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Schoof H, Ernst R, Mayer KFX. The PlaNet Consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource. Comp Funct Genomics 2011; 5:184-9. [PMID: 18629059 PMCID: PMC2447343 DOI: 10.1002/cfg.374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Accepted: 11/24/2003] [Indexed: 11/17/2022] Open
Abstract
The completion of the Arabidopsis genome and the large collections of other plant
sequences generated in recent years have sparked extensive functional genomics
efforts. However, the utilization of this data is inefficient, as data sources are
distributed and heterogeneous and efforts at data integration are lagging behind.
PlaNet aims to overcome the limitations of individual efforts as well as the
limitations of heterogeneous, independent data collections. PlaNet is a distributed
effort among European bioinformatics groups and plant molecular biologists to
establish a comprehensive integrated database in a collaborative network. Objectives
are the implementation of infrastructure and data sources to capture plant genomic
information into a comprehensive, integrated platform. This will facilitate the
systematic exploration of Arabidopsis and other plants. New methods for data
exchange, database integration and access are being developed to create a highly
integrated, federated data resource for research. The connection between the
individual resources is realized with BioMOBY. BioMOBY provides an architecture
for the discovery and distribution of biological data through web services. While
knowledge is centralized, data is maintained at its primary source without a need for
warehousing. To standardize nomenclature and data representation, ontologies and
generic data models are defined in interaction with the relevant communities.Minimal
data models should make it simple to allow broad integration, while inheritance allows
detail and depth to be added to more complex data objects without losing integration.
To allow expert annotation and keep databases curated, local and remote annotation
interfaces are provided. Easy and direct access to all data is key to the project.
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Affiliation(s)
- H Schoof
- Technische Universität München, Chair of Genome-oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan D-85350, Germany.
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de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One 2009; 4:e5764. [PMID: 19503618 PMCID: PMC2685480 DOI: 10.1371/journal.pone.0005764] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 04/16/2009] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Genome level analyses have enhanced our view of phylogenetics in many areas of the tree of life. With the production of whole genome DNA sequences of hundreds of organisms and large-scale EST databases a large number of candidate genes for inclusion into phylogenetic analysis have become available. In this work, we exploit the burgeoning genomic data being generated for plant genomes to address one of the more important plant phylogenetic questions concerning the hierarchical relationships of the several major seed plant lineages (angiosperms, Cycadales, Gingkoales, Gnetales, and Coniferales), which continues to be a work in progress, despite numerous studies using single, few or several genes and morphology datasets. Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group. METHODOLOGY We exploited the EST database to construct a supermatrix of DNA sequences (over 1,200 concatenated orthologous gene partitions for 17 taxa) to examine non-flowering seed plant relationships. This analysis employed programs that offer rapid and robust orthology determination of novel, short sequences from plant ESTs based on reference seed plant genomes. Our phylogenetic analysis retrieved an unbiased (with respect to gene choice), well-resolved and highly supported phylogenetic hypothesis that was robust to various outgroup combinations. CONCLUSIONS We evaluated character support and the relative contribution of numerous variables (e.g. gene number, missing data, partitioning schemes, taxon sampling and outgroup choice) on tree topology, stability and support metrics. Our results indicate that while missing characters and order of addition of genes to an analysis do not influence branch support, inadequate taxon sampling and limited choice of outgroup(s) can lead to spurious inference of phylogeny when dealing with phylogenomic scale data sets. As expected, support and resolution increases significantly as more informative characters are added, until reaching a threshold, beyond which support metrics stabilize, and the effect of adding conflicting characters is minimized.
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Affiliation(s)
- Jose Eduardo de la Torre-Bárcena
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Cullman Molecular Systematics Laboratory and Genomics Laboratory, The New York Botanical Garden, Bronx, New York, United States of America
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Ernest K. Lee
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Dennis Wm. Stevenson
- Cullman Molecular Systematics Laboratory and Genomics Laboratory, The New York Botanical Garden, Bronx, New York, United States of America
| | - Eric D. Brenner
- Cullman Molecular Systematics Laboratory and Genomics Laboratory, The New York Botanical Garden, Bronx, New York, United States of America
| | - Manpreet S. Katari
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Gloria M. Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
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Grossman AR. In the Grip of Algal Genomics. TRANSGENIC MICROALGAE AS GREEN CELL FACTORIES 2008; 616:54-76. [DOI: 10.1007/978-0-387-75532-8_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Borges JC, Cagliari TC, Ramos CHI. Expression and variability of molecular chaperones in the sugarcane expressome. JOURNAL OF PLANT PHYSIOLOGY 2007; 164:505-13. [PMID: 16687190 DOI: 10.1016/j.jplph.2006.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 03/19/2006] [Indexed: 05/09/2023]
Abstract
Molecular chaperones perform folding assistance in newly synthesized polypeptides preventing aggregation processes, recovering proteins from aggregates, among other important cellular functions. Thus their study presents great biotechnological importance. The present work discusses the mining for chaperone-related sequences within the sugarcane EST genome project database, which resulted in approximately 300 different sequences. Since molecular chaperones are highly conserved in most organisms studied so far, the number of sequences related to these proteins in sugarcane was very similar to the number found in the Arabidopsis thaliana genome. The Hsp70 family was the main molecular chaperone system present in the sugarcane expressome. However, many other relevant molecular chaperones systems were also present. A digital RNA blot analysis showed that 5'ESTs from all molecular chaperones were found in every sugarcane library, despite their heterogeneous expression profiles. The results presented here suggest the importance of molecular chaperones to polypeptide metabolism in sugarcane cells, based on their abundance and variability. Finally, these data have being used to guide more in deep analysis, permitting the choice of specific targets to study.
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Affiliation(s)
- Júlio C Borges
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, 13084-971 Campinas SP, Brazil.
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Madishetty K, Condamine P, Svensson JT, Rodriguez E, Close TJ. An improved method to identify BAC clones using pooled overgos. Nucleic Acids Res 2006; 35:e5. [PMID: 17151072 PMCID: PMC1761434 DOI: 10.1093/nar/gkl920] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Hybridization using overgo probes is an established approach for screening arrayed bacterial artificial chromosome (BAC) libraries. We have improved the use of overgos by increasing the yield of positive clones using reduced levels of radioisotopes and enzyme. The strategy involves labeling with all four radiolabeled nucleotides in a hot pulse followed by a cold nucleotide chase and then extending the exposure time to compensate for reduced specific activity of the probes. The resulting cost savings and reduced human exposure to radiation make the use of highly pooled overgo probes a more attractive approach for screening of BAC libraries from organisms with large genomes.
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Affiliation(s)
| | | | | | | | - Timothy J. Close
- To whom correspondence should be addressed. Tel: +1 951 827 3318; Fax: +1 951 827 4437; E-mail:
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Suchánková P, Kubaláková M, Kovárová P, Bartos J, Cíhalíková J, Molnár-Láng M, Endo TR, Dolezel J. Dissection of the nuclear genome of barley by chromosome flow sorting. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:651-9. [PMID: 16810504 DOI: 10.1007/s00122-006-0329-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 05/27/2006] [Indexed: 05/10/2023]
Abstract
Isolation of mitotic chromosomes using flow cytometry is an attractive way to dissect nuclear genomes into their individual chromosomal components or portions of them. This approach is especially useful in plants with complex genomes, where it offers a targeted and hence economical approach to genome analysis and gene cloning. In several plant species, DNA of flow-sorted chromosomes has been used for isolation of molecular markers from specific genome regions, for physical mapping using polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH), for integration of genetic and physical maps and for construction of chromosome-specific DNA libraries, including those cloned in bacterial artificial chromosome vectors. Until now, chromosome analysis and sorting using flow cytometry (flow cytogenetics) has found little application in barley (2n = 14, 1C approximately 5,100 Mbp) because of the impossibility of discriminating and sorting individual chromosomes, except for the smallest chromosome 1H and some translocation chromosomes with DNA content significantly different from the remaining chromosomes. In this work, we demonstrate that wheat-barley ditelosomic addition lines can be used to sort any arm of barley chromosomes 2H-7H. Thus, the barley genome can be dissected into fractions representing only about 6-12% of the total genome. This advance makes the flow cytogenetics an attractive tool, which may greatly facilitate genome analysis and gene cloning in barley.
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Affiliation(s)
- Pavla Suchánková
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, 77200 Olomouc, Czech Republic
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Mrácek J, Greiner S, Cho WK, Rauwolf U, Braun M, Umate P, Altstätter J, Stoppel R, Mlcochová L, Silber MV, Volz SM, White S, Selmeier R, Rudd S, Herrmann RG, Meurer J. Construction, database integration, and application of an Oenothera EST library. Genomics 2006; 88:372-80. [PMID: 16829020 DOI: 10.1016/j.ygeno.2006.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 04/20/2006] [Accepted: 05/30/2006] [Indexed: 11/18/2022]
Abstract
Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.
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Affiliation(s)
- Jaroslav Mrácek
- Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, 80638 München, Germany
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de la Torre JEB, Egan MG, Katari MS, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R. ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol 2006; 6:48. [PMID: 16776834 PMCID: PMC1564041 DOI: 10.1186/1471-2148-6-48] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 06/15/2006] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. RESULTS A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. CONCLUSION Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products.
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Affiliation(s)
- Jose EB de la Torre
- Department of Biology, New York University, 100 Washington Sq East, New York NY 10003, USA
| | - Mary G Egan
- American Museum of Natural History, Central Park West @79St., New York, NY 10024, USA
| | - Manpreet S Katari
- Department of Biology, New York University, 100 Washington Sq East, New York NY 10003, USA
| | - Eric D Brenner
- Department of Biology, New York University, 100 Washington Sq East, New York NY 10003, USA
- New York Botanical Garden Bronx, 200th Street and Kazimiroff Boulevard, Bronx, NY 10458, USA
| | - Dennis W Stevenson
- New York Botanical Garden Bronx, 200th Street and Kazimiroff Boulevard, Bronx, NY 10458, USA
| | - Gloria M Coruzzi
- Department of Biology, New York University, 100 Washington Sq East, New York NY 10003, USA
| | - Rob DeSalle
- American Museum of Natural History, Central Park West @79St., New York, NY 10024, USA
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9
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Strizh IG. Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. Bioessays 2006; 28:199-210. [PMID: 16435295 DOI: 10.1002/bies.20368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Modern technologies have rapidly transformed biology into a data-intensive discipline. In addition to the enormous amounts of existing experimental data in the literature, every new study can produce a large amount of new data, resulting in novel ideas and more publications. In order to understand a biological process as completely as possible, scientists should be able to combine and analyze all such information. Not only molecular biology and bioinformatics, but all the other domains of biology including plant biology, require tools and technologies that enable experts to capture knowledge within distributed and heterogeneous sources of information. Ontologies have proven to be one of the most-useful means of constructing and formalizing expert knowledge. The key feature of an ontology is that it represents a computer-interpretable model of a particular subject area. This article outlines the importance of ontologies for systems biology, data integration and information analyses, as illustrated through the example of reactive oxygen species (ROS) signaling networks in plants.
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Affiliation(s)
- Irina G Strizh
- Plant Physiology Department, Biology Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory, 119992 Moscow, Russia.
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Glinski M, Weckwerth W. The role of mass spectrometry in plant systems biology. MASS SPECTROMETRY REVIEWS 2006; 25:173-214. [PMID: 16284938 DOI: 10.1002/mas.20063] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Large-scale analyses of proteins and metabolites are intimately bound to advancements in MS technologies. The aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. Here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and multidimensional liquid chromatography coupled to mass spectrometry (LC-MS). The analysis of (i) proteins (ii) phosphoproteins, and (iii) metabolites is discussed in the context of plant physiology and environment and with a focus on novel method developments. Recently published studies measuring dynamic (quantitative) behavior at these levels are summarized; for these works, the completely sequenced plants Arabidopsis thaliana and Oryza sativa (rice) have been the primary models of choice. Particular emphasis is given to key physiological processes such as metabolism, development, stress, and defense. Moreover, attempts to combine spatial, tissue-specific resolution with systematic profiling are described. Finally, we summarize the initial steps to characterize the molecular plant phenotype as a corollary of environment and genotype.
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Affiliation(s)
- Mirko Glinski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Vij S, Gupta V, Kumar D, Vydianathan R, Raghuvanshi S, Khurana P, Khurana JP, Tyagi AK. Decoding the rice genome. Bioessays 2006; 28:421-32. [PMID: 16547947 DOI: 10.1002/bies.20399] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rice cultivation is one of the most important agricultural activities on earth, with nearly 90% of it being produced in Asia. It belongs to the family of crops that includes wheat, maize and barley, and it supplies more than 50% of calories consumed by the world population. Its immense economic value and a relatively small genome size makes it a focal point for scientific investigations, so much so that four whole genome sequence drafts with varying qualities have been generated by both public and privately funded ventures. The availability of a complete and high-quality map-based sequence has provided the opportunity to study genome organization and evolution. Most importantly, the order and identity of 37,544 genes of rice have been unraveled. The sequence provides the required ingredients for functional genomics and molecular breeding programs aimed at unraveling intricate cellular processes and improving rice productivity.
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Affiliation(s)
- Shubha Vij
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India
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12
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Affiliation(s)
- Arthur R Grossman
- The Carnegie Institution, Department of Plant Biology, Stanford, California 94305, USA.
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Abstract
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family. Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes
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Vassilev D, Leunissen J, Atanassov A, Nenov A, Dimov G. Application of Bioinformatics in Plant Breeding. BIOTECHNOL BIOTEC EQ 2005. [DOI: 10.1080/13102818.2005.10817293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Cagliari TC, Tiroli AO, Borges JC, Ramos CH. Identification and in silico expression pattern analysis of Eucalyptus expressed sequencing tags (ESTs) encoding molecular chaperones. Genet Mol Biol 2005. [DOI: 10.1590/s1415-47572005000400006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Thiago C. Cagliari
- Centro de Biologia Molecular Estrutural, Brazil; Universidade Estadual de Campinas, Brazil
| | - Ana O. Tiroli
- Centro de Biologia Molecular Estrutural, Brazil; Universidade Estadual de Campinas, Brazil
| | - Júlio C. Borges
- Centro de Biologia Molecular Estrutural, Brazil; Universidade Estadual de Campinas, Brazil
| | - Carlos H.I. Ramos
- Centro de Biologia Molecular Estrutural, Brazil; Universidade Estadual de Campinas, Brazil
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Meyers BC, Scalabrin S, Morgante M. Mapping and sequencing complex genomes: let's get physical! Nat Rev Genet 2004; 5:578-88. [PMID: 15266340 DOI: 10.1038/nrg1404] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
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Ferrol N, Azcón-Aguilar C, Bago B, Franken P, Gollotte A, González-Guerrero M, Harrier LA, Lanfranco L, van Tuinen D, Gianinazzi-Pearson V. Genomics of Arbuscular Mycorrhizal Fungi. FUNGAL GENOMICS 2004. [DOI: 10.1016/s1874-5334(04)80019-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KFX, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM. Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol 2003; 4:R78. [PMID: 14659015 PMCID: PMC329417 DOI: 10.1186/gb-2003-4-12-r78] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Revised: 10/03/2003] [Accepted: 10/23/2003] [Indexed: 11/10/2022] Open
Abstract
Analysis of cycad ESTs has uncovered conserved and potentially novel genes. The presence of a glutamate receptor agonist, as well as a glutamate receptor-like gene in cycads, supports the hypothesis that such neuroactive plant products are not merely herbivore deterrents but may also serve a role in plant signaling. Background Cycads are ancient seed plants (living fossils) with origins in the Paleozoic. Cycads are sometimes considered a 'missing link' as they exhibit characteristics intermediate between vascular non-seed plants and the more derived seed plants. Cycads have also been implicated as the source of 'Guam's dementia', possibly due to the production of S(+)-beta-methyl-alpha, beta-diaminopropionic acid (BMAA), which is an agonist of animal glutamate receptors. Results A total of 4,200 expressed sequence tags (ESTs) were created from Cycas rumphii and clustered into 2,458 contigs, of which 1,764 had low-stringency BLAST similarity to other plant genes. Among those cycad contigs with similarity to plant genes, 1,718 cycad 'hits' are to angiosperms, 1,310 match genes in gymnosperms and 734 match lower (non-seed) plants. Forty-six contigs were found that matched only genes in lower plants and gymnosperms. Upon obtaining the complete sequence from the clones of 37/46 contigs, 14 still matched only gymnosperms. Among those cycad contigs common to higher plants, ESTs were discovered that correspond to those involved in development and signaling in present-day flowering plants. We purified a cycad EST for a glutamate receptor (GLR)-like gene, as well as ESTs potentially involved in the synthesis of the GLR agonist BMAA. Conclusions Analysis of cycad ESTs has uncovered conserved and potentially novel genes. Furthermore, the presence of a glutamate receptor agonist, as well as a glutamate receptor-like gene in cycads, supports the hypothesis that such neuroactive plant products are not merely herbivore deterrents but may also serve a role in plant signaling.
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Affiliation(s)
- Eric D Brenner
- The New York Botanical Garden, 200th Street and Kazimiroff, Bronx, NY 10458-5126, USA.
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Pedra JHF, Brandt A, Li HM, Westerman R, Romero-Severson J, Pollack RJ, Murdock LL, Pittendrigh BR. Transcriptome identification of putative genes involved in protein catabolism and innate immune response in human body louse (Pediculicidae: Pediculus humanus). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2003; 33:1135-1143. [PMID: 14563364 DOI: 10.1016/s0965-1748(03)00133-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genomics information relating to human body lice is surprisingly scarce, and this has constrained studies of their physiology, immunology and vector biology. To identify novel body louse genes, we used engorged adult lice to generate a cDNA library. Initially, 1152 clones were screened for inserts, edited for removal of vector sequences and base pairs of poor quality, and viewed for splicing variations, gene families and polymorphism. Computational methods identified 506 inferred open reading frames including the first predicted louse defensin. The inferred defensin aligns well with other insect defensins and has highly conserved cysteine residues, as are known for other defensin sequences. Two cysteine and five serine proteinases were categorized according to their inferred catalytic sites. We also discovered seven putative ubiquitin-pathway genes and four iron metabolizing deduced enzymes. Finally, glutathione-S-transferases and cytochrome P450 genes were among the detoxification enzymes found. Results from this first systematic effort to discover human body louse genes should promote further studies in Phthiraptera and lice.
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Affiliation(s)
- Joao H F Pedra
- Indiana Center for Insect Genomics, University of Notre Dame, Notre Dame, IN 46556-0369, USA
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Tang W, Luo X, Nelson A, Collver H, Kinken K. Functional genomics of wood quality and properties. GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:263-78. [PMID: 15629055 PMCID: PMC5172417 DOI: 10.1016/s1672-0229(03)01032-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide. In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus. The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.
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Affiliation(s)
- Wei Tang
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA.
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Birch PR, Avrova AO, Armstrong M, Venter E, Taleb N, Gilroy EM, Phillips MS, Whisson SC. The potato – Phytophthora infestans interaction transcriptome. CANADIAN JOURNAL OF PLANT PATHOLOGY 2003. [PMID: 0 DOI: 10.1080/07060660309507074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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Rudd S. Expressed sequence tags: alternative or complement to whole genome sequences? TRENDS IN PLANT SCIENCE 2003; 8:321-9. [PMID: 12878016 DOI: 10.1016/s1360-1385(03)00131-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Over three million sequences from approximately 200 plant species have been deposited in the publicly available plant expressed sequence tag (EST) sequence databases. Many of the ESTs have been sequenced as an alternative to complete genome sequencing or as a substrate for cDNA array-based expression analyses. This creates a formidable resource from both biodiversity and gene-discovery standpoints. Bioinformatics-based sequence analysis tools have extended the scope of EST analysis into the fields of proteomics, marker development and genome annotation. Although EST collections are certainly no substitute for a whole genome scaffold, this "poor man's genome" resource forms the core foundations for various genome-scale experiments within the as yet unsequenceable plant genomes.
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Affiliation(s)
- Stephen Rudd
- Institut für Bioinformatik, GSF Forschungszentrum für Umwelt und Gesundheit, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.
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Abstract
The multitude of metabolites found in living organisms and the calculated, unexpected small number of genes identified during genome sequencing projects discomfit biologists. Several processes on the transcription and translation level lead to the formation of isoenzymes and can therefore explain at least parts of this surprising result. However, poor enzyme specificity may also contribute to metabolome diversity. In former studies, when enzymes were isolated from natural sources, impure protein preparations were hold responsible for broad enzyme specificity. Nowadays, highly purified enzymes are available by molecular biological methods such as heterologous expression in host organisms and they can be thoroughly analyzed. During biochemical analysis of heterologously expressed enzymes poor specificity was observed for enzymes involved in fruit ripening, e.g. in flavour and color formation. Surprisingly broad specificity was shown for the reactants in the case of alcohol acyl-CoA transferase, O-methyltransferase, glucosyltransferase, P450 monooxygenases as well as polyketide synthases and for the product in the case of monoterpene synthases. Literature data confirm the assumption of limited specificity for enzymes involved in metabolism and bioformation of secondary metabolites. It is concluded that metabolome diversity is caused by low enzyme specificity but availability of suitable substrates due to compartmentation has also taken into account.
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Affiliation(s)
- Wilfried Schwab
- Lehrstuhl für Lebensmittelchemie, Universität Würzburg, Am Hubland, D-97074, Würzburg, Germany.
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Wei F, Wing RA, Wise RP. Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. THE PLANT CELL 2002; 14:1903-17. [PMID: 12172030 PMCID: PMC151473 DOI: 10.1105/tpc.002238] [Citation(s) in RCA: 165] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2002] [Accepted: 04/30/2002] [Indexed: 05/18/2023]
Abstract
Genes that confer defense against pathogens often are clustered in the genome and evolve via diverse mechanisms. To evaluate the organization and content of a major defense gene complex in cereals, we determined the complete sequence of a 261-kb BAC contig from barley cv Morex that spans the Mla (powdery mildew) resistance locus. Among the 32 predicted genes on this contig, 15 are associated with plant defense responses; 6 of these are associated with defense responses to powdery mildew disease but function in different signaling pathways. The Mla region is organized as three gene-rich islands separated by two nested complexes of transposable elements and a 45-kb gene-poor region. A heterochromatic-like region is positioned directly proximal to Mla and is composed of a gene-poor core with 17 families of diverse tandem repeats that overlap a hypermethylated, but transcriptionally active, gene-dense island. Paleontology analysis of long terminal repeat retrotransposons indicates that the present Mla region evolved over a period of >7 million years through a variety of duplication, inversion, and transposon-insertion events. Sequence-based recombination estimates indicate that R genes positioned adjacent to nested long terminal repeat retrotransposons, such as Mla, do not favor recombination as a means of diversification. We present a model for the evolution of the Mla region that encompasses several emerging features of large cereal genomes.
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Affiliation(s)
- Fusheng Wei
- Interdepartmental Genetics Program and Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA
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