- Email: [email protected]
Genome studies and molecular genetics
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Genome studies and molecular genetics/Plant biotechnology Web alert Robyn M Perrin* and Philip A Wigge† A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Plant Biology. Addresses *Laboratory of Genetics, Room 3330 Genetics/Biotechnology Building, 445 Henry Mall, Madison, Wisconsin 53706, USA; e-mail: [email protected] † Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; e-mail: [email protected] Current Opinion in Plant Biology 2002, 5:89–90
Plant genome-sequencing projects Plant Genomes Central — Genome Projects in Progress http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/PlantList.html This is the National Center for Biotechnology Information’s collection of links to plant genome and expressed sequence tag (EST) sequencing projects. The website features links to sequence databases for Arabidopsis, rice and Medicago truncatula; to genetic maps of barley, tomato, bread wheat and maize; and to a number of plant EST databases.
Arabidopsis functional genomics Arabidopsis 2010 Project http://www.arabidopsis.org/workshop1.html Arabidopsis Functional Genomics Network http://www.uni-frankfurt.de/fb15/botanik/mcb/AFGN/ AFGNHome.html The Arabidopsis 2010 project and its European counterpart, the Arabidopsis Functional Genomics Network, seek to provide functional information on the large number of genes that have not yet been characterized and on gene families that have been revealed by the Arabidopsis genome-sequencing project. These sites provide detailed mission statements for these ambitious projects, and detail the grants already awarded and the criteria that will be used to award future grants. Plant Functional Genomics Research Group http://www.gsc.riken.go.jp/e/group/plantgrE.html This site outlines the approach taken by the Japanese plant functional genomics program at the RIKEN Research Institute. A two-pronged approach is being used to try to determine the function of all of the estimated 25 000 gene products in Arabidopsis. A collection of full-length cDNAs is being generated, and knock-out lines for every gene are being constructed.
Tomato genetics and genomics CM Rick Tomato Genetic Resource Center http://tgrc.ucdavis.edu The CM Rick Tomato Genetic Resource Center (TGRC) maintains a gene bank of tomato mutants, wild relatives of tomato (including all nine Lycopersicum spp. and four related Solanum spp.) and additional miscellaneous genetic stocks. Seed stocks are available to researchers upon request and have been used to identify genes conferring disease resistance, insect resistance, abiotic stress tolerance and improved horticultural traits. Other uses for these genetic resources include basic research into physiology, development, genetics and genomics. Users may search the database by accession, gene or researcher. A set of
archived images of wild relatives and some monogenic mutants is available on the web site. The site also presents information to aid in the cultivation of various wild species. Solanaceae Genomics Network http://www.sgn.cornell.edu/ The Solanaceae Genomics Network (SGN), supported by the National Science Foundation and housed at Cornell University, provides tools and resources for Solanaceae researchers. The SGN website allows users to retrieve the full set of expressed sequence tag (EST) sequences generated by the NSF-funded Tomato Genome Project and the Potato Genome Project, as well as EST sequences generated at Cornell for tomato, eggplant and petunia that have not been deposited in GenBank. A list of conserved orthologous set (COS) markers is also available, which allows researchers to conduct comparativemapping studies between tomato and Arabidopsis. SolGenes http://genome.cornell.edu/solgenes/welcome.html SolGenes is a plant genome database supported by the US Department of Agriculture and housed at Cornell University. The database is maintained in the ACEDB software format and users may freely download both the database itself and the software necessary for creating a copy of the database on their own computer. Web-based queries of the database, which can be searched by 31 categories, are also available. Information on gene nomenclature is provided, and users may download botanical drawings of various Solanaceous spp.
Tropical crop genomics Sugar Cane EST Genome Project http://sucest.lad.ic.unicamp.br/en/ Seedquest http://www.seedquest.com/News/releases/europe/ cropdesign/n3771.htm As described in the review by Grivet and Arruda (pp 122–127), the first of these two websites hosts the sugarcane expressed sequence tag (EST) project. SUCEST is part of ONSA, a network of research laboratories in the state of São Paulo (Brazil). The goal of the project is to identify 50 000 sugarcane genes. The project will be concluded when this goal is reached or when 300 000 reads have been deposited in the database. Currently, access to SUCEST data requires registration as a project participant. In the autumn of 2001, SUCEST and CropDesign signed an agreement for a functional genomics alliance, which is described in a press release found at the second URL. Plant Genomics at CIRAD: Sugarcane http://www.cirad.fr/presentation/programmes/biotrop/ resultats/biositecirad/sugar.htm This site describes the research on sugarcane genomics conducted by CIRAD, a French scientific organization specializing in agricultural research for the tropics and subtropics. In collaboration with SUCEST (see above), researchers at CIRAD have tried to characterize the structure of the interspecific aneuploid genome of modern sugarcane cultivars. Their work has involved using restriction fragment length polymorphisms (RFLPs) to analyze genetic diversity in various Saccharum spp. and mapping RFLP and amplified fragment length polymorphism (AFLP) markers in one sugarcane cultivar.
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SorghumDb Data Collection Site http://algodon.tamu.edu/sorghumdb.html The SorghumDb homepage is hosted by the US Department of Agriculture–Agricultural Research Service. Researchers at USDA–ARS and Texas A & M University develop and maintain the database. Users may search the database by map locus, probe, clone, sequence, allele, research article or author. Forms are also available for users to submit information on sorghum genetics or interactions, metabolic pathways, research articles, or colleague contact details. The Klein Group: Pioneering the Field of Sorghum Genetics http://sorghumgenome.tamu.edu/ This site provides graphical displays of ten sorghum linkage groups. By clicking on loci of interest, users may view a table of framework (LOD>3) or placed (LOD<3) markers for that linkage group. From there, users may access simple sequence repeat (SSR) or amplified fragment length polymorphism (AFLP) data for each marker, allowing them to reproduce PCR conditions and identify markers within their own samples. The site is hosted at Texas A & M University and is linked to the SorghumDB homepage (see above). Biodiversity Analysis of Tropical Crop Plants by DNA Marker Technology http://www.mpiz-koeln.mpg.de/~rohde/biodiversity.html This site summarizes the work of Dieter Becker and Wolfgang Rohde in using DNA-marker technology that is based on PCR techniques, such as the use of restriction fragment length polymorphisms (RFLPs) and randomly amplified polymorphic DNA (RAPD). These and other approaches are being applied to produce genetic maps for exotic species such as henequén, coconut, mango, avocado and guava. Resources for the Analysis of Arabidopsis Genechip™ Data www-biology.ucsd.edu/labs/schroeder/genechip.html The Schroeder Lab have updated the Arabidopsis index file, provided by Affymetrix for the Arabidopsis chip, thereby facilitating automated analyses of Genechip™ expression profiles. The index file available at this website provides the position of each element with reference to Arabidopsis chromosomes, and the Arabidopsis Genome Initiative (AGI) identifiers for most elements. Files containing DNA sequences and protein sequences corresponding to most elements on the Affymetrix chip are also available. The files that can be downloaded from this site will allow more rapid and automated analyses of Affymetrix GeneChipTM data using software packages (e.g. GeneSpring or others). Furthermore, the chromosome-location function for each gene on the Affymetrix chip can help in mapping gene-deletion mutations. The Schroeder group has also developed web-based tools for the extraction of upstream promoter sequences using Affymetrix gene and/or AGI
identifiers. The recovered sequences can either be directly sent to a ‘MEME’ website (i.e. a web-based promoter analysis tool) for regulatory element searches or copied for export into other regulatory-motif search and analysis tools.
Epigenetics Science Magazine Special Issue on Epigenetics http://www.sciencemag.org/content/vol293/issue5532/ A special issue of Science (published on August 10, 2001) is devoted in part to the topic of epigenetics. The issue includes news, viewpoints and reviews on epigenetic inheritance in plants, fungi and mammals. A web supplement to the edition provides links to websites on related topics and a selection of research papers, news items and reviews on epigenetics published in Science over the past five years. Some items require a subscription for full-text access. Peter Meyer Lab — Plant Epigenetics http://www.biology.leeds.ac.uk/centres/liba/pmgrp/home.htm The laboratory homepage of Peter Meyer (University of Leeds, UK) includes background information on the epigenetic silencing of gene expression in plants. A list of publications from the Meyer laboratory is also provided. The Meaning of Epigenetics http://www.the-scientist.com/yr2001/sep/ comm1_010917.html This article in The Scientist by Joshua Lederberg explores the semantics of the term ‘epigenetics’. A term that dates back to 1942, ‘epigenetics’ has been defined in various and sometimes confusing ways. Lederberg describes the history of the debate in this commentary, which can be accessed without charge by registering at The Scientist Magazine website. Ambion: RNA Interference and Gene Silencing http://www.ambion.com/hottopics/RNAi/ Produced by Ambion, Inc., this site provides links to a review article on RNA interference (RNAi) and gene silencing, as well as a list of relevant references. Ambion specializes in the development of products and resources for research involving RNA.
Disease resistance Joe Chappell’s Research: Biochemical and Molecular Insights from Studies of Plant–Pathogen Interactions http://www.uky.edu/~lfrals0/joespiel.html Joe Chappell’s website describes his work in studying how plants defend themselves against microbial pathogens. In particular, research in Chappell’s group has examined how plants control the synthesis of antimicrobial phytoalexins, yielding many novel insights into the mechanisms of plant disease resistance.
Genome studies and molecular genetics/Plant biotechnology Web alert Robyn M Perrin* and Philip A Wigge† A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Plant Biology. Addresses *Laboratory of Genetics, Room 3330 Genetics/Biotechnology Building, 445 Henry Mall, Madison, Wisconsin 53706, USA; e-mail: [email protected] † Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; e-mail: [email protected] Current Opinion in Plant Biology 2002, 5:89–90
Plant genome-sequencing projects Plant Genomes Central — Genome Projects in Progress http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/PlantList.html This is the National Center for Biotechnology Information’s collection of links to plant genome and expressed sequence tag (EST) sequencing projects. The website features links to sequence databases for Arabidopsis, rice and Medicago truncatula; to genetic maps of barley, tomato, bread wheat and maize; and to a number of plant EST databases.
Arabidopsis functional genomics Arabidopsis 2010 Project http://www.arabidopsis.org/workshop1.html Arabidopsis Functional Genomics Network http://www.uni-frankfurt.de/fb15/botanik/mcb/AFGN/ AFGNHome.html The Arabidopsis 2010 project and its European counterpart, the Arabidopsis Functional Genomics Network, seek to provide functional information on the large number of genes that have not yet been characterized and on gene families that have been revealed by the Arabidopsis genome-sequencing project. These sites provide detailed mission statements for these ambitious projects, and detail the grants already awarded and the criteria that will be used to award future grants. Plant Functional Genomics Research Group http://www.gsc.riken.go.jp/e/group/plantgrE.html This site outlines the approach taken by the Japanese plant functional genomics program at the RIKEN Research Institute. A two-pronged approach is being used to try to determine the function of all of the estimated 25 000 gene products in Arabidopsis. A collection of full-length cDNAs is being generated, and knock-out lines for every gene are being constructed.
Tomato genetics and genomics CM Rick Tomato Genetic Resource Center http://tgrc.ucdavis.edu The CM Rick Tomato Genetic Resource Center (TGRC) maintains a gene bank of tomato mutants, wild relatives of tomato (including all nine Lycopersicum spp. and four related Solanum spp.) and additional miscellaneous genetic stocks. Seed stocks are available to researchers upon request and have been used to identify genes conferring disease resistance, insect resistance, abiotic stress tolerance and improved horticultural traits. Other uses for these genetic resources include basic research into physiology, development, genetics and genomics. Users may search the database by accession, gene or researcher. A set of
archived images of wild relatives and some monogenic mutants is available on the web site. The site also presents information to aid in the cultivation of various wild species. Solanaceae Genomics Network http://www.sgn.cornell.edu/ The Solanaceae Genomics Network (SGN), supported by the National Science Foundation and housed at Cornell University, provides tools and resources for Solanaceae researchers. The SGN website allows users to retrieve the full set of expressed sequence tag (EST) sequences generated by the NSF-funded Tomato Genome Project and the Potato Genome Project, as well as EST sequences generated at Cornell for tomato, eggplant and petunia that have not been deposited in GenBank. A list of conserved orthologous set (COS) markers is also available, which allows researchers to conduct comparativemapping studies between tomato and Arabidopsis. SolGenes http://genome.cornell.edu/solgenes/welcome.html SolGenes is a plant genome database supported by the US Department of Agriculture and housed at Cornell University. The database is maintained in the ACEDB software format and users may freely download both the database itself and the software necessary for creating a copy of the database on their own computer. Web-based queries of the database, which can be searched by 31 categories, are also available. Information on gene nomenclature is provided, and users may download botanical drawings of various Solanaceous spp.
Tropical crop genomics Sugar Cane EST Genome Project http://sucest.lad.ic.unicamp.br/en/ Seedquest http://www.seedquest.com/News/releases/europe/ cropdesign/n3771.htm As described in the review by Grivet and Arruda (pp 122–127), the first of these two websites hosts the sugarcane expressed sequence tag (EST) project. SUCEST is part of ONSA, a network of research laboratories in the state of São Paulo (Brazil). The goal of the project is to identify 50 000 sugarcane genes. The project will be concluded when this goal is reached or when 300 000 reads have been deposited in the database. Currently, access to SUCEST data requires registration as a project participant. In the autumn of 2001, SUCEST and CropDesign signed an agreement for a functional genomics alliance, which is described in a press release found at the second URL. Plant Genomics at CIRAD: Sugarcane http://www.cirad.fr/presentation/programmes/biotrop/ resultats/biositecirad/sugar.htm This site describes the research on sugarcane genomics conducted by CIRAD, a French scientific organization specializing in agricultural research for the tropics and subtropics. In collaboration with SUCEST (see above), researchers at CIRAD have tried to characterize the structure of the interspecific aneuploid genome of modern sugarcane cultivars. Their work has involved using restriction fragment length polymorphisms (RFLPs) to analyze genetic diversity in various Saccharum spp. and mapping RFLP and amplified fragment length polymorphism (AFLP) markers in one sugarcane cultivar.
90
Web alert
SorghumDb Data Collection Site http://algodon.tamu.edu/sorghumdb.html The SorghumDb homepage is hosted by the US Department of Agriculture–Agricultural Research Service. Researchers at USDA–ARS and Texas A & M University develop and maintain the database. Users may search the database by map locus, probe, clone, sequence, allele, research article or author. Forms are also available for users to submit information on sorghum genetics or interactions, metabolic pathways, research articles, or colleague contact details. The Klein Group: Pioneering the Field of Sorghum Genetics http://sorghumgenome.tamu.edu/ This site provides graphical displays of ten sorghum linkage groups. By clicking on loci of interest, users may view a table of framework (LOD>3) or placed (LOD<3) markers for that linkage group. From there, users may access simple sequence repeat (SSR) or amplified fragment length polymorphism (AFLP) data for each marker, allowing them to reproduce PCR conditions and identify markers within their own samples. The site is hosted at Texas A & M University and is linked to the SorghumDB homepage (see above). Biodiversity Analysis of Tropical Crop Plants by DNA Marker Technology http://www.mpiz-koeln.mpg.de/~rohde/biodiversity.html This site summarizes the work of Dieter Becker and Wolfgang Rohde in using DNA-marker technology that is based on PCR techniques, such as the use of restriction fragment length polymorphisms (RFLPs) and randomly amplified polymorphic DNA (RAPD). These and other approaches are being applied to produce genetic maps for exotic species such as henequén, coconut, mango, avocado and guava. Resources for the Analysis of Arabidopsis Genechip™ Data www-biology.ucsd.edu/labs/schroeder/genechip.html The Schroeder Lab have updated the Arabidopsis index file, provided by Affymetrix for the Arabidopsis chip, thereby facilitating automated analyses of Genechip™ expression profiles. The index file available at this website provides the position of each element with reference to Arabidopsis chromosomes, and the Arabidopsis Genome Initiative (AGI) identifiers for most elements. Files containing DNA sequences and protein sequences corresponding to most elements on the Affymetrix chip are also available. The files that can be downloaded from this site will allow more rapid and automated analyses of Affymetrix GeneChipTM data using software packages (e.g. GeneSpring or others). Furthermore, the chromosome-location function for each gene on the Affymetrix chip can help in mapping gene-deletion mutations. The Schroeder group has also developed web-based tools for the extraction of upstream promoter sequences using Affymetrix gene and/or AGI
identifiers. The recovered sequences can either be directly sent to a ‘MEME’ website (i.e. a web-based promoter analysis tool) for regulatory element searches or copied for export into other regulatory-motif search and analysis tools.
Epigenetics Science Magazine Special Issue on Epigenetics http://www.sciencemag.org/content/vol293/issue5532/ A special issue of Science (published on August 10, 2001) is devoted in part to the topic of epigenetics. The issue includes news, viewpoints and reviews on epigenetic inheritance in plants, fungi and mammals. A web supplement to the edition provides links to websites on related topics and a selection of research papers, news items and reviews on epigenetics published in Science over the past five years. Some items require a subscription for full-text access. Peter Meyer Lab — Plant Epigenetics http://www.biology.leeds.ac.uk/centres/liba/pmgrp/home.htm The laboratory homepage of Peter Meyer (University of Leeds, UK) includes background information on the epigenetic silencing of gene expression in plants. A list of publications from the Meyer laboratory is also provided. The Meaning of Epigenetics http://www.the-scientist.com/yr2001/sep/ comm1_010917.html This article in The Scientist by Joshua Lederberg explores the semantics of the term ‘epigenetics’. A term that dates back to 1942, ‘epigenetics’ has been defined in various and sometimes confusing ways. Lederberg describes the history of the debate in this commentary, which can be accessed without charge by registering at The Scientist Magazine website. Ambion: RNA Interference and Gene Silencing http://www.ambion.com/hottopics/RNAi/ Produced by Ambion, Inc., this site provides links to a review article on RNA interference (RNAi) and gene silencing, as well as a list of relevant references. Ambion specializes in the development of products and resources for research involving RNA.
Disease resistance Joe Chappell’s Research: Biochemical and Molecular Insights from Studies of Plant–Pathogen Interactions http://www.uky.edu/~lfrals0/joespiel.html Joe Chappell’s website describes his work in studying how plants defend themselves against microbial pathogens. In particular, research in Chappell’s group has examined how plants control the synthesis of antimicrobial phytoalexins, yielding many novel insights into the mechanisms of plant disease resistance.