The Sequenced Angiosperm Genomes and Genome Databases
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Oryza Longistaminata) ECOTYPES and CULTIVATED RICE (Otyza Sativa) CULTIVARS from the COASTAL REGION of KENYA '!
\ X INTERACTIVE EFFECT ON MORPHOLOGY, PHENOLOGY AND GROWTH OF THE WILD RICE (Oryza longistaminata) ECOTYPES AND CULTIVATED RICE (Otyza sativa) CULTIVARS FROM THE COASTAL REGION OF KENYA '! BY NJERU S. MWINGI (B.Sc. Hons, Egerton ) A THESIS SUBMITTED TO UNIVERSITY OF NAIROBI, SCHOOL OF BIOLOGICAL SCIENCES, IN PARTIAL FULFILLMENT OF A MASTERS OF SCIENCE DEGREE IN BOTANY University ot NAIROBI Library DECLARATION 1, Serah Mwingi Njeru, hereby declare that this thesis is my original work and has not been presented for a Master of Science degree in any other university Signature _____ ___________ Date__ ______1;f) <rl We the undersigned declare that this thesis has been submitted with our approval as the university supervisors Prof. J. I. Kinyamario Signature Date Ig'/g'/CLO// Dr J. K. Mworia Signature Date f g / g / i 0 / / d e d ic a t io n This thesis is dedicated to my mother, Retisia Kivutu, for her great dedication towards all my academic achievements. Her efforts are always appreciated and will remain a challenge to me forever. Mama you have done a great job. acknowledgements I wish to express my sincere appreciation and gratitude to my supervisor Prof. J. I. Kinyamario for his contribution, support, guidance and motivation as I did this work. Also, I wish to thank him for introducing me to the Biosafe-Train Project and the larger DAN1DA ENRECA research group. Without him it would have been very difficult to accomplish my objectives. I am also very grateful to my other suprvisor, Dr. J. K. Mworia for his support and guidance throughout my M.Sc. -
Characterisation of an Intron-Split Solanales Microrna
Characterisation of an intron-split Solanales microRNA Zahara Medina Calzada A thesis submitted for the degree of Doctor of Philosophy University of East Anglia School of Biological Sciences September 2017 This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution “Doing science is very romantic… when it works!” (the friend of a friend of mine) 2 Abstract MicroRNAs (miRNAs) are a distinct class of short endogenous RNAs with central roles in post-transcriptional regulation of gene expression that make them essential for the development and normal physiology of several groups of eukaryotes, including plants. In the last 15 years, hundreds of miRNA species have been identified in plants and great advances have been achieved in the understanding of plant miRNA biogenesis and mode of action. However, many miRNAs, generally those with less conventional features, still remain to be discovered. Likewise, further layers that regulate the pathway from miRNA biogenesis to function and turnover are starting to be revealed. In the present work we have studied the tomato miRNA “top14”, a miRNA with a non-canonical pri-miRNA structure in which an intron is in between miRNA and miRNA*. We have found that this miRNA is conserved within the economically important Solanaceae family and among other members of the Solanales order also agriculturally relevant, like in sweet potato, while its peculiar intron-split pri-miRNA structure is exclusively kept in the more closely related genera Solanum , Capsicum and Nicotiana . -
Identification of Anther Length QTL and Construction of Chromosome
plants Article Identification of Anther Length QTL and Construction of Chromosome Segment Substitution Lines of Oryza longistaminata Takayuki Ogami, Hideshi Yasui, Atsushi Yoshimura and Yoshiyuki Yamagata * Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University. 744, Motooka, Nishi-ku, Fukuoka 819-0395, Japan; [email protected] (T.O.); [email protected] (H.Y.); [email protected] (A.Y.) * Correspondence: [email protected]; Tel.: +81-92-802-4553 Received: 30 August 2019; Accepted: 29 September 2019; Published: 29 September 2019 Abstract: Life histories and breeding systems strongly affect the genetic diversity of seed plants, but the genetic architectures that promote outcrossing in Oryza longistaminata, a perennial wild species in Africa, are not understood. We conducted a genetic analysis of the anther length of O. longistaminata accession W1508 using advanced backcross quantitative trait locus (QTL) analysis and chromosomal segment substitution lines (CSSLs) in the genetic background of O. sativa Taichung 65 (T65), with simple sequence repeat markers. QTL analysis of the BC3F1 population (n = 100) revealed that four main QTL regions on chromosomes 3, 5, and 6 were associated to anther length. We selected a minimum set of BC3F2 plants for the development of CSSLs to cover as much of the W1508 genome as possible. The additional minor QTLs were suggested in the regional QTL analysis, using 21 to 24 plants in each of the selected BC3F2 population. The main QTLs found on chromosomes 3, 5, and 6 were validated and designated qATL3, qATL5, qATL6.1, and qATL6.2, as novel QTLs identified in O. -
Research Article Ecological Observations of Native Geocoris Pallens and G
Hindawi Publishing Corporation Psyche Volume 2013, Article ID 465108, 11 pages http://dx.doi.org/10.1155/2013/465108 Research Article Ecological Observations of Native Geocoris pallens and G. punctipes Populations in the Great Basin Desert of Southwestern Utah Meredith C. Schuman, Danny Kessler, and Ian T. Baldwin Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoll-Straße¨ 8, 07745 Jena, Germany Correspondence should be addressed to Ian T. Baldwin; [email protected] Received 5 November 2012; Accepted 16 April 2013 Academic Editor: David G. James Copyright © 2013 Meredith C. Schuman 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. Big-eyed bugs (Geocoris spp. Fallen,´ Hemiptera: Lygaeidae) are ubiquitous, omnivorous insect predators whose plant feeding behavior raises the question of whether they benefit or harm plants. However, several studies have investigated both the potential of Geocoris spp. to serve as biological control agents in agriculture and their importance as agents of plant indirect defense in nature. These studies have demonstrated that Geocoris spp. effectively reduce herbivore populations and increase plant yield. Previous work has also indicated that Geocoris spp. respond to visual and olfactory cues when foraging and choosing their prey and that associative learning of prey and plant cues informs their foraging strategies. For these reasons, Geocoris spp. have become models for the study of tritrophic plant-herbivore-predator interactions. Here, we present detailed images and ecological observations of G. pallens Stal˚ and G. -
Genome Skimming for Phylogenomics
Genome skimming for phylogenomics Steven Andrew Dodsworth School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. Submitted in partial fulfilment of the requirements of the degree of Doctor of Philosophy November 2015 1 Statement of originality I, Steven Andrew Dodsworth, confirm that the research included within this thesis is my own work or that where it has been carried out in collaboration with, or supported by others, that this is duly acknowledged and my contribution indicated. Previously published material is also acknowledged and a full list of publications is given in the Appendix. Details of collaboration and publications are given at the start of each chapter, as appropriate. I attest that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge break any UK law, infringe any third party’s copyright or other Intellectual Property Right, or contain any confidential material. I accept that the College has the right to use plagiarism detection software to check the electronic version of the thesis. I confirm that this thesis has not been previously submitted for the award of a degree by this or any other university. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. Signature: Date: 16th November 2015 2 Frontispiece: Nicotiana burbidgeae Symon at Dalhousie Springs, South Australia. 2014. Photo: S. Dodsworth. 3 Acknowledgements Firstly, I would like to thank my PhD supervisors, Professor Andrew Leitch and Professor Mark Chase. -
Appendix Color Plates of Solanales Species
Appendix Color Plates of Solanales Species The first half of the color plates (Plates 1–8) shows a selection of phytochemically prominent solanaceous species, the second half (Plates 9–16) a selection of convol- vulaceous counterparts. The scientific name of the species in bold (for authorities see text and tables) may be followed (in brackets) by a frequently used though invalid synonym and/or a common name if existent. The next information refers to the habitus, origin/natural distribution, and – if applicable – cultivation. If more than one photograph is shown for a certain species there will be explanations for each of them. Finally, section numbers of the phytochemical Chapters 3–8 are given, where the respective species are discussed. The individually combined occurrence of sec- ondary metabolites from different structural classes characterizes every species. However, it has to be remembered that a small number of citations does not neces- sarily indicate a poorer secondary metabolism in a respective species compared with others; this may just be due to less studies being carried out. Solanaceae Plate 1a Anthocercis littorea (yellow tailflower): erect or rarely sprawling shrub (to 3 m); W- and SW-Australia; Sects. 3.1 / 3.4 Plate 1b, c Atropa belladonna (deadly nightshade): erect herbaceous perennial plant (to 1.5 m); Europe to central Asia (naturalized: N-USA; cultivated as a medicinal plant); b fruiting twig; c flowers, unripe (green) and ripe (black) berries; Sects. 3.1 / 3.3.2 / 3.4 / 3.5 / 6.5.2 / 7.5.1 / 7.7.2 / 7.7.4.3 Plate 1d Brugmansia versicolor (angel’s trumpet): shrub or small tree (to 5 m); tropical parts of Ecuador west of the Andes (cultivated as an ornamental in tropical and subtropical regions); Sect. -
Great Basin Native Plant Project: 2015 Progress Report
GREAT BASIN NATIVE PLANT PROJECT 2015 PROGRESS REPORT USDA FOREST SERVICE, ROCKY MOUNTAIN RESEARCH STATION AND USDI BUREAU OF LAND MANAGEMENT, BOISE, ID APRIL 2016 COOPERATORS USDA Forest Service, Rocky Mountain Research Station Grassland, Shrubland and Desert Ecosystem Research Program, Boise, ID, Provo, UT, and Albuquerque, NM USDI Bureau of Land Management, Plant Conservation Program, Washington, DC Boise State University, Boise, ID Brigham Young University, Provo, UT College of Western Idaho, Nampa, ID Eastern Oregon Stewardship Services, Prineville, OR Northern Arizona University, Flagstaff, AZ Oregon State University, Bend, OR Oregon State University Malheur Experiment Station, Ontario, OR Private Contractors and Land Owners Native Seed Industry Texas Tech University, Lubbock, TX University of California, Browns Valley, CA University of Idaho, Moscow, ID University of Nevada, Reno, NV University of Nevada Cooperative Extension, Elko and Reno, NV Utah State University, Logan, UT US Army Corps of Engineers, Junction City, OR USDA Agricultural Research Service, Pollinating Insects Research Center, Logan, UT USDA Agricultural Research Service, Eastern Oregon Agriculture Research Center, Burns, OR USDA Agricultural Research Service, Forage and Range Research Laboratory, Logan, UT USDA Agricultural Research Service, Great Basin Rangelands Research Unit, Reno, NV USDA Agricultural Research Service, Western Regional Plant Introduction Center, Pullman, WA USDA Forest Service, National Seed Laboratory, Dry Branch, GA USDA Forest Service, -
Transcriptome Profiling of Agrobacterium‑Mediated Infiltration of Transcription Factors to Discover Gene Function and Expression Networks in Plants Donna M
Bond et al. Plant Methods (2016) 12:41 DOI 10.1186/s13007-016-0141-7 Plant Methods RESEARCH Open Access Infiltration‑RNAseq: transcriptome profiling of Agrobacterium‑mediated infiltration of transcription factors to discover gene function and expression networks in plants Donna M. Bond1*, Nick W. Albert2, Robyn H. Lee1, Gareth B. Gillard1,4, Chris M. Brown1, Roger P. Hellens3 and Richard C. Macknight1,2* Abstract Background: Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct pheno- typic outputs. The identification of genes and transcriptional networks regulated by a TF often requires stable trans- formation and expression changes in plant cells. However, the production of stable transformants can be slow and laborious with no guarantee of success. Furthermore, transgenic plants overexpressing a TF of interest can present pleiotropic phenotypes and/or result in a high number of indirect gene expression changes. Therefore, fast, efficient, high-throughput methods for assaying TF function are needed. Results: Agroinfiltration is a simple plant biology method that allows transient gene expression. It is a rapid and powerful tool for the functional characterisation of TF genes in planta. High throughput RNA sequencing is now a widely used method for analysing gene expression profiles (transcriptomes). By coupling TF agroinfiltration with RNA sequencing (named here as Infiltration-RNAseq), gene expression networks and gene function can be identified within a few weeks rather than many months. As a proof of concept, we agroinfiltrated Medicago truncatula leaves with M. truncatula LEGUME ANTHOCYANIN PRODUCITION 1 (MtLAP1), a MYB transcription factor involved in the regula- tion of the anthocyanin pathway, and assessed the resulting transcriptome. -
Morphological and Molecular Dissection of Wild Rices from Eastern India Suggests Distinct Speciation Received: 8 May 2017 Accepted: 22 January 2018 Between O
www.nature.com/scientificreports OPEN Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation Received: 8 May 2017 Accepted: 22 January 2018 between O. rufpogon and O. nivara Published: xx xx xxxx populations Rashmita Samal, Pritesh Sundar Roy, Auromira Sahoo, Meera Kumari Kar, Bhaskar Chandra Patra, Bishnu Charan Marndi & Jwala Narasimha Rao Gundimeda The inter relationships between the two progenitors is interesting as both wild relatives are known to be the great untapped gene reservoirs. The debate continues on granting a separate species status to Oryza nivara. The present study was conducted on populations of Oryza rufpogon and Oryza nivara from Eastern India employing morphological and molecular characteristics. The cluster analysis of the data on morphological traits could clearly classify the two wild forms into two separate discrete groups without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Amplifcation of hyper variable regions of the genome could reveal 144 alleles suggesting high genetic diversity values (average He = 0.566). Moreover, with 42.37% of uncommon alleles between the two wild relatives, the molecular variance analysis (AMOVA) could detect only 21% of total variation (p < 0.001) among them and rest 59% was within them. The population structure analysis clearly classifed these two wild populations into two distinct sub-populations (K = 2) without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Clear diferentiation into two distinct groups indicates that O. rufpogon and O. nivara could be treated as two diferent species. -
Chenopodium Ucrainicum (Chenopodiaceae / Amaranthaceae Sensu APG), a New Diploid Species: a Morphological Description and Pictorial Guide
https://doi.org/10.15407/ukrbotj77.04.237 Chenopodium ucrainicum (Chenopodiaceae / Amaranthaceae sensu APG), a new diploid species: a morphological description and pictorial guide Sergei L. MOSYAKIN1, Bohumil MANDÁK2, 3 1 M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine 2 Tereschenkivska Str., Kyiv 01601, Ukraine [email protected] 2 Faculty of Environmental Sciences, Czech University of Life Sciences Prague 129 Kamýcká, Praha 6 – Suchdol 165 21, Czech Republic [email protected] 3 Institute of Botany, Czech Academy of Sciences 1 Zámek, Průhonice 252 43, Czech Republic [email protected] Mosyakin S.L., Mandák B. 2020. Chenopodium ucrainicum (Chenopodiaceae / Amaranthaceae sensu APG), a new diploid species: a morphological description and pictorial guide. Ukrainian Botanical Journal, 77(4): 237–248. Abstract. A morphological description is provided for Chenopodium ucrainicum Mosyakin & Mandák (Chenopodiaceae / Amaranthaceae sensu APG), a new species allied to C. suecicum and C. ficifolium. At present this new species is reliably known from several localities in Ukraine (three areas in Kyiv city, one in Kyiv Region, one in Rivne Region), but it is probably more widespread, or could be even alien in Eastern Europe. Comparison of our plants with other taxa [such as C. suecicum (incl. C. neumanii, etc.), C. ficifolium, several morphotypes of C. album, as well as plants known as C. borbasii, C. missouriense (sensu stricto and sensu auct. europ.), C. lobodontum, etc.], demonstrated that C. ucrainicum is morphologically different from all these known and named taxa. It is also a late-flowering and late-fruiting species: in Kyiv fruits/seeds normally develop during late September – early November. -
2641-3182 08 Catalogo1 Dicotyledoneae4 Pag2641 ONAG
2962 - Simaroubaceae Dicotyledoneae Quassia glabra (Engl.) Noot. = Simaba glabra Engl. SIPARUNACEAE Referencias: Pirani, J. R., 1987. Autores: Hausner, G. & Renner, S. S. Quassia praecox (Hassl.) Noot. = Simaba praecox Hassl. Referencias: Pirani, J. R., 1987. 1 género, 1 especie. Quassia trichilioides (A. St.-Hil.) D. Dietr. = Simaba trichilioides A. St.-Hil. Siparuna Aubl. Referencias: Pirani, J. R., 1987. Número de especies: 1 Siparuna guianensis Aubl. Simaba Aubl. Referencias: Renner, S. S. & Hausner, G., 2005. Número de especies: 3, 1 endémica Arbusto o arbolito. Nativa. 0–600 m. Países: PRY(AMA). Simaba glabra Engl. Ejemplares de referencia: PRY[Hassler, E. 11960 (F, G, GH, Sin.: Quassia glabra (Engl.) Noot., Simaba glabra Engl. K, NY)]. subsp. trijuga Hassl., Simaba glabra Engl. var. emarginata Hassl., Simaba glabra Engl. var. inaequilatera Hassl. Referencias: Basualdo, I. Z. & Soria Rey, N., 2002; Fernández Casas, F. J., 1988; Pirani, J. R., 1987, 2002c; SOLANACEAE Sleumer, H. O., 1953b. Arbusto o árbol. Nativa. 0–500 m. Coordinador: Barboza, G. E. Países: ARG(MIS); PRY(AMA, CAA, CON). Autores: Stehmann, J. R. & Semir, J. (Calibrachoa y Ejemplares de referencia: ARG[Molfino, J. F. s.n. (BA)]; Petunia), Matesevach, M., Barboza, G. E., Spooner, PRY[Hassler, E. 10569 (G, LIL, P)]. D. M., Clausen, A. M. & Peralta, I. E. (Solanum sect. Petota), Barboza, G. E., Matesevach, M. & Simaba glabra Engl. var. emarginata Hassl. = Simaba Mentz, L. A. glabra Engl. Referencias: Pirani, J. R., 1987. 41 géneros, 500 especies, 250 especies endémicas, 7 Simaba glabra Engl. var. inaequilatera Hassl. = Simaba especies introducidas. glabra Engl. Referencias: Pirani, J. R., 1987. Acnistus Schott Número de especies: 1 Simaba glabra Engl. -
NJ Native Plants - USDA
NJ Native Plants - USDA Scientific Name Common Name N/I Family Category National Wetland Indicator Status Thermopsis villosa Aaron's rod N Fabaceae Dicot Rubus depavitus Aberdeen dewberry N Rosaceae Dicot Artemisia absinthium absinthium I Asteraceae Dicot Aplectrum hyemale Adam and Eve N Orchidaceae Monocot FAC-, FACW Yucca filamentosa Adam's needle N Agavaceae Monocot Gentianella quinquefolia agueweed N Gentianaceae Dicot FAC, FACW- Rhamnus alnifolia alderleaf buckthorn N Rhamnaceae Dicot FACU, OBL Medicago sativa alfalfa I Fabaceae Dicot Ranunculus cymbalaria alkali buttercup N Ranunculaceae Dicot OBL Rubus allegheniensis Allegheny blackberry N Rosaceae Dicot UPL, FACW Hieracium paniculatum Allegheny hawkweed N Asteraceae Dicot Mimulus ringens Allegheny monkeyflower N Scrophulariaceae Dicot OBL Ranunculus allegheniensis Allegheny Mountain buttercup N Ranunculaceae Dicot FACU, FAC Prunus alleghaniensis Allegheny plum N Rosaceae Dicot UPL, NI Amelanchier laevis Allegheny serviceberry N Rosaceae Dicot Hylotelephium telephioides Allegheny stonecrop N Crassulaceae Dicot Adlumia fungosa allegheny vine N Fumariaceae Dicot Centaurea transalpina alpine knapweed N Asteraceae Dicot Potamogeton alpinus alpine pondweed N Potamogetonaceae Monocot OBL Viola labradorica alpine violet N Violaceae Dicot FAC Trifolium hybridum alsike clover I Fabaceae Dicot FACU-, FAC Cornus alternifolia alternateleaf dogwood N Cornaceae Dicot Strophostyles helvola amberique-bean N Fabaceae Dicot Puccinellia americana American alkaligrass N Poaceae Monocot Heuchera americana