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Karla C Gendler

Bio: Karla C Gendler is an academic researcher from University of Arizona. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 7, co-authored 7 publications receiving 7293 citations.
Topics: Genome, Gene, Populus trichocarpa, Proteome, Flagellum

Papers
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Journal ArticleDOI
Gerald A. Tuskan1, Gerald A. Tuskan2, Stephen P. DiFazio1, Stephen P. DiFazio3, Stefan Jansson4, Joerg Bohlmann5, Igor V. Grigoriev6, Uffe Hellsten6, Nicholas H. Putnam6, Steven G. Ralph5, Stephane Rombauts7, Asaf Salamov6, Jacquie Schein, Lieven Sterck7, Andrea Aerts6, Rishikeshi Bhalerao4, Rishikesh P. Bhalerao8, Damien Blaudez9, Wout Boerjan7, Annick Brun9, Amy M. Brunner10, Victor Busov11, Malcolm M. Campbell12, John E. Carlson13, Michel Chalot9, Jarrod Chapman6, G.-L. Chen1, Dawn Cooper5, Pedro M. Coutinho14, Jérémy Couturier9, Sarah F. Covert15, Quentin C. B. Cronk5, R. Cunningham1, John M. Davis16, Sven Degroeve7, Annabelle Déjardin9, Claude W. dePamphilis13, John C. Detter6, Bill Dirks17, Inna Dubchak6, Inna Dubchak18, Sébastien Duplessis9, Jürgen Ehlting5, Brian E. Ellis5, Karla C Gendler19, David Goodstein6, Michael Gribskov20, Jane Grimwood21, Andrew Groover22, Lee E. Gunter1, Björn Hamberger5, Berthold Heinze, Yrjö Helariutta23, Yrjö Helariutta24, Yrjö Helariutta8, Bernard Henrissat14, D. Holligan15, Robert A. Holt, Wenyu Huang6, N. Islam-Faridi22, Steven J.M. Jones, M. Jones-Rhoades25, Richard A. Jorgensen19, Chandrashekhar P. Joshi11, Jaakko Kangasjärvi24, Jan Karlsson4, Colin T. Kelleher5, Robert Kirkpatrick, Matias Kirst16, Annegret Kohler9, Udaya C. Kalluri1, Frank W. Larimer1, Jim Leebens-Mack15, Jean-Charles Leplé9, Philip F. LoCascio1, Y. Lou6, Susan Lucas6, Francis Martin9, Barbara Montanini9, Carolyn A. Napoli19, David R. Nelson26, C D Nelson22, Kaisa Nieminen24, Ove Nilsson8, V. Pereda9, Gary F. Peter16, Ryan N. Philippe5, Gilles Pilate9, Alexander Poliakov18, J. Razumovskaya1, Paul G. Richardson6, Cécile Rinaldi9, Kermit Ritland5, Pierre Rouzé7, D. Ryaboy18, Jeremy Schmutz21, J. Schrader27, Bo Segerman4, H. Shin, Asim Siddiqui, Fredrik Sterky, Astrid Terry6, Chung-Jui Tsai11, Edward C. Uberbacher1, Per Unneberg, Jorma Vahala24, Kerr Wall13, Susan R. Wessler15, Guojun Yang15, T. Yin1, Carl J. Douglas5, Marco A. Marra, Göran Sandberg8, Y. Van de Peer7, Daniel S. Rokhsar17, Daniel S. Rokhsar6 
15 Sep 2006-Science
TL;DR: The draft genome of the black cottonwood tree, Populus trichocarpa, has been reported in this paper, with more than 45,000 putative protein-coding genes identified.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

4,025 citations

Journal ArticleDOI
Sabeeha S. Merchant1, Simon E. Prochnik2, Olivier Vallon3, Elizabeth H. Harris4, Steven J. Karpowicz1, George B. Witman5, Astrid Terry2, Asaf Salamov2, Lillian K. Fritz-Laylin6, Laurence Maréchal-Drouard7, Wallace F. Marshall8, Liang-Hu Qu9, David R. Nelson10, Anton A. Sanderfoot11, Martin H. Spalding12, Vladimir V. Kapitonov13, Qinghu Ren, Patrick J. Ferris14, Erika Lindquist2, Harris Shapiro2, Susan Lucas2, Jane Grimwood15, Jeremy Schmutz15, Pierre Cardol3, Pierre Cardol16, Heriberto Cerutti17, Guillaume Chanfreau1, Chun-Long Chen9, Valérie Cognat7, Martin T. Croft18, Rachel M. Dent6, Susan K. Dutcher19, Emilio Fernández20, Hideya Fukuzawa21, David González-Ballester22, Diego González-Halphen23, Armin Hallmann, Marc Hanikenne16, Michael Hippler24, William Inwood6, Kamel Jabbari25, Ming Kalanon26, Richard Kuras3, Paul A. Lefebvre11, Stéphane D. Lemaire27, Alexey V. Lobanov17, Martin Lohr28, Andrea L Manuell29, Iris Meier30, Laurens Mets31, Maria Mittag32, Telsa M. Mittelmeier33, James V. Moroney34, Jeffrey L. Moseley22, Carolyn A. Napoli33, Aurora M. Nedelcu35, Krishna K. Niyogi6, Sergey V. Novoselov17, Ian T. Paulsen, Greg Pazour5, Saul Purton36, Jean-Philippe Ral7, Diego Mauricio Riaño-Pachón37, Wayne R. Riekhof, Linda A. Rymarquis38, Michael Schroda, David B. Stern39, James G. Umen14, Robert D. Willows40, Nedra F. Wilson41, Sara L. Zimmer39, Jens Allmer42, Janneke Balk18, Katerina Bisova43, Chong-Jian Chen9, Marek Eliáš44, Karla C Gendler33, Charles R. Hauser45, Mary Rose Lamb46, Heidi K. Ledford6, Joanne C. Long1, Jun Minagawa47, M. Dudley Page1, Junmin Pan48, Wirulda Pootakham22, Sanja Roje49, Annkatrin Rose50, Eric Stahlberg30, Aimee M. Terauchi1, Pinfen Yang51, Steven G. Ball7, Chris Bowler25, Carol L. Dieckmann33, Vadim N. Gladyshev17, Pamela J. Green38, Richard A. Jorgensen33, Stephen P. Mayfield29, Bernd Mueller-Roeber37, Sathish Rajamani30, Richard T. Sayre30, Peter Brokstein2, Inna Dubchak2, David Goodstein2, Leila Hornick2, Y. Wayne Huang2, Jinal Jhaveri2, Yigong Luo2, Diego Martinez2, Wing Chi Abby Ngau2, Bobby Otillar2, Alexander Poliakov2, Aaron Porter2, Lukasz Szajkowski2, Gregory Werner2, Kemin Zhou2, Igor V. Grigoriev2, Daniel S. Rokhsar6, Daniel S. Rokhsar2, Arthur R. Grossman22 
University of California, Los Angeles1, United States Department of Energy2, University of Paris3, Duke University4, University of Massachusetts Medical School5, University of California, Berkeley6, Centre national de la recherche scientifique7, University of California, San Francisco8, Sun Yat-sen University9, University of Tennessee Health Science Center10, University of Minnesota11, Iowa State University12, Genetic Information Research Institute13, Salk Institute for Biological Studies14, Stanford University15, University of Liège16, University of Nebraska–Lincoln17, University of Cambridge18, Washington University in St. Louis19, University of Córdoba (Spain)20, Kyoto University21, Carnegie Institution for Science22, National Autonomous University of Mexico23, University of Münster24, École Normale Supérieure25, University of Melbourne26, University of Paris-Sud27, University of Mainz28, Scripps Research Institute29, Ohio State University30, University of Chicago31, University of Jena32, University of Arizona33, Louisiana State University34, University of New Brunswick35, University College London36, University of Potsdam37, Delaware Biotechnology Institute38, Boyce Thompson Institute for Plant Research39, Macquarie University40, Oklahoma State University Center for Health Sciences41, İzmir University of Economics42, Academy of Sciences of the Czech Republic43, Charles University in Prague44, St. Edward's University45, University of Puget Sound46, Hokkaido University47, Tsinghua University48, Washington State University49, Appalachian State University50, Marquette University51
12 Oct 2007-Science
TL;DR: Analyses of the Chlamydomonas genome advance the understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
Abstract: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

2,554 citations

Journal ArticleDOI
TL;DR: It is speculated that this latter process may be involved in altering the cell-surface characteristics of each species, and selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
Abstract: The smallest known eukaryotes, at ≈1-μm diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.

612 citations

Journal ArticleDOI
TL;DR: Testing whether long-distance movement of FLOWERING LOCUS T (FT) mRNA or FT is required for floral induction showed consistent with FT functioning as a component of the florigenic signaling system in the cucurbits.
Abstract: Cucurbita moschata, a cucurbit species responsive to inductive short-day (SD) photoperiods, and Zucchini yellow mosaic virus (ZYMV) were used to test whether long-distance movement of FLOWERING LOCUS T (FT) mRNA or FT is required for floral induction. Ectopic expression of FT by ZYMV was highly effective in mediating floral induction of long-day (LD)–treated plants. Moreover, the infection zone of ZYMV was far removed from floral meristems, suggesting that FT transcripts do not function as the florigenic signal in this system. Heterografting demonstrated efficient transmission of a florigenic signal from flowering Cucurbita maxima stocks to LD-grown C. moschata scions. Real-time RT-PCR performed on phloem sap collected from C. maxima stocks detected no FT transcripts, whereas mass spectrometry of phloem sap proteins revealed the presence of Cm-FTL1 and Cm-FTL2. Importantly, studies on LD- and SD-treated C. moschata plants established that Cmo-FTL1 and Cmo-FTL2 are regulated by photoperiod at the level of movement into the phloem and not by transcription. Finally, mass spectrometry of florally induced heterografted C. moschata scions revealed that C. maxima FT, but not FT mRNA, crossed the graft union in the phloem translocation stream. Collectively, these studies are consistent with FT functioning as a component of the florigenic signaling system in the cucurbits.

455 citations

01 Sep 2006
TL;DR: Analyzing the draft genome of the black cottonwood tree, Populus trichocarpa, revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

355 citations


Cited by
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates and has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation.
Abstract: The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.cazy.org/.

6,028 citations

Journal ArticleDOI
14 Jan 2010-Nature
TL;DR: An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

3,743 citations

Journal ArticleDOI
TL;DR: Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.
Abstract: The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

3,728 citations

Journal ArticleDOI
TL;DR: A brief summary of the current knowledge on oleaginous algae and their fatty acid and TAG biosynthesis, algal model systems and genomic approaches to a better understanding of TAG production, and a historical perspective and path forward for microalgae-based biofuel research and commercialization are provided.
Abstract: Microalgae represent an exceptionally diverse but highly specialized group of micro-organisms adapted to various ecological habitats. Many microalgae have the ability to produce substantial amounts (e.g. 20-50% dry cell weight) of triacylglycerols (TAG) as a storage lipid under photo-oxidative stress or other adverse environmental conditions. Fatty acids, the building blocks for TAGs and all other cellular lipids, are synthesized in the chloroplast using a single set of enzymes, of which acetyl CoA carboxylase (ACCase) is key in regulating fatty acid synthesis rates. However, the expression of genes involved in fatty acid synthesis is poorly understood in microalgae. Synthesis and sequestration of TAG into cytosolic lipid bodies appear to be a protective mechanism by which algal cells cope with stress conditions, but little is known about regulation of TAG formation at the molecular and cellular level. While the concept of using microalgae as an alternative and renewable source of lipid-rich biomass feedstock for biofuels has been explored over the past few decades, a scalable, commercially viable system has yet to emerge. Today, the production of algal oil is primarily confined to high-value specialty oils with nutritional value, rather than commodity oils for biofuel. This review provides a brief summary of the current knowledge on oleaginous algae and their fatty acid and TAG biosynthesis, algal model systems and genomic approaches to a better understanding of TAG production, and a historical perspective and path forward for microalgae-based biofuel research and commercialization.

3,479 citations