A Multi-Step Comparison of Short-Read Full Plastome Sequence Assembly Methods in Grasses
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Understory Community Shifts in Response to Repeated Fire and Fire Surrogate Treatments in the Southern Appalachian Mountains, USA Emily C
Oakman et al. Fire Ecology (2021) 17:7 Fire Ecology https://doi.org/10.1186/s42408-021-00097-1 ORIGINAL RESEARCH Open Access Understory community shifts in response to repeated fire and fire surrogate treatments in the southern Appalachian Mountains, USA Emily C. Oakman1, Donald L. Hagan1* , Thomas A. Waldrop2 and Kyle Barrett1 Abstract Background: Decades of fire exclusion in the southern Appalachian Mountains, USA, has led to changing forest structure and species composition over time. Forest managers and scientists recognize this and are implementing silvicultural treatments to restore forest communities. In this study, conducted at the southern Appalachian Fire and Fire Surrogate Study site in Green River Game Land, North Carolina, USA, we assessed the effects of four fuel- reduction methods (burned four times, B; mechanical treatment two times, M; mechanical treatment two times plus burned four times, MB; and control, C) on the changes in understory community from pre-treatment to post- treatment years (2001 to 2016). We used non-metric multidimensional scaling (NMDS) to determine overall understory community heterogeneity, agglomerative hierarchical cluster analyses (AHCA) to determine finer-scale changes in understory community structure, and indicator species analyses (ISA) to identify the species that were associated with the different fuel reduction treatments over time. Results: The NMDS ordination showed little separation between treatment polygons. The AHCA resulted in two main categories of understory species responses based on how treatment plots clustered together: (1) species apparently unaffected by the treatments (i.e., no treatment pattern present within cluster); and (2) species that responded to B, M, or MB treatments (i.e., pattern of treatment plots present within cluster). -
Bamboo: a Versatile Plant the Journal of the Greens and Gardens, Volume 01, No
An International Journal of Floriculture Science and Landscaping Bamboo: a versatile plant The Journal of the Greens and Gardens, Volume 01, No. 02 : 24-26. 2019 Short Communication Bamboo: a versatile plant Anurag Bajpay* and Kulveer Singh Yadav School of Agricultural Sciences and Technology, Regional Institute of Management and Technology (RIMT) University, Mandi Gobindgarh, Punjab-147301, INDIA *Corresponding Author: [email protected] Received: March 12, 2019 Accepted: March 30, 2019 Abstract This paper deals with the versatile uses of bamboo plant species. It has many useful properties and used for various purposes. Bamboos are used in landscaping, fencing, housing, raw materials for crafts, pulp for paper industry and fabrics for cloth industry besides culinary products, fodder etc. The young shoots of bamboo are used for preparing various delicious foods, processed products and also used as medicines. Various bamboo species are also utilized in herbal and traditional medication. It also has huge potential for solving many problems of environmental and social needs. Key words: Bamboo, environment, culinary, medicine and ornamental use. Introduction: pulp for the paper industry, storage and transportation Bamboo (Bamboo Schreb.) is an evergreen perennial baskets, used in flooring and roofing, preparation of fabrics flowering plant belonging to the monocots family Poaceae. etc. Young rhizomes of Bamboo are widely used to preparing This woody grass widely grows in tropical, subtropical and many kinds of food products. The products of Bamboos are also in temperate zones of India and world as well. The genus gaining popularity among the people and bamboo industries is mainly in distributed Asia, Africa, and Tropical America. -
Preliminary Checklist of the Terrestrial Flora and Fauna of Fern Cave
Preliminary Checklist of the Terrestrial Flora and Fauna of Fern Cave National Wildlife Refuge ______________________________________________ Prepared for: United States Fish & Wildlife Service Prepared by: J. Kevin England, MAT David Richardson, MS Completed: as of 22 Sep 2019 All rights reserved. Phone: 256-565-4933 Email: [email protected] Flora & Fauna of FCNWR2 ABSTRACT I.) Total Biodiversity Data The main objective of this study was to inventory and document the total biodiversity of terrestrial habitats located at Fern Cave National Wildlife Refuge (FCNWR). Table 1. Total Biodiversity of Fern Cave National Wildlife Refuge, Jackson Co., AL, USA Level of Classification Families Genera Species Lichens and Allied Fungi 14 21 28 Bryophytes (Bryophyta, Anthocerotophyta, Marchantiophyta) 7 9 9 Vascular Plants (Tracheophytes) 76 138 176 Insects (Class Insecta) 9 9 9 Centipedes (Class Chilopoda) 1 1 1 Millipedes (Class Diplopoda) 2 3 3 Amphibians (Class Amphibia) 3 4 5 Reptiles (Class Reptilia) 2 3 3 Birds (Class Aves) 1 1 1 Mammals (Class Mammalia) 2 2 2 Total 117 191 237 II. Vascular Flora (Appendix 3) Methods and Materials To compile a thorough vascular flora survey, several examples of different plant communities at numerous sites were visited and sampled during the study. Approximately 45 minutes was spent documenting community structure at each site. Lastly, all habitats, ecological systems, and plant associations found within the property boundaries were defined based on floristic content, soil characteristics (soil maps) and other abiotic factors. Flora & Fauna of FCNWR3 The most commonly used texts for specimen identification in this study were Flora of North America (1993+), Mohr (1901), Radford et al. -
Natural Vegetation of the Carolinas: Classification and Description of Plant Communities of the Far Western Mountains of North Carolina
Natural vegetation of the Carolinas: Classification and Description of Plant Communities of the Far Western Mountains of North Carolina A report prepared for the Ecosystem Enhancement Program, North Carolina Department of Environment and Natural Resources in partial fulfillments of contract D07042. By M. Forbes Boyle, Robert K. Peet, Thomas R. Wentworth, Michael P. Schafale, and Michael Lee Carolina Vegetation Survey Curriculum in Ecology, CB#3275 University of North Carolina Chapel Hill, NC 27599‐3275 Version 1. April, 2011 1 INTRODUCTION In mid June 2010, the Carolina Vegetation Survey conducted an initial inventory of natural communities along the far western montane counties of North Carolina. There had never been a project designed to classify the diversity of natural upland (and some wetland) communities throughout this portion of North Carolina. Furthermore, the data captured from these plots will enable us to refine the community classification within the broader region. The goal of this report is to determine a classification structure based on the synthesis of vegetation data obtained from the June 2010 sampling event, and to use the resulting information to develop restoration targets for disturbed ecosystems location in this general region of North Carolina. STUDY AREA AND FIELD METHODS From June 13‐20 2010, a total of 48 vegetation plots were established throughout the far western mountains of North Carolina (Figure 1). Focus locations within the study area included the Pisgah National Forest (NF) (French Broad and Pisgah Ranger Districts), the Nantahala NF (Tusquitee Ranger District), and Sandymush Game Land. Target natural communities throughout the week included basic oak‐hickory forest, rich cove forest, northern hardwood and boulderfield forest, chestnut oak forest, montane red cedar woodland, shale slope woodland, montane alluvial slough forest, and low elevation xeric pine forest. -
Macro-Propagation of Native Cane (Arundinaria Spp.) in Central Kentucky and Restoration Out-Plantings in Western Tennessee and Southern Alabama
Macro-propagation of native cane (Arundinaria spp.) in central Kentucky and restoration out-plantings in western Tennessee and southern Alabama. by Rachel Elizabeth Conley A thesis submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Master of Science Auburn, Alabama August 1, 2015 Keywords: Arundinaria, canebrake, ethnobotany, macro-propagation, restoration, rhizome Copyright 2015 by Rachel Elizabeth Conley Approved by Mark Smith, Chair, Associate Professor, School of Forestry and Wildlife Sciences Nancy Loewenstein, Research Fellow IV, School of Forestry and Wildlife Sciences Christopher Anderson, Associate Professor, School of Forestry and Wildlife Sciences Abstract Canebrakes, monodominant stands of native bamboo (Arundinaria spp.; hereafter cane), are a critically endangered ecosystem in the Southeastern United States. Canebrakes have declined to <2% of their former range from overgrazing by livestock, land conversion, habitat fragmentation, and fire suppression. Canebrakes are important for wildlife habitat, riparian buffers, and Native American ethnobotany. In cane macro- propagation trials, I investigated mother plant collection site and time-since- transplantation effects on rhizome production. Additionally, I assessed the effects of collection site and container type on propagule survival, growth rate, and final aboveground growth. In out-planting trials, I investigated the effects of shade, mulch, and fertilizer on survival and growth of propagules. My results indicate that an interaction between time and collection site affected rhizome production. Propagule survival was affected by collection site and final size was affected by collection site and container type. I suggest using macro-propagation for small-scale canebrake restoration (<10 ha). ii Acknowledgments I would like to thank The Nature Conservancy and the USDA NRCS for project funding, particularly Jeff Fore for his help and interest and David Elliott for his help with the Atmore site coordination. -
The Journal of the American Bamboo Society Volume 26
152065 ABS BSCv26 Cover 12/30/13 2:49 PM Page 1 The Journal of the American Bamboo Society Volume 26 152065 ABS BSCv26 Cover 12/30/13 2:49 PM Page 2 BAMBOO SCIENCE & CULTURE The Journal of the American Bamboo Society is published by the American Bamboo Society Copyright 2013 ISSN 0197– 3789 Bamboo Science and Culture: The Journal of the American Bamboo Society is the continuation of The Journal of the American Bamboo Society President of the Society Board of Directors James Clever David Benfield Ariel Dubov Vice President Carole Meckes Tom Harlow Luc Boeraeve Karlyn M. Bradshaw Treasurer Norm Bezona Dawn Weaver Andy Ringle Daniel Fox Secretary Scott Ritchie David King David King Anna Foleen Membership John Tkach Tom Harlow Danielo Ramos Artie Turner Membership Information Membership in the American Bamboo Society and one ABS chapter is for the calendar year and includes a subscription to the bimonthly Newsletter and annual Journal. See http://www.bamboo.org for current rates. Cover photo: Yushania alpina, Rwenzori, Uganda (Photo by Dr. Peter Gill). Bamboo Science and Culture: The Journal of the American Bamboo Society 26(1): 1-12 © Copyright 2013 by the American Bamboo Society Canebrake fauna revisited: additional records of species diversity in a critically endangered ecosystem Steven G. Platt1, Thomas R. Rainwater2*, Ruth M. Elsey3, and Christopher G. Brantley4 1Wildlife Conservation Society, Myanmar Program, Aye Yeik Mon 1st Street, Yadanamon Hosuing Ave., Yangon, Myanmar 2U.S. Fish and Wildlife Service, Ecological Services Field Office, 176 Croghan Road, Suite 200, Charleston, South Carolina 29407, USA 3Louisiana Department of Wildlife and Fisheries, Rockefeller Wildlife Refuge, 5476 Grand Chenier, Louisiana 70643, USA 4United States Army Corps of Engineers Bonnet Carré Spillway, P.O. -
Evolution of the Bamboos
Wysocki et al. BMC Evolutionary Biology (2015) 15:50 DOI 10.1186/s12862-015-0321-5 RESEARCH ARTICLE Open Access Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis William P Wysocki1*, Lynn G Clark2, Lakshmi Attigala2, Eduardo Ruiz-Sanchez3 and Melvin R Duvall1 Abstract Background: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae. Results: Here a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots. Conclusions: Phylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues. -
Based Probes Reveals a Large-Scale Phylogeny of 412 Bamboos
Wang et al. BMC Plant Biology (2021) 21:76 https://doi.org/10.1186/s12870-020-02779-5 RESEARCH ARTICLE Open Access Targeted enrichment of novel chloroplast- based probes reveals a large-scale phylogeny of 412 bamboos Jiongliang Wang1,2†, Weixue Mu3†, Ting Yang3, Yue Song3, Yin Guang Hou1,2, Yu Wang1,2, Zhimin Gao1,2, Xin Liu3, Huan Liu3 and Hansheng Zhao1,2* Abstract Background: The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution. Results: To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15 M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. -
PIEDMONT/MOUNTAIN CANEBRAKE Concept
PIEDMONT/MOUNTAIN CANEBRAKE Concept: Piedmont/Mountain Canebrakes are communities dominated by dense thickets of Arundinaria gigantea, treeless or with an open canopy. No well-developed examples are known to remain in North Carolina. Distinguishing Features: Piedmont/Mountain Canebrakes are distinguished by having a dense shrub layer of Arundinaria gigantea, occurring with limited tree cover. Areas of cane that appear to be naturally developed, or are restored in plausible natural settings, should be regarded as this type. Areas where Arundinaria occurs at low to moderate density under a typical forest canopy are not included, nor are stands of Arundinaria appalachiana in uplands. Abundance of Arundinaria gigantea in a forest may suggest past occurrence of a canebrake but should not be taken as proof of a former canebrake without additional evidence. Methods of finding sites of past canebrakes, other than definitive site-species historical descriptions, are not known. Piedmont/Mountain Canebrakes are distinguished from Peatland Canebrakes by occurring different regions, different environments, and in being dominated by Arundinaria gigantea rather than Arundinaria tecta. Synonyms: Arundinaria gigantea ssp. gigantea Shrubland (CEGL003836). Ecological Systems: South-Central Interior Small Stream and Riparian (CES202.706); South- Central Interior Large Floodplain (CES202.705). Sites: Piedmont/Mountain Canebrakes may potentially occur in either small or large floodplains. They are believed to be primarily in the Mountain Region but could occur in the upper Piedmont. Soils: Piedmont/Mountain Canebrakes could potentially occur on any floodplain soil. If particular soil conditions are necessary, they are not known. Hydrology: Canebrakes occurred on drier floodplain sites; they presumably were flooded intermittently for brief periods. -
Grasses Endemic to the Conterminous United States
Humboldt State University Digital Commons @ Humboldt State University Botanical Studies Open Educational Resources and Data 12-26-2019 Grasses Endemic to the Conterminous United States James P. Smith Jr Humboldt State University, [email protected] Follow this and additional works at: https://digitalcommons.humboldt.edu/botany_jps Part of the Botany Commons Recommended Citation Smith, James P. Jr, "Grasses Endemic to the Conterminous United States" (2019). Botanical Studies. 89. https://digitalcommons.humboldt.edu/botany_jps/89 This Grasses-United States is brought to you for free and open access by the Open Educational Resources and Data at Digital Commons @ Humboldt State University. It has been accepted for inclusion in Botanical Studies by an authorized administrator of Digital Commons @ Humboldt State University. For more information, please contact [email protected]. GRASSES ENDEMIC TO THE CONTERMINOUS UNITED STATES James P. Smith, Jr. Professor Emeritus of Botany Department of Biological Sciences Humboldt State University Arcata, California 26 December 2019 INTRODUCTION Agrostis densiflora • CA, OR Agrostis hallii • CA, OR For a grass to be an endemic, it must be native and be Agrostis hendersonii • CA, OR restricted to the area specified, in this case the Agrostis hooveri • CA conterminous United States. Native plants cultivated or Agrostis howellii • OR introduced outside their natural range are still treated as Agrostis lacuna-vernalis: CA (Monterey Co.) endemic. There are degrees of endemism. A grass may be Agrostis rossiae • WY known from a single historical collection, one or a few Alopecurus aequalis var. sonomensis • CA extant populations, a county, a state, a few contiguous Alopecurus saccatus • CA, ID, OR, WA states, a region (e. -
Environmental Assessment United States Department of Agriculture Land Bridge Road Forest Service Bridge Relocation Project
Environmental Assessment United States Department of Agriculture Land Bridge Road Forest Service Bridge Relocation Project April 9,2014 Andrew Pickens Ranger District Sumter National Forest Oconee County South Carolina Land Bridge Road – Bridge Relocation Project Environmental Assessment Location of Action: Sumter National Forest, Andrew Pickens Ranger District, Oconee County, South Carolina Type of Document: Environmental Assessment Lead Agency: USDA Forest Service Responsible Official: John Richard Lint, Forest Supervisor, Francis Marion and Sumter National Forest Contact Person: Victor Wyant Silviculturist / TMA USDA Forest Service 112 Andrew Pickens Circle Mountain Rest, SC 29664 Phone: 864-638-9568 The U.S. Department of Agriculture (USDA) prohibits discrimination in all its programs and activities on the basis of race, color, national origin, age, disability, and where applicable, sex, marital status, familial status, parental status, religion, sexual orientation, genetic information, political beliefs, reprisal, or because all or part of an individual’s income is derived from any public assistance program. (Not all prohibited bases apply to all programs.) Persons with disabilities who require alternative means for communication of program information (Braille, large print, audiotape, etc.) should contact USDA’s TARGET Center at (202) 720-2600 (voice and TDD). To file a complaint of discrimination, write to USDA, Director, Office of Civil Rights, 1400 Independence Avenue, S.W., Washington, D.C. 20250-9410, or call (800) 795-3272 -
A 250 Plastome Phylogeny of the Grass Family (Poaceae): Topological Support Under Different Data Partitions
A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions Jeffery M. Saarela1, Sean V. Burke2, William P. Wysocki3, Matthew D. Barrett4,5, Lynn G. Clark6, Joseph M. Craine7, Paul M. Peterson8, Robert J. Soreng8, Maria S. Vorontsova9 and Melvin R. Duvall2 1 Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, ON, Canada 2 Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA 3 Center for Data Intensive Sciences, University of Chicago, Chicago, IL, USA 4 Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, Australia 5 School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia 6 Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA 7 Jonah Ventures, Manhattan, KS, USA 8 Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA 9 Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UK ABSTRACT The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries Submitted 8 August 2017 and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal Accepted 8 January 2018 Published 2 February 2018 was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single Corresponding authors Jeffery M.