Convergent Molecular Evolution of Multiple Chloroplast Genes in C4
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Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight Into Interspecific Relationship and Phylogeny
biology Article Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny Fengjiao Zhang 1,2, Ning Wang 1,2, Guanghao Cheng 1,2, Xiaochun Shu 1,2, Tao Wang 1,2 , Weibing Zhuang 1,2, Ruisen Lu 1,2,* and Zhong Wang 1,2,* 1 Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; [email protected] (F.Z.); [email protected] (N.W.); [email protected] (G.C.); [email protected] (X.S.); [email protected] (T.W.); [email protected] (W.Z.) 2 The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China * Correspondence: [email protected] (R.L.); [email protected] (Z.W.) Simple Summary: The genus Lycoris (Amaryllidaceae) comprises about 20 species with high orna- mental and medicinal value. However, germplasm identification is still difficult due to frequent interspecific hybridization and intraspecific morphological variation within this genus. Plastid genome sequencing has been proven to be a useful tool to identify closely related species and is widely used in the field of plant evolution and phylogeny. In the present study, we provided four Citation: Zhang, F.; Wang, N.; chloroplast genomes of Lycoris and retrieved seven published species in the genus for comparative Cheng, G.; Shu, X.; Wang, T.; Zhuang, genomics and phylogenetic analyses. All these chloroplast genomes possess the typical quadripartite W.; Lu, R.; Wang, Z. -
Complete Chloroplast Genomes Shed Light on Phylogenetic
www.nature.com/scientificreports OPEN Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae) Ju Namgung1,4, Hoang Dang Khoa Do1,2,4, Changkyun Kim1, Hyeok Jae Choi3 & Joo‑Hwan Kim1* Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, fve of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein‑coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA , psbA upstream, rpl32- trnL-UAG , ycf1, rpl22, matK, and ndhF, were identifed in the studied Allium species. Additionally, we present the frst phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, fve species of Amaryllidoideae, one species of Agapanthoideae, and fve species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae‑Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae‑ Gilliesieae‑Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by diferentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. -
Phylogeny and Subfamilial Classification of the Grasses (Poaceae) Author(S): Grass Phylogeny Working Group, Nigel P
Phylogeny and Subfamilial Classification of the Grasses (Poaceae) Author(s): Grass Phylogeny Working Group, Nigel P. Barker, Lynn G. Clark, Jerrold I. Davis, Melvin R. Duvall, Gerald F. Guala, Catherine Hsiao, Elizabeth A. Kellogg, H. Peter Linder Source: Annals of the Missouri Botanical Garden, Vol. 88, No. 3 (Summer, 2001), pp. 373-457 Published by: Missouri Botanical Garden Press Stable URL: http://www.jstor.org/stable/3298585 Accessed: 06/10/2008 11:05 Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available at http://www.jstor.org/page/info/about/policies/terms.jsp. JSTOR's Terms and Conditions of Use provides, in part, that unless you have obtained prior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content in the JSTOR archive only for your personal, non-commercial use. Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained at http://www.jstor.org/action/showPublisher?publisherCode=mobot. Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printed page of such transmission. JSTOR is a not-for-profit organization founded in 1995 to build trusted digital archives for scholarship. We work with the scholarly community to preserve their work and the materials they rely upon, and to build a common research platform that promotes the discovery and use of these resources. For more information about JSTOR, please contact [email protected]. -
Ndhf Sequence Evolution and the Major Clades in the Sunflower Family KI-JOONG KIM* and ROBERT K
Proc. Natl. Acad. Sci. USA Vol. 92, pp. 10379-10383, October 1995 Evolution ndhF sequence evolution and the major clades in the sunflower family KI-JOONG KIM* AND ROBERT K. JANSENt Department of Botany, University of Texas, Austin, TX 78713-7640 Communicated by Peter H. Raven, Missouri Botanical Garden, St. Louis, MO, June 21, 1995 ABSTRACT An extensive sequence comparison of the either too short or too conserved to provide adequate numbers chloroplast ndhF gene from all major clades of the largest of characters in recently evolved families. A number of alter- flowering plant family (Asteraceae) shows that this gene native genes have been suggested as potential candidates for provides -3 times more phylogenetic information than rbcL. phylogenetic comparisons at lower taxonomic levels (9). The This is because it is substantially longer and evolves twice as phylogenetic utility of one of these, matK, has been recently fast. The 5' region (1380 bp) ofndhF is very different from the demonstrated (10). Comparison of sequences of two chloro- 3' region (855 bp) and is similar to rbcL in both the rate and plast genomes (rice and tobacco), however, revealed only two the pattern of sequence change. The 3' region is more A+T- genes, rpoCl and ndhF, that are considerably longer and evolve rich, has higher levels of nonsynonymous base substitution, faster than rbcL (9, 11). We selected ndhF because it is longer and shows greater transversion bias at all codon positions. and evolves slightly faster than rpoCl (11), because rpoCl has These differences probably reflect different functional con- an intron that may require additional effort in DNA amplifi- straints on the 5' and 3' regions of nduhF. -
Sequencing of Cdna
ORIGINAL RESEARCH ARTICLE published: 07 March 2011 doi: 10.3389/fmicb.2011.00041 Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC 7002 by Next-Gen (SOLiD™) sequencing of cDNA Marcus Ludwig and Donald A. Bryant* Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA Edited by: The genome of the unicellular, euryhaline cyanobacterium Synechococcus sp. PCC 7002 encodes Thomas E. Hanson, University of about 3200 proteins. Transcripts were detected for nearly all annotated open reading frames Delaware, USA by a global transcriptomic analysis by Next-Generation (SOLiD™) sequencing of cDNA. In the Reviewed by: Martin Hagemann, University Rostock, cDNA samples sequenced, ∼90% of the mapped sequences were derived from the 16S and Germany 23S ribosomal RNAs and ∼10% of the sequences were derived from mRNAs. In cells grown Jack Meeks, University of California, photoautotrophically under standard conditions [38°C, 1% (v/v) CO2 in air, 250 μmol photons USA m−2 s−1], the highest transcript levels (up to 2% of the total mRNA for the most abundantly *Correspondence: transcribed genes; e.g., cpcAB, psbA, psaA) were generally derived from genes encoding Donald A. Bryant, Department of Biochemistry and Molecular Biology, structural components of the photosynthetic apparatus. High-light exposure for 1 h caused The Pennsylvania State University, changes in transcript levels for genes encoding proteins of the photosynthetic apparatus, Type-1 S-235 Frear Building, University Park, NADH dehydrogenase complex and ATP synthase, whereas dark incubation for 1 h resulted PA 16802, USA. in a global decrease in transcript levels for photosynthesis-related genes and an increase in e-mail: [email protected] transcript levels for genes involved in carbohydrate degradation. -
82167915.Pdf
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1837 (2014) 954–963 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbabio Characterization of the type 2 NADH:menaquinone oxidoreductases from Staphylococcus aureus and the bactericidal action of phenothiazines☆ Lici A. Schurig-Briccio a, Takahiro Yano b,HarveyRubinb,RobertB.Gennisa,⁎ a Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA b Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA article info abstract Article history: Methicillin-resistant Staphylococcus aureus (MRSA) is currently one of the principal multiple drug resistant Received 21 March 2014 bacterial pathogens causing serious infections, many of which are life-threatening. Consequently, new therapeutic Received in revised form 27 March 2014 targets are required to combat such infections. In the current work, we explore the type 2 Nicotinamide adenine Accepted 28 March 2014 dinucleotide reduced form (NADH) dehydrogenases (NDH-2s) as possible drug targets and look at the effects Available online 5 April 2014 of phenothiazines, known to inhibit NDH-2 from Mycobacterium tuberculosis. NDH-2s are monotopic fl Keywords: membrane proteins that catalyze the transfer of electrons from NADH via avin adenine dinucleotide (FAD) to + Bioenergetics/electron transfer complex the quinone pool. They are required for maintaining the NADH/Nicotinamide adenine dinucleotide (NAD ) Enzyme inhibitor redox balance and contribute indirectly to the generation of proton motive force. NDH-2s are not present in Respiratory chain mammals, but are the only form of respiratory NADH dehydrogenase in several pathogens, including S. -
Sotwp 2016.Pdf
STATE OF THE WORLD’S PLANTS OF THE WORLD’S STATE 2016 The staff and trustees of the Royal Botanic Gardens, Kew and the Kew Foundation would like to thank the Sfumato Foundation for generously funding the State of the World’s Plants project. State of the World’s Plants 2016 Citation This report should be cited as: RBG Kew (2016). The State of the World’s Plants Report – 2016. Royal Botanic Gardens, Kew ISBN: 978-1-84246-628-5 © The Board of Trustees of the Royal Botanic Gardens, Kew (2016) (unless otherwise stated) Printed on 100% recycled paper The State of the World’s Plants 1 Contents Introduction to the State of the World’s Plants Describing the world’s plants 4 Naming and counting the world’s plants 10 New plant species discovered in 2015 14 Plant evolutionary relationships and plant genomes 18 Useful plants 24 Important plant areas 28 Country focus: status of knowledge of Brazilian plants Global threats to plants 34 Climate change 40 Global land-cover change 46 Invasive species 52 Plant diseases – state of research 58 Extinction risk and threats to plants Policies and international trade 64 CITES and the prevention of illegal trade 70 The Nagoya Protocol on Access to Genetic Resources and Benefit Sharing 76 References 80 Contributors and acknowledgments 2 Introduction to the State of the World’s Plants Introduction to the State of the World’s Plants This is the first document to collate current knowledge on as well as policies and international agreements that are the state of the world’s plants. -
Molecular and Functional Analysis of Nicotinate Catabolism in Eubacterium Barkeri
Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri Ashraf Alhapel, Daniel J. Darley, Nadine Wagener, Elke Eckel, Nora Elsner, and Antonio J. Pierik* Laboratorium fu¨r Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universita¨t, D-35032 Marburg, Germany Edited by Perry A. Frey, University of Wisconsin, Madison, WI, and approved June 29, 2006 (received for review March 1, 2006) The anaerobic soil bacterium Eubacterium barkeri catabolizes nic- complex (see Fig. 1). Based on the identified intermediates, otinate to pyruvate and propionate via a unique fermentation. A several anticipated enzymes were purified and characterized: full molecular characterization of nicotinate fermentation in this nicotinate dehydrogenase (12), 6-hydroxynicotinate reductase organism was accomplished by the following results: (i) A 23.2-kb (7), 2-methyleneglutarate mutase, and 3-methylitaconate DNA segment with a gene cluster encoding all nine enzymes was isomerase (13, 14). These findings outlined the nicotinate fer- cloned and sequenced, (ii) two chiral intermediates were discov- mentation pathway and placed the identified intermediates in an ered, and (iii) three enzymes were found, completing the hitherto enzymatic framework. unknown part of the pathway. Nicotinate dehydrogenase, a (non- The nicotinate dehydrogenase contains [2Fe-2S] clusters (15), selenocysteine) selenium-containing four-subunit enzyme, is en- FAD and molybdopterin cytosine dinucleotide (16), and has an coded by ndhF (FAD subunit), ndhS (2 x [2Fe-2S] subunit), and by unusual subunit composition [50, 37, 33, and 23 kDa (17)]. It has the ndhL͞ndhM genes. In contrast to all enzymes of the xanthine labile (nonselenocysteine) selenium (18) also identified in pu- dehydrogenase family, the latter two encode a two-subunit mo- rine dehydrogenase from Clostridium purinolyticum and xanthine lybdopterin protein. -
Physiological and Proteomic Responses of Diploid and Tetraploid Black Locust (Robinia Pseudoacacia L.) Subjected to Salt Stress
Int. J. Mol. Sci. 2013, 14, 20299-20325; doi:10.3390/ijms141020299 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Physiological and Proteomic Responses of Diploid and Tetraploid Black Locust (Robinia pseudoacacia L.) Subjected to Salt Stress Zhiming Wang 1,†, Mingyue Wang 1,†, Likun Liu2 and Fanjuan Meng 1,* 1 College of Life Science, Northeast Forestry University, Harbin 150040, China; E-Mails: [email protected] (Z.W.); [email protected] (M.W.) 2 Department of Medical Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Gangwon-do 200-701, Korea; E-Mail: [email protected] † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-451-8219-2170; Fax: +86-451-8643-3905. Received: 17 June 2013; in revised form: 31 August 2013 / Accepted: 9 September 2013 / Published: 14 October 2013 Abstract: Tetraploid black locust (Robinia pseudoacacia L.) is adaptable to salt stress. Here, we compared morphological, physiological, ultrastructural, and proteomic traits of leaves in tetraploid black locust and its diploid relatives under salt stress. The results showed that diploid (2×) plants suffered from greater negative effects than those of tetraploid (4×) plants. After salt treatment, plant growth was inhibited, photosynthesis was reduced, reactive oxygen species, malondialdehyde content, and relative electrolyte leakage increased, and defense-related enzyme activities decreased in 2× compared to those in 4×. In addition, salt stress resulted in distorted chloroplasts, swollen thylakoid membranes, accumulation of plastoglobules, and increased starch grains in 2× compared to those in 4×. -
Interplay Between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces Ambofaciens
antibiotics Article Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens Eva Pinatel 1,†, Matteo Calcagnile 2,† , Adelfia Talà 2, Fabrizio Damiano 2 , Luisa Siculella 2 , Clelia Peano 3,4, Giuseppe Egidio De Benedetto 5 , Antonio Pennetta 5 , Gianluca De Bellis 1 and Pietro Alifano 2,* 1 Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Italy; [email protected] (E.P.); [email protected] (G.D.B.) 2 Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy; [email protected] (M.C.); adelfi[email protected] (A.T.); [email protected] (F.D.); [email protected] (L.S.) 3 Institute for Genetic and Biomedical Research, Operative Unit (UoS) of Milan, National Research Council, 20089 Rozzano, Italy; [email protected] 4 Human Technopole, 20157 Milan, Italy; [email protected] 5 Department of Cultural Heritage, University of Salento, Via Monteroni, 73100 Lecce, Italy; [email protected] (G.E.D.B.); [email protected] (A.P.) * Correspondence: [email protected] † These authors contributed equally to this work. Citation: Pinatel, E.; Calcagnile, M.; Abstract: While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene Talà, A.; Damiano, F.; Siculella, L.; expression has become increasingly evident, their interaction with the global regulatory circuits is Peano, C.; De Benedetto, G.E.; still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces Pennetta, A.; De Bellis, G.; Alifano, P. -
Supporting Information
Supporting Information Christin et al. 10.1073/pnas.1216777110 SI Materials and Methods blades were then embedded in resin (JB-4; Polysciences), Phylogenetic Inference. A previously published 545-taxa dataset of following the manufacturer’s instructions. Five-micrometer the grasses based on the plastid markers rbcL, ndhF,andtrnK-matK thick cross-sections of the embedded leaf fragments were cut (1) was expanded and used for phylogenetic inference. For species with a microtome and stained with saturated cresyl violet sampled for anatomical cross-sections but not included in the acetate (CVA). Some samples were fixed in formalin-pro- published dataset, the markers ndhF and/or trnK-matK were either pionic acid-alcohol (FPA), embedded in paraffin, sectioned at retrieved from GenBank when available or were newly sequenced 10 μm, and stained with a safranin O-orange G series (11) as from extracted genomic DNA with the method and primers de- described in (12). All slides were made permanent and are scribed previously (1, 2). These new sequences were aligned to the available on request. dataset, excluding the regions that were too variable as described previously (1). The final dataset totaled 604 taxa and was used for Anatomical Measurements. All C3 grasses possess a double BS, with “ phylogenetic inference as implemented in the software Bayesian the outer layer derived from ground meristem to form a paren- ” Evolutionary Analysis by Sampling Trees (BEAST) (3). chyma sheath, and the internal layer derived from the vascular “ ” The phylogenetic tree was inferred under a general time-re- procambium to form a mestome sheath (13). Many C4 grasses versible substitution model with a gamma-shape parameter and also possess these two BS layers, with one of them specialized in “ ” a proportion of invariants (GTR+G+I). -
A New Species of Sartidia (Graminae), Endemic to Ultramafic Soils ⁎ K
Available online at www.sciencedirect.com South African Journal of Botany 77 (2011) 598–607 www.elsevier.com/locate/sajb A new species of Sartidia (Graminae), endemic to ultramafic soils ⁎ K. Balkwill a, , G.J. Campbell-Young a, L. Fish b, J. Munday a, M.L. Frean a, M. Stalmans a,c a C.E. Moss Herbarium, School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Private Bag 3, Wits 2050, South Africa b National Herbarium, Pretoria (PRE), South African National Biodiversity Institute, Private Bag X101, Pretoria 0001, South Africa c International Conservation Services, PO Box 19139, Nelspruit 1200, South Africa Received 4 November 2009; received in revised form 27 November 2010; accepted 7 December 2010 Abstract A species of Sartidia De Winter, first collected by P.J. Muller in 1972 in the Cythna Letty Nature Reserve in Mpumalanga, does not match existing material of Sartidia, a genus comprising four species. The new species, S. dewinteri J. Munday & L. Fish, is most similar to S. jucunda (Schweick.) De Winter but differs in the leaf sheath colour, lower leaf blade surface texture, spikelet length and upper glume length. It differs also from all other species in the genus in the shape and branching of the inflorescence, the relative length of the lateral awns to the median awn, lemma body surface texture, callus shape and hair arrangement, palea shape and distribution. Sartidia dewinteri differs anatomically from S. angolensis and S. vanderystii in that the stereome strands in the leaf blades project partly or almost completely into the first order vascular bundles rather than not at all, and from S.