Author
Udaya C. Kalluri
Other affiliations: Michigan Technological University, Georgia Institute of Technology, Oak Ridge Associated Universities
Bio: Udaya C. Kalluri is an academic researcher from Oak Ridge National Laboratory. The author has contributed to research in topics: Arabidopsis & Lignin. The author has an hindex of 25, co-authored 59 publications receiving 7153 citations. Previous affiliations of Udaya C. Kalluri include Michigan Technological University & Georgia Institute of Technology.
Topics: Arabidopsis, Lignin, Cellulose, Proteome, Genome
Papers published on a yearly basis
Papers
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Oak Ridge National Laboratory1, University of Tennessee2, West Virginia University3, Umeå University4, University of British Columbia5, United States Department of Energy6, Ghent University7, Swedish University of Agricultural Sciences8, Institut national de la recherche agronomique9, Virginia Tech10, Michigan Technological University11, University of Toronto12, Pennsylvania State University13, University of Provence14, University of Georgia15, University of Florida16, University of California, Berkeley17, Lawrence Berkeley National Laboratory18, University of Arizona19, Purdue University20, Stanford University21, United States Department of Agriculture22, University of Helsinki23, University of Turku24, Massachusetts Institute of Technology25, University of Tennessee Health Science Center26, University of Tübingen27
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
Agricultural Research Service1, Oregon State University2, University of California, Berkeley3, John Innes Centre4, United States Department of Energy5, United States Department of Agriculture6, University of California, Davis7, University of Silesia in Katowice8, China Agricultural University9, Iowa State University10, Washington State University11, University of Florida12, University of Massachusetts Amherst13, University of Wisconsin-Madison14, Technische Universität München15, Cornell University16, University of Zurich17, University of Helsinki18, Universidade Federal de Pelotas19, Purdue University20, University of Texas at Arlington21, National Center for Genome Resources22, University of Delaware23, Joint BioEnergy Institute24, University of Copenhagen25, Kyung Hee University26, Ghent University27, Centre national de la recherche scientifique28, Oak Ridge National Laboratory29, Ohio State University30, Institut national de la recherche agronomique31, University of Picardie Jules Verne32, Illinois State University33, Sabancı University34, Donald Danforth Plant Science Center35
TL;DR: The high-quality genome sequence will help Brachypodium reach its potential as an important model system for developing new energy and food crops and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat.
Abstract: Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.
1,603 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
TL;DR: Examination of the extent of conservation and divergence in the structure and evolution of Populus Aux/IAA and ARF gene families with respect to Arabidopsis and rice shows that several Aux/ IAA andARF subgroups have differentially expanded or contracted between the two dicotyledonous plants.
Abstract: Background
Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants We identified the suites of genes in the two gene families in Populus and performed comparative genomic analysis with Arabidopsis and rice
214 citations
TL;DR: The present review seeks to survey and summarize the scattered evidence in support of known host root modifications brought about by beneficial microorganisms and implicate the role of auxin synthesis, transport and signal transduction in modulating beneficial effects in plants.
Abstract: A wide variety of microorganisms known to produce auxin and auxin precursors form beneficial relationships with plants and alter host root development. Moreover, other signals produced by microorganisms affect auxin pathways in host plants. However, the precise role of auxin and auxin-signalling pathways in modulating plant-microbe interactions is unknown. Dissecting out the auxin synthesis, transport and signalling pathways resulting in the characteristic molecular, physiological and developmental response in plants will further illuminate upon how these intriguing inter-species interactions of environmental, ecological and economic significance occur. The present review seeks to survey and summarize the scattered evidence in support of known host root modifications brought about by beneficial microorganisms and implicate the role of auxin synthesis, transport and signal transduction in modulating beneficial effects in plants. Finally, through a synthesis of the current body of work, we present outstanding challenges and potential future research directions on studies related to auxin signalling in plant-microbe interactions.
167 citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
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
University of Tennessee1, Oak Ridge National Laboratory2, West Virginia University3, Umeå University4, University of British Columbia5, United States Department of Energy6, Ghent University7, Swedish University of Agricultural Sciences8, Institut national de la recherche agronomique9, Virginia Tech10, Michigan Technological University11, University of Toronto12, Pennsylvania State University13, University of Provence14, University of Georgia15, University of Florida16, University of California, Berkeley17, Lawrence Berkeley National Laboratory18, University of Arizona19, Purdue University20, Stanford University21, United States Department of Agriculture22, University of Helsinki23, University of Turku24, Massachusetts Institute of Technology25, University of Tennessee Health Science Center26, University of Tübingen27
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
Agricultural Research Service1, Purdue University2, University of North Carolina at Charlotte3, University of California, Berkeley4, University of Arizona5, University of Maryland, College Park6, University of Missouri7, Joint Genome Institute8, National Center for Genome Resources9, Iowa State University10, University of Wisconsin–Stevens Point11, University of Nebraska–Lincoln12
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
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