The Rice Genome Knowledgebase
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Establishment of a Global Network for the in Situ Conservation of Crop Wild Relatives: Status and Needs
THEMATIC BACKGROUND STUDY Establishment of a Global Network for the In Situ Conservation of Crop Wild Relatives: Status and Needs Nigel Maxted and Shelagh Kell BACKGROUND STUDY PAPER NO. 39 October 2009 COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE ESTABLISHMENT OF A GLOBAL NETWORK FOR THE IN SITU CONSERVATION OF CROP WILD RELATIVES: STATUS AND NEEDS by *By Nigel Maxted and Shelagh Kell The content of this document is entirely the responsibility of the authors, and does not .necessarily represent the views of the FAO, or its Members 2 * School of Biosciences, University of Birmingham. Disclaimer The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the Food and Agriculture Organization of the United Nations (FAO), or its Members. The designations employed and the presentation of material do not imply the expression of any opinion whatsoever on the part of FAO concerning legal or development status of any country, territory, city or area or of its authorities or concerning the delimitation of its frontiers or boundaries. The mention of specific companies or products of manufacturers, whether or not these have been patented, does not imply that these have been endorsed by FAO in preference to others of a similar nature that are not mentioned. CONTENTS SUMMARY 6 ACKNOWLEDGEMENTS 7 PART 1: INTRODUCTION 8 1.1 Background and scope 8 1.2 The global and local importance of crop wild relatives 10 1.3 Definition of a crop wild relative 12 1.4 Global numbers of crop -
Databases and Bioinformatics Tools for Rice Research
Current Plant Biology 7–8 (2016) 39–52 Contents lists available at ScienceDirect Current Plant Biology jo urnal homepage: www.elsevier.com/locate/cpb ଝ Databases and bioinformatics tools for rice research ∗ Priyanka Garg, Pankaj Jaiswal Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USA a r t i c l e i n f o a b s t r a c t Keywords: Rice is one of the most important agricultural crop in the world and widely studied model plant. The Biological database completion of whole genome sequence of rice (Oryza sativa) and high-throughput experimental plat- Rice forms have led to the generation of the tremendous amount of data, and development of the specialized Gene expression databases and bioinformatics tools for data processing, efficient organization, analysis, and visualiza- Biocuration tion. In this article, we discuss a collection of biological databases that host genomics data on sequence, Ontology Pathways gene expression, genetic variation, gene-interactomes, and pathways, and facilitate data analysis and visualization. © 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). 1. Introduction organisms including rice. In contrast community-specific databases cater to the need of a specific research community such as plant Over the last decades, an increasing amount of genome-scale databases, e.g. PlantGDB [8], ENSEMBL Plants [9], Gramene [10], experimental data sets became available and several online and PLEXdb [11], Gene Expression Atlas [12], Planteome [13], etc. The open source, biology databases have emerged. -
EFFECT of WEEDY RICE (Oryza Sativa L.)
EFFECT OF WEEDY RICE (Oryza sativa L.) ON THE YIELD OF CULTIVATED RICE (Oryza sativa L.) IN GREENHOUSE AND FIELD ENVIRONMENT SALMAH BINTI TAJUDDIN UNIVERSITI SAINS MALAYSIA 2014 EFFECT OF WEEDY RICE (Oryza sativa L.) ON THE YIELD OF CULTIVATED RICE (Oryza sativa L.) IN GREENHOUSE AND FIELD ENVIRONMENT by SALMAH BINTI TAJUDDIN Thesis submitted in fulfilment of the requirements for the degree of Master of Science AUGUST 2014 ACKNOWLEDGEMENTS My postgraduate (MSc) study at the Universiti Sains Malaysia (School of Biological Sciences) was a great challenge. It was made possible with the kind assistance of many individuals, either directly or indirectly, to whom I am indebted, not all of whom are mentioned in this page. First and foremost, my deepest appreciation goes to Prof. Mashhor Mansor for his strong support, unweary supervision and motivating guidance during the course of my study. In addition, I was also trained in writing scientific papers and had the opportunity to present scientific papers in seminars and conferences. Other academicians had also given support through inspirational motivations and guidance, particularly Dr. Azmi Man, Prof. Nashriyah Mat and Dr. Asyraf Mansor, my co-supervisors, to all of whom I am very grateful. I wish to thank the staff of the Malaysian Meteorological Department Pulau Pinang for providing me the necessary meteorological data needed for my thesis. The staff of MARDI (Seberang Perai) had been very helpful in my experimental work, especially En. Awang, En. Ebnil, En. Mustafa, Pn. Norhayati and Pn. Aqilah. The staff of USM for help me solve statistics analysis problems, particularly Dr. -
2178-IJBCS-Article-Chinyere Nwokeocha
Available online at http://ajol.info/index.php/ijbcs Int. J. Biol. Chem. Sci. 9(1): 35-47, February 2015 ISSN 1997-342X (Online), ISSN 1991-8631 (Print) Original Paper http://indexmedicus.afro.who.int Botanical indices of ploidy levels in some African accessions of Oryza punctata Kotschy ex Steud Chinyere Constance NWOKEOCHA Obafemi Awolowo University, Institute of Natural History Museum, Ile–Ife, Nigeria. E-mail: [email protected]; Tel: +234(0)8138338473 ABSTRACT Twenty-nine accessions of Oryza punctata Kotschy ex Steud, from local and other African habitats were studied to establish the attributes that can delineate the two ploidy levels based on agro-botanical, foliar epidermal and nodal anatomical characteristics. The diploid plants of O. punctata are early-maturing annuals with a small biomass, while the tetraploids are large, vigorous perennials. From the anatomical and morphological traits: the diploids have narrower leaves (0.95 - 1.36 cm wide) than the tetraploids (1.9 - 2.3 cm); the culms of diploids are generally thin (0.28 - 0.35 cm in diameter) compared to the tetraploids (0.37 - 0.57 cm); the diploids have longer spikelets (6.20 - 7.04 mm) with length/breadth > 3; longer awns (52 - 86 mm) than the tetraploids (20 - 31 mm). The basal cells of microhairs in the diploids are about twice the length of apical cells, but only slightly longer than the apical cells in the tetraploids; prickle hairs are sparse in the intercostal zone of diploids, but abundant in tetraploids; short cells are paired and abundant in the intercostal zone of diploids, but sparse and solitary in the tetraploids. -
Why Are Momilactones Always Associated with Biosynthetic Gene Clusters in Plants? COMMENTARY Juan Zhanga,B and Reuben J
COMMENTARY Why are momilactones always associated with biosynthetic gene clusters in plants? COMMENTARY Juan Zhanga,b and Reuben J. Petersa,1 There is an emerging realization that plant genomes intriguing hints about the distinct evolutionary pres- contain biosynthetic gene clusters (BGCs) for more sures leading to not only their assembly but also that specialized metabolism in certain cases (1). However, of BGCs in plants more generally. while horizontal gene transfer seems to drive the as- As labdane-related diterpenoids, the momilac- sembly of self-sufficient BGCs in microbes, the limita- tones require dual cyclization reactions (9). Notably, tions of strict vertical gene transmission necessitate a identification of the two relevant cyclases revealed distinct driving force for the assembly of BGCs in that the genes for these consecutively acting enzymes plants. The evidence for horizontal gene transfer of are close together in the rice genome (2). Moreover, BGCs in microbes is derived from the appearance of the only other genes in the region encode two closely homologous such loci, leading to biosynthesis of the related cytochrome P450 (CYP) monooxygenases same (or very closely related) natural products, in phy- (CYP99A2 and CYP99A3) and two short-chain alcohol logenetically distinct species. By contrast, there has dehydrogenases/reductases (SDRs) (10). The two been much less investigation of such occurrences in SDRs also are closely related, and both can catalyze plants. This is a result of many fewer examples of oxidation of the penultimate intermediate 3β-hydroxy- BGCs, as well as instances of natural products that skip syn-pimaradien-19,6β-olide to form the characteristic across phylogenetic distances in this kingdom. -
Table S1 PF00931 Species Abbreviated Species
Table S1 PF00931 Species_abbreviated Species Taxon Database 223 Acoerulea Aquilegia coerulea dicot phytozome12.1.6 152 Acomosus Ananas comosus monocot phytozome12.1.6 124 Ahalleri Arabidopsis halleri dicot phytozome12.1.6 119 Ahypochondriacus Amaranthus hypochondriacus dicot phytozome12.1.6 105 Ahypochondriacus_v2.1 Amaranthus hypochondriacus dicot phytozome12.1.6 177 Alyrata Arabidopsis lyrata dicot phytozome12.1.6 376 Aoccidentale_v0.9 Anacardium occidentale dicot phytozome12.1.6 35 Aofficinalis_V1.1 Asparagus officinalis monocot phytozome12.1.6 160 Athaliana Arabidopsis thaliana columbia dicot phytozome12.1.6 160 Athaliana_Araport11 Arabidopsis thaliana columbia dicot phytozome12.1.6 99 Atrichopoda Amborella trichopoda Amborellales phytozome12.1.6 16 Bbraunii_v2.1 Botryococcus braunii Chlorophyta phytozome12.1.6 308 Bdistachyon Brachypodium distachyon monocot phytozome12.1.6 331 BdistachyonBD21-3_v1.1 Brachypodium distachyon Bd21-3 monocot phytozome12.1.6 535 Bhybridum_v1.1 Brachypodium hybridum monocot phytozome12.1.6 114 Boleraceacapitata Brassica oleracea capitata dicot phytozome12.1.6 187 BrapaFPsc Brassica rapa FPsc dicot phytozome12.1.6 235 Bstacei Brachypodium stacei monocot phytozome12.1.6 297 Bstricta Boechera stricta dicot phytozome12.1.6 414 Bsylvaticum_v1.1 Brachypodium sylvaticum monocot phytozome12.1.6 766 Carabica_v0.5 Coffea arabica dicot phytozome12.1.6 99 Carietinum_v1.0 Cicer arietinum dicot phytozome12.1.6 342 Cclementina Citrus clementina dicot phytozome12.1.6 96 Cgrandiflora Capsella grandiflora dicot phytozome12.1.6 -
Why Are Momilactones Always Associated with Biosynthetic Gene Clusters in Plants?
Biochemistry, Biophysics and Molecular Biology Publications Biochemistry, Biophysics and Molecular Biology 6-2-2020 Why are momilactones always associated with biosynthetic gene clusters in plants? Juan Zhang Iowa State University Reuben J. Peters Iowa State University, [email protected] Follow this and additional works at: https://lib.dr.iastate.edu/bbmb_ag_pubs Part of the Biochemistry, Biophysics, and Structural Biology Commons, Genetics and Genomics Commons, and the Plant Sciences Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ bbmb_ag_pubs/282. For information on how to cite this item, please visit http://lib.dr.iastate.edu/howtocite.html. This Article is brought to you for free and open access by the Biochemistry, Biophysics and Molecular Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Biochemistry, Biophysics and Molecular Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Why are momilactones always associated with biosynthetic gene clusters in plants? Abstract There is an emerging realization that plant genomes contain biosynthetic gene clusters (BGCs) for more specialized metabolism in certain cases (1). However, while horizontal gene transfer seems to drive the assembly of self-sufficient BGCs in microbes, the limitations of strict vertical gene transmission necessitates a distinct driving force for the assembly of BGCs in plants. The evidence for horizontal gene transfer of BGCs in microbes is derived from the appearance of homologous such loci, leading to biosynthesis of the same (or very closely related) natural products, in phylogenetically distinct species. -
Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation Across the Genus Oryza
ARTICLES https://doi.org/10.1038/s41588-018-0040-0 Corrected: Publisher Correction Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza Joshua C. Stein1, Yeisoo Yu2,21, Dario Copetti2,3, Derrick J. Zwickl4, Li Zhang 5, Chengjun Zhang 5, Kapeel Chougule1,2, Dongying Gao6, Aiko Iwata6, Jose Luis Goicoechea2, Sharon Wei1, Jun Wang7, Yi Liao8, Muhua Wang2,22, Julie Jacquemin2,23, Claude Becker 9, Dave Kudrna2, Jianwei Zhang2, Carlos E. M. Londono2, Xiang Song2, Seunghee Lee2, Paul Sanchez2,24, Andrea Zuccolo 2,25, Jetty S. S. Ammiraju2,26, Jayson Talag2, Ann Danowitz2, Luis F. Rivera2,27, Andrea R. Gschwend5, Christos Noutsos1, Cheng-chieh Wu10,11, Shu-min Kao10,28, Jhih-wun Zeng10, Fu-jin Wei10,29, Qiang Zhao12, Qi Feng 12, Moaine El Baidouri13, Marie-Christine Carpentier13, Eric Lasserre 13, Richard Cooke13, Daniel da Rosa Farias14, Luciano Carlos da Maia14, Railson S. dos Santos14, Kevin G. Nyberg15, Kenneth L. McNally3, Ramil Mauleon3, Nickolai Alexandrov3, Jeremy Schmutz16, Dave Flowers16, Chuanzhu Fan7, Detlef Weigel9, Kshirod K. Jena3, Thomas Wicker17, Mingsheng Chen8, Bin Han12, Robert Henry 18, Yue-ie C. Hsing10, Nori Kurata19, Antonio Costa de Oliveira14, Olivier Panaud 13, Scott A. Jackson 6, Carlos A. Machado15, Michael J. Sanderson4, Manyuan Long 5, Doreen Ware 1,20 and Rod A. Wing 2,3,4* The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. -
The State of Sudan's Biodiversity for Food and Agriculture
COUNTRY REPORTS THE STATE OF SUDAN’S BIODIVERSITY FOR FOOD AND AGRICULTURE This country report has been prepared by the national authorities as a contribution to the FAO publication, The State of the World’s Biodiversity for Food and Agriculture. The report is being made available by the Food and Agriculture Organization of the United Nations (FAO) as requested by the Commission on Genetic Resources for Food and Agriculture. The information in this report has not been verified by FAO, and the content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of FAO, or its Members. The designations employed and the presentation of material do not imply the expression of any opinion whatsoever on the part of FAO concerning legal or development status of any country, territory, city or area or of its authorities or concerning the delimitation of its frontiers or boundaries. The mention of specific companies or products of manufacturers, whether or not these have been patented, does not imply that these have been endorsed by FAO in preference to others of a similar nature that are not mentioned. FOREWORD Sudan is a part to the FAO Commission on Genetic Resources for Food and Agriculture, the only intergovernmental forum which deals with whole range of genetic resources for food and agriculture. The importance of the genetic resources for food and agriculture stems from the fact that it is building block of biodiversity. It is realized that biodiversity provides the basis for livelihood and sustainable social and economic development; and safe ecological safety and food security. -
Production and Cytological Characterization of Oryza Sativa and Oryza Punctata Derived Synthetic Amphiploids
Genome Production and cytological characterization of Oryza sativa and Oryza punctata derived synthetic amphiploids Journal: Genome Manuscript ID gen-2019-0062.R1 Manuscript Type: Article Date Submitted by the 28-Jun-2019 Author: Complete List of Authors: Kumar, Kishor; Punjab Agricultural University, School of Agricultural Biotechnology Neelam, Kumari; Punjab Agricultural University, School of Agricultural Biotechnology Singh, Gurpreet;Draft Punjab Agricultural University, School of Agricultural Biotechnology Mathan, Jyotirmaya; NIPGR Ranjan, Aashish; NIPGR Brar, Darshan; Punjab Agricultural University, School of Agricultural Biotechnology Singh, Kuldeep; Punjab Agricultural University, School of Agricultural Biotechnology; National Bureau of Plant Genetic Resources Oryza punctata, Synthetic Amphiploids, Aneuploids, Cytology, Flow Keyword: Cytometery Is the invited manuscript for consideration in a Special Not applicable (regular submission) Issue? : https://mc06.manuscriptcentral.com/genome-pubs Page 1 of 28 Genome 1 Production and cytological characterization of Oryza sativa and Oryza punctata derived synthetic 2 amphiploids 3 Kishor Kumar1,3, Kumari Neelam1,#, Gurpreet Singh1 , Jyotirmaya Mathan2, Aashish Ranjan2 Darshan 4 Singh Brar1 and Kuldeep Singh1,4 5 1 School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, 6 India. 7 2 National Institute of Plant Genome Research, New Delhi, 110067, India 8 3 Faculty Centre on Integrated Rural Development and Management, Ramakrishna Mission 9 Vivekanada Educational and Research Institute, Narendrapur, Kolkata, 700103, India 10 4 ICAR- National Bureau of Plant Genetic Resources, PUSA, New Delhi, 110012, India 11 12 # Author for correspondence 13 Kumari Neelam Draft 14 School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, 15 India 16 Email: [email protected] 17 Mobile No.: +917986044964 18 19 20 21 22 23 24 25 26 27 28 1 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 2 of 28 29 Abstract 30 Oryza punctata Kotschy ex Steud. -
Dynamic Differential Evolution Schemes of WRKY Transcription
www.nature.com/scientificreports OPEN Dynamic diferential evolution schemes of WRKY transcription factors in domesticated and wild rice Anne J. Villacastin, Keeley S. Adams, Rin Boonjue, Paul J. Rushton, Mira Han & Jefery Q. Shen* WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identifed prevalence of Group III WRKYs despite diferences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that fnely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversifcation of an important gene family under strong selective pressure for biotechnological improvements of the world’s most valued food crop. -
The Genome Sequence of African Rice (Oryza Glaberrima) and Evidence for Independent Domestication
ARTICLES OPEN The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication Muhua Wang1,16, Yeisoo Yu1,16, Georg Haberer2,16, Pradeep Reddy Marri3,16, Chuanzhu Fan1,4, Jose Luis Goicoechea1, Andrea Zuccolo5, Xiang Song1, Dave Kudrna1, Jetty S S Ammiraju1,6, Rosa Maria Cossu7, Carlos Maldonado1, Jinfeng Chen8, Seunghee Lee1, Nick Sisneros1, Kristi de Baynast1, Wolfgang Golser1, Marina Wissotski1, Woojin Kim1, Paul Sanchez1,9, Marie-Noelle Ndjiondjop10, Kayode Sanni10, Manyuan Long11, Judith Carney12, Olivier Panaud13, Thomas Wicker14, Carlos A Machado15, Mingsheng Chen8, Klaus F X Mayer2, Steve Rounsley3 & Rod A Wing1 The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes. O. glaberrima Steud. is an African species of rice that was inde- Here we present a high-quality assembly and annotation of the pendently domesticated from the wild progenitor O.