diversity of wild orchids in the southern slope of Mount Merapi, Yogyakarta, Indonesia eight years after the 2010 eruption FEBRI YUDA KURNIAWAN1,2,♥, FAUZANA PUTRI2,3, AHMAD SUYOKO2,3, HIMAWAN MASYHURI2,3, MAYA PURQI SULISTIANINGRUM2,3, ENDANG SEMIARTI3,♥♥ 1Postgraduate School, Universitas Gadjah Mada. Jl. Teknika Utara, Sleman 55281, Yogyakarta, Indonesia. Tel./fax. +62-274-544975, email: [email protected] 2Biology Orchid Study Club (BiOSC), Faculty of Biology, Universitas Gadjah Mada. Jl. Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia 3Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada. Jl. Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia. Tel./fax.: +62-274-580839, email: [email protected] Manuscript received: 21 August 2020. Revision accepted: 31 August 2020. Abstract. Kurniawan FY, Putri F, Suyoko A, Masyhuri H, Sulistianingrum MP, Semiarti E. 2020. The diversity of wild orchids in the southern slope of Mount Merapi, Yogyakarta, Indonesia eight years after the 2010 eruption. Biodiversitas 21: 4457-4465. The ecosystem of the slopes of Mount Merapi is mountain tropical forest which is frequently affected by volcanic activities. The dynamics of the volcano affect the diversity and abundance of orchids in the ecosystem. Tritis is an area included in the Turgo Hill of the southern slope of Mount Merapi and is under the management of Mount Merapi National Park. The ecosystem in Tritis area classified as lower mountain forest and it has been affected by Mount Merapi eruption. This study aimed to do an inventory of orchid species in Tritis to know the diversity and abundance of orchids that exist in this area. -
Disperis and Epipogium (Orchidaceae): Two New Generic Record for the Flora of Odisha Fmlisfjl ,Oa Bfiiksft;E ¼Vkwfdzmslh½ : Vk
Nelumbo Vol 59(2), (159-163) 2017 ISSN (Print) : 0976-5069 DOI : 10.20324/nelumbo/v32/2017/120461 ISSN (Online) : 2455-376X Disperis and Epipogium (Orchidaceae): two new generic record for the flora of Odisha Truptirekha Kar1, Maloth Mohan1 and Kishore Kumar Mandal2 1Similipal Tiger Reserve, Bhanjpur, Baripada, Odisha -757002, India 2P. G. Department of Botany, North Orissa University, Baripada, Odisha -757003, India Corresponding author: [email protected] fMLisfjl ,oa bfiiksft;e ¼vkWfdZMslh½ : vksM+h’kk ds ouLifrtkr ds fy, nks u, oa’kijd vfHkys[k =qfIrjs[kk dj] ekyksFk eksgu ,oa fd’kksj dqekj eaMy lkjka’k vksfM+lk jkT; ds fy, nks uohu oa'kijd vfHkys[k ds :Ik esa nks vkWfdZM tkfr;ka fMLisfjl uhy?ksjsfUll okbV ,oa bfiiksft;e jksft;e ¼Mh- MkWu ½ fyaMy çFke ckj ntZ fd;s x;s A çLrqr 'kks/k i= esa bu nksuksa tkfr;ksa dk foLr`r ofxZdh fooj.k] forj.k ij fVIi.kh ,oa vklkuh ls igpku ds fy, ,d QksVksIysV nh x;h gS A ABSTRACT Two orchid species viz. Disperis neilgherrensis Wight and Epipogium roseum (D. Don) Lindl. are reported as new distributional record for the state of Odisha. These genera are recorded first time for the flora of Odisha. Detailed taxonomic description, notes on distribution and photo plates are provided for easy identification. Keywords: Disperis, Epipogium , Flora, Orchidaceae, Similipal INTRODUCTION (Seidenfaden, 1969). The genus is well known for its extremely complicated flower morphology and structure; The genus Disperis Sw. with about 70 species is well rep- with various fused floral parts and highly elaborated lip resented in Africa, Madagascar and its adjacent Indian bearing appendages (Kurzweil & Linder, 1991; Kurz- Ocean islands (Manning, 1999; La Croix & al., 2002). -
Fungal Diversity Driven by Bark Features Affects Phorophyte
www.nature.com/scientificreports OPEN Fungal diversity driven by bark features afects phorophyte preference in epiphytic orchids from southern China Lorenzo Pecoraro1*, Hanne N. Rasmussen2, Sofa I. F. Gomes3, Xiao Wang1, Vincent S. F. T. Merckx3, Lei Cai4 & Finn N. Rasmussen5 Epiphytic orchids exhibit varying degrees of phorophyte tree specifcity. We performed a pilot study to investigate why epiphytic orchids prefer or avoid certain trees. We selected two orchid species, Panisea unifora and Bulbophyllum odoratissimum co-occurring in a forest habitat in southern China, where they showed a specifc association with Quercus yiwuensis and Pistacia weinmannifolia trees, respectively. We analysed a number of environmental factors potentially infuencing the relationship between orchids and trees. Diference in bark features, such as water holding capacity and pH were recorded between Q. yiwuensis and P. weinmannifolia, which could infuence both orchid seed germination and fungal diversity on the two phorophytes. Morphological and molecular culture-based methods, combined with metabarcoding analyses, were used to assess fungal communities associated with studied orchids and trees. A total of 162 fungal species in 74 genera were isolated from bark samples. Only two genera, Acremonium and Verticillium, were shared by the two phorophyte species. Metabarcoding analysis confrmed the presence of signifcantly diferent fungal communities on the investigated tree and orchid species, with considerable similarity between each orchid species and its host tree, suggesting that the orchid-host tree association is infuenced by the fungal communities of the host tree bark. Epiphytism is one of the most common examples of commensalism occurring in terrestrial environments, which provides advantages, such as less competition and increased access to light, protection from terrestrial herbivores, and better fower exposure to pollinators and seed dispersal 1,2. -
RNA-Seq Highlights Parallel and Contrasting Patterns in the Evolution of the Nuclear Genome of Fully Mycoheterotrophic Plants Mikhail I
Schelkunov et al. BMC Genomics (2018) 19:602 https://doi.org/10.1186/s12864-018-4968-3 RESEARCH ARTICLE Open Access RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants Mikhail I. Schelkunov1* , Aleksey A. Penin1,2,3 and Maria D. Logacheva1,4,5* Abstract Background: While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels. Results: Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related fully heterotrophic plants. In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated nucleotide substitutions twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H. monotropa. Conclusions: Full heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants. -
A Third Species of Epipogium (Orchidaceae) Added to the Indian Flora
A third species of Epipogium (Orchidaceae) added to the Indian flora Anant Kumar1, Gopal Krishna1 & Vinay Ranjan1* ________________________________ 1Botanical Survey of India, Central National Herbarium, Howrah-711103, West Bengal, India *corresponding author: [email protected] ________________________________ Abstract Epipogium japonicum Makino was recently observed in Neora Valley National Park, Darjeeling, West Bengal, India. Its presence as a new addition to Indian flora brings to 3 the number of known species on the Indian territory. A brief description with an illustration, a determination key and a geographical distribution map of the three species known in India are proposed. Résumé Epipogium japonicum Makino a récemment été observé dans le Parc National Neora Valley (Darjeeling, West Bengal) en Inde. Ceci constitue une addition nouvelle à la flore indienne et porte à 3 le nombre d'espèces connues sur le territoire indien. Nous en donnons ici une brève description, accompagnée d'une illustration et d'une carte de distribution géographique en Inde des trois espèces en question. Une clé de détermination de ces trois espèces est également proposée. Keywords: Flora of India, Neora Valley National Park, new record, taxonomy. Mots clés : flore d'Inde, nouvel enregistrement, Parc national Neora Valley, taxinomie. Manuscrit reçu le 15/10/2018 Article mis en ligne le 13/02/2019 – pp. 17-24 Introduction According to the world checklist of Orchidaceae (Govaerts et al., 2018), the mycotrophic genus Epipogium Gmelin ex Borkhausen (1792: 139) is comprised of three species. Later, this number increases up to 5 after the recent discovery of new species from Taiwan (Lin et al., 2016; Hsieh et al., 2018): Epipogium aphyllum Swartz (1814:32), Epipogium japonicum Makino (1904: 131), Epipogium kentingensis T.P.Lin & S.H.Wu (2012: 378), Epipogium meridianus T.P.Lin in Hsieh et al. -
An Annotated Checklist of the Orchids of Sri Lanka, by Fernando And
Rheedea Vol. 18(1) 1-28 2008 An Annotated Checklist of the Orchids of Sri Lanka 1 Samantha Suranjan Fernando and Paul Ormerod Post Graduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka. E-mail: [email protected] 1P.O. Box 8210, Cairns 4870, Queensland, Australia. E-mail: [email protected] Abstract A general description of Sri Lanka and its bioclimatic zones are presented. The history of the Island’s orchid taxonomy is briefly reviewed. An updated checklist is presented for the country’s orchid flora using recent information. New species, new records and nomenclatural changes from previous lists are annotated with appropriate references. This work lists 188 species belonging to 78 genera with one endemic genus (Adrorhizon Hook. f.) and 55 endemic species. A new name, Bulbophyllum jayaweerae Fernando et Ormerod, is proposed for Cirrhopetalum roseum Jayaweera. Illegitimacy of the name Saccolabium virescens Gardner ex Lindl. is discussed and this species is described as a new taxon, Robiquetia virescens Ormerod et Fernando. Keywords: Sri Lanka, Orchids, Bulbophyllum jayaweerae, Robiquetia virescens, New name, New taxon Introduction Sri Lanka is a pear shaped island in the Indian Ocean lying in the southern tip of the Indian Peninsula (Fig. 1). It lies between 5° 55’ - 9°51’ North latitudes and 79° 41’ - 81°54’ East longitudes and covers a total area of 65,609.8 km² consisting of 64,453.6 km² of land area and 1,156. 2 km² of inland waters. The island has a maximum length of about 435 km and a maximum width of about 225 km. -
Parallel Evolution of Highly Conserved Plastid Genome Architecture in Red Seaweeds and Seed Plants
Lee et al. BMC Biology (2016) 14:75 DOI 10.1186/s12915-016-0299-5 RESEARCH ARTICLE Open Access Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants JunMo Lee1, Chung Hyun Cho1, Seung In Park1, Ji Won Choi1, Hyun Suk Song1, John A. West2, Debashish Bhattacharya3† and Hwan Su Yoon1*† Abstract Background: The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results: We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions: Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. -
RNA-Seq Highlights Parallel and Contrasting Patterns in the Evolution of the Nuclear Genome of Holo-Mycoheterotrophic Plants
bioRxiv preprint doi: https://doi.org/10.1101/183202; this version posted September 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of holo-mycoheterotrophic plants M.I. Schelkunov 1, 2,*, A.A. Penin 1, 2, 3, M.D. Logacheva 1, 2,* 1 - Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia 2 - Lomonosov Moscow State University, A.N Belozersky Institute of Physico-Chemical Biology, Moscow, Russia 3 - Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia * - corresponding authors, [email protected], [email protected] Summary While photosynthesis is the most notable trait of plants, several lineages of plants (so-called holo- heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels. Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related holo-heterotrophic plants. In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. -
Differing Life-History Strategies of Two Mycoheterotrophic Orchid Species Associated with Leaf Litter- and Wood-Decaying Fungi
diversity Article Differing Life-History Strategies of Two Mycoheterotrophic Orchid Species Associated with Leaf Litter- and Wood-Decaying Fungi Yuki Ogura-Tsujita 1,2,* , Kenshi Tetsuka 3, Shuichiro Tagane 4, Miho Kubota 1, Shuichiro Anan 1, Yumi Yamashita 5 , Koichi Tone 6 and Tomohisa Yukawa 5 1 Faculty of Agriculture, Saga University, 1 Honjyo-machi, Saga 840-8502, Japan; [email protected] (M.K.); [email protected] (S.A.) 2 The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan 3 Yakushima Evergreen Broad-Leaved Forest Network, Isso, Yakushima-machi, Kumage-gun, Kagoshima 891-4203, Japan; [email protected] 4 The Kagoshima University Museum, 1-21-30 Korimoto, Kagoshima 890-0065, Japan; [email protected] 5 Tsukuba Botanical Garden, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan; [email protected] (Y.Y.); [email protected] (T.Y.) 6 Okinawa Municipal Museum, 2-19-6 Uechi, Okinawa 904-0031, Japan; [email protected] * Correspondence: [email protected] Abstract: Mycoheterotrophic orchids depend completely on mycorrhizal fungi for their supply of carbon. The life-history traits of mycoheterotrophic plants (MHPs) can differ according to the characteristics of the associated mycorrhizal fungi. We compared the life-history strategies of two Citation: Ogura-Tsujita, Y.; Tetsuka, mycoheterotrophic orchids associated with wood- and leaf litter-decaying fungi over a maximum K.; Tagane, S.; Kubota, M.; Anan, S.; of six years of field monitoring. Seventy percent of the aboveground stems of Erythrorchis altissima, Yamashita, Y.; Tone, K.; Yukawa, T. -
An Orchid Checklist of Mt. Popa, Central Myanmar
Bull. Natl. Mus. Nat. Sci., Ser. B, 41(2), pp. 69–89, May 22, 2015 An Orchid Checklist of Mt. Popa, Central Myanmar Nobuyuki Tanaka1, Tomohisa Yukawa2,*, Khin Myo Htwe3 and Jin Murata4 1 Kochi Prefectural Makino Botanical Garden, Godaisan 4200–6, Kochi 781–8125, Japan; Present address: Department of Botany, National Museum of Nature and Science, Amakubo 4–1–1, Tsukuba, Ibaraki 305–0005, Japan 2 Department of Botany, National Museum of Nature and Science, Amakubo 4–1–1, Tsukuba, Ibaraki 305–0005, Japan 3 Popa Mountain Park, Nature and Wildlife Conservation Division, Environmental Conservation and Forestry, Kyaukpadaung Township, Mandalay Region, Union of Myanmar 4 Botanical Gardens, Graduate School of Sciences, the University of Tokyo, Hakusan 3–7–1, Bunkyo-ku, Tokyo 112–0001, Japan * E-mail: [email protected] (Received 20 February 2015; accepted 25 March 2015) Abstract As part of floristic inventory work of Myanmar, a preliminary orchid flora of Mt. Popa, central Myanmar, is provided. We herein record 102 taxa of orchids representing 42 genera from this region. Key words : checklist, Orchidaceae, Mt. Popa, Myanmar Introduction central Myanmar (Fig. 1). Working in the 1930s, Frederik Garrett Dickason was probably the first Myanmar (old Burma) is located south of the botanist to make collections on Mt. Popa (Tanaka Himalayan region and, with a land area of et al., 2006). Yin Yin Kyi reported on the vegeta- 676,500 km2 (approximately twice the size of Japan), spans tropical evergreen, mixed decidu- ous, savanna and alpine vegetation types (Tanaka, 2005). An updated checklist of the gym- nosperms and flowering plants of Myanmar has been published (Kress et al., 2003) based on pre- vious or preceding works by Lace (1912), Rod- ger (1922), Hundley and Chit (1961) and Hund- ley (1987), and with additional records accumulated from floras of neighbouring regions. -
Ectomycorrhizal Inocybe Species Associate with the Mycoheterotrophic Orchid Epipogium Aphyllum but Not Its Asexual Propagules
Annals of Botany 104: 595–610, 2009 doi:10.1093/aob/mcn269, available online at www.aob.oxfordjournals.org Ectomycorrhizal Inocybe species associate with the mycoheterotrophic orchid Epipogium aphyllum but not its asexual propagules Melanie Roy1,†, Takahiro Yagame2, Masahide Yamato3, Koji Iwase4, Christine Heinz5, Antonella Faccio6, Paola Bonfante6 and Marc-Andre Selosse1,†,* 1Centre d’Ecologie Fonctionnelle et Evolutive (CNRS, UMR 5175), Equipe Interactions Biotiques, 1919 Route de Mende, 34293 Montpellier ce´dex 5, France, 2Orchid Museum Takamori, 512-73 Izuhara, Shimoina, Nagano 399-3107, Japan, 3Environment Department, The General Environmental Technos Co., Ltd, 1-3-5 Azuchimachi Chuo-ku, Osaka 541-0052, Japan, 4Fungus/ Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-minami, Tottori 680-8553, Japan, 5Universite´ Montpellier 2, UMR AMAP Botanique et bioinformatique de l’Architecture des Plantes, 34000 Montpellier, France and 6Dipartimento di Biologia Vegetale dell’Universita`, Istituto per la Protezione delle Piante – CNR, Viale Mattioli 25, 10125 Torino, Italy Received: 1 June 2008 Returned for revision: 22 September 2008 Accepted: 25 November 2008 Published electronically: 19 January 2009 † Background and Aims Epipogium aphyllum is a Eurasian achlorophyllous, mycoheterotrophic forest orchid. Due to its rarity, it is often protected, and its biology is poorly known. The identity and pattern of colonization of fungal associates providing carbon to this orchid have not been studied previously. † Methods Using samples from 34 individuals from 18 populations in Japan, Russia and France, the following were investigated: (a) colonization patterns of fungal associates of E. aphyllum by microscopy; (b) their identity by PCR amplification of nuclear ribosomal ITS carried out on rhizome fragments and hyphal pelotons.