Progress 01/01/08 to 12/31/11
Outputs
OUTPUTS: Collectively, the Solanaceae are a valuable component of U.S. agriculture. The major Solanaceae crop species share both sequence identity and gene order thereby providing the basis for leveraging genomic resources across taxa. Transcriptome and genome sequencing projects have been initiated for the major crop species. The potato genome has been completed and is now publicly available. To improve the ability of researchers to interpret the genome and transcriptome resources for the Solanaceae, it is essential that all of the partial Solanaceae transcript and genome sequence be integrated at the family level and linked to other model dicot species to provide contextual information on the putative function of Solanaceae homologs. In this project, we have created a central web portal for accessing sequence data for the Solanaceae (http://solanaceae.plantbiology.msu.edu/). In our Species Overview pages, we provide a central resource for sequence, transcript, expression, publications, and analyses/tools for species in the Solanaceae. We have identified Single Nucleotide Polymorphisms and Simple Sequence Repeats within the Solanaceae transcriptome sequence datasets for use as potential genetic markers. We have identified putative orthologs, paralogs, and lineage-specific genes within the Solanaceae to facilitate intra- and inter-species comparisons. We have annotated bacterial artificial chromosome (BAC) clones primarily from potato and tomato as well as other Solanaceae species and made these available on our Solanaceae Genome Browser. We have mapped sequences from the Solanaceae species to the genomes of multiple dicot species to permit leveraging resources from these model species to the Solanaceae. In the last year, we added the potato genome data provided by the Potato Genome Sequencing Consortium. We support a genome browser for potato that includes 68 tracks of annotation including Single Nucleotide Polymorphisms, Simple Sequence Repeats, and comparative alignments with other plant species. The comparative alignments include alignments to Solanaceae transcript assemblies and the Arabidopsis, poplar, grapevine, and soybean proteomes to permit leveraging of the functional annotation data from these species to potato and other Solanaceae species. Another major component of the genome browser is the expression data from two potato genotypes. The RNA-seq data provides a qualitative and quantitative annotation of the potato genome. Users can determine if empirically detected transcripts are consistent with computationally-derived gene annotation and determine expression levels in a wide range of development and abiotic/biotic stress conditions. Additional updates to the entire site are in progress and will be released in early 2012. PARTICIPANTS: Individuals Project Director: C. Robin Buell, Michigan State University, performed oversight and management to the project. Bioinformaticists: Brett Whitty, John Hamilton, Kevin Childs, Cory Hirsch, and Faerlin Pulido performed computational analyses on the project. Partners: Michigan State University, East Lansing MI; Collaborators: Dave Douches, USDA SolCAP project; Lukas Mueller, SGN project. Potato Genome Sequencing Consortium (http://potatogenome.net). Training We have disseminated our knowledge on comparative genomics for the Solanaceae through the project website. TARGET AUDIENCES: The target audience is plant biologists, molecular biologists, breeders, and genomics experts. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
This project provides tools for translational genomics that are essential to elevate Solanaceae from a morphologically diverse set of important vegetable species with distributed genomics resources to a suite of crop species integrated through the commonality of their genomes. We have provided a suite of tools and analyses for maximizing use of sequence data from the Solanaceae by biologists. These are available through a public website (Solanaceae Genomics Resource; http://solanaceae.plantbiology.msu.edu/) that provides search and browsing tools, downloadable datasets, and value-added annotation of Solanaceae sequences. Major tools and datasets of use by the public are candidate markers including simple sequence repeats and single nucleotide polymorphisms, orthologous linkages across the Solanaceae and model dicot species, paralogous relationships within each species, and a large set of functional annotations. Another major tool that we have provided is a suite of genome browsers in which not only Solanaceae sequences are presented in a graphical format with annotation, but also in which we have provided major model dicot genomes with linkages to Solanaceae sequences. With the addition of the potato genome sequence and annotation, we have been able to provide users with a substantially more complete and useful genomic resource for not only potato researchers but also all Solanaceae users. Based on site usage data tracked by Google Analytics from the period Jan 1 2011 to December 31 2011, the Solanaceae Genomics Resource web site had a total of 6,793 unique visitors for a total of 16,179 visits with an average of 2.4 unique site visits per day. The total number of page views in this period was 124,229. The site visitors were from 111 countries/territories ( 4,532 users within the U.S.). The average user uses the site for 10 minutes and accesses 7.8 pages per visit. In the previous year were 4,518 unique visitors, 8.584 visits, and 41,678 total page views suggesting a broadening of interest in the site by the scientific community.
Publications
- No publications reported this period
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Collectively, the Solanaceae are a valuable component of US agriculture. The major Solanaceae crop species share both sequence identity and gene order thereby providing the basis for leveraging genomic resources across taxa. Transcriptome and genome sequencing projects have been initiated for the major crop species and draft genome sequences are now available for potato and tomato. To improve the ability of researchers to interpret these incomplete resources, it is essential that all of the partial Solanaceae transcript and genome sequence be integrated at the family level and linked to other model dicot species to provide contextual information on the putative function of Solanaceae homologs. In this project, we have created a central web portal for accessing sequence data for the Solanaceae (http://solanaceae.plantbiology.msu.edu/). In our Species Overview pages, we provide a central resource for sequence, transcript, expression, publications, and analyses/tools for species in the Solanaceae. We have identified Single Nucleotide Polymorphisms and Simple Sequence Repeats within the Solanaceae transcriptome sequence datasets for use as potential genetic markers. We have identified putative orthologs, paralogs, and lineage-specific genes within the Solanaceae to facilitate intra- and inter-species comparisons. We have annotated bacterial artificial chromosome (BAC) clones primarily from potato and tomato as well as other Solanaceae species and made these available on our Solanaceae Genome Browser. We have mapped sequences from the Solanaceae species to the genomes of four dicot species to permit leveraging resources from these model species to the Solanaceae. In the last year, we began hosting the Potato Genome Sequencing Consortium (PGSC) potato genome browser and integrating the Solanaceae comparative site with incoming links from the PGSC genome browser. Since Release 3 of our resource, we have added to site resources 171 Mbp (in 1792 assemblies) of new Solanaceae BAC sequences (126% more new or updated sequence, including additional species) and 78 Mbp of new Solanaceae transcript assemblies (39% more transcript sequences available, including additional species). In addition, we have added the following new features: improved annotation of the transcript assemblies, improved annotation of the BAC sequences, improved functionality of annotation keyword and accession searching of site resources. These resources and features will be made available in our December, 2010 update of the external website. Based on site usage data tracked by Google Analytics from the period Dec. 1st 2009 - Dec. 1st 2010, the Solanaceae Genomics Resource web site had a total of 4,463 absolute unique visitors from 102 countries/territories (2,622 users within the U.S.), with an average of 22 site visits per day. Absolute unique visitors for the previous year were 3,306, meaning the user base served by our resource increased 35% over the past year. A significant number of site users were frequent users of site resources, with 1,108 users (25%) accessing the site >15 times over the year; 317 (7%) site users accessed the resource >50 times over the year. PARTICIPANTS: Individuals Project Director: C. Robin Buell, Michigan State University, performed oversight and management to the project. Bioinformaticists: Brett Whitty performed computational analyses on the project. Partners: Michigan State University, East Lansing MI; Collaborators: Dave Douches, USDA SolCAP project; Lukas Mueller, SGN project. Potato Genome Sequencing Consortium (http://potatogenome.net) Training We have disseminated our knowledge on comparative genomics for the Solanaceae through the project website. TARGET AUDIENCES: The target audience is plant biologists, molecular biologists, breeders, and genomics experts. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
This project provides tools for translational genomics that are essential to elevate Solanaceae from a morphologically diverse set of important vegetable species with distributed genomics resources to a suite of crop species integrated through the commonality of their genomes. We have provided a suite of tools and analyses for maximizing use of sequence data from the Solanaceae by biologists. These are available through a public website (Solanaceae Genomics Resource; http://solanaceae.plantbiology.msu.edu/) that provides search and browsing tools, downloadable datasets, and value-added annotation of Solanaceae sequences. Major tools and datasets of use by the public are candidate markers including simple sequence repeats and single nucleotide polymorphisms, orthologous linkages across the Solanaceae and model dicot species, paralogous relationships within each species, and a large set of functional annotations. Another major tool that we have provided is a suite of genome browsers in which not only Solanaceae sequences are presented in a graphical format with annotation, but also in which we have provided major model dicot genomes with linkages to Solanaceae sequences. In the last year, we have continued to update and improve the content and tools available through our resource.
Publications
- No publications reported this period
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: Collectively, the Solanaceae are a valuable component of US agriculture. The major Solanaceae crop species share both sequence identity and gene order thereby providing the basis for leveraging genomic resources across taxa. Transcriptome and genome sequencing projects have been initiated for the major crop species and draft genome sequences are now available for potato and tomato. To improve the ability of researchers to interpret these incomplete resources, it is essential that all of the partial Solanaceae transcript and genome sequence be integrated at the family level and linked to other model dicot species to provide contextual information on the putative function of Solanaceae homologs. In this project, we have created a central web portal for accessing sequence data for the Solanaceae (http://solanaceae.plantbiology.msu.edu/). In our Species Overview pages, we provide a central resource for sequence, transcript, expression, publications, and analyses/tools for species in the Solanaceae. We have identified Single Nucleotide Polymorphisms and Simple Sequence Repeats within the Solanaceae transcriptome sequence datasets for use as potential genetic markers. We have identified putative orthologs, paralogs, and lineage-specific genes within the Solanaceae to facilitate intra- and inter-species comparisons. We have annotated bacterial artificial chromosome clones primarily from potato and tomato as well as other Solanaceae species and made these available on our Solanaceae Genome Browser. We have mapped sequences from the Solanaceae species to the genomes of four dicot species (Arabidopsis, Medicago, GrapeVine, Poplar) to permit leveraging resources from these model species to the Solanaceae. PARTICIPANTS: Individuals: Project Director: C. Robin Buell, Michigan State University, performed oversight and management to the project. Bioinformaticists: Brett Whitty and Morgan Chaires performed computational analyses on the project. Partners: Michigan State University, East Lansing MI. Collaborators: Sergio Feingold, Argentina; Dave Douches, USDA SolCAP project; Lukas Mueller, SGN project. Training: We have disseminated our knowledge on comparative genomics for the Solanaceae through the project website. TARGET AUDIENCES: The target audience is plant biologists, molecular biologists, breeders, and genomics experts. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
This project provides tools for translational genomics that are essential to elevate Solanaceae from a morphologically diverse set of important vegetable species with distributed genomics resources to a suite of crop species integrated through the commonality of their genomes. We have provided a suite of tools and analyses for maximizing use of sequence data from the Solanaceae by biologists. These are available through a public website (Solanaceae Genomics Resource; http://solanaceae.plantbiology.msu.edu/) that provides search and browsing tools, downloadable datasets, and value-added annotation of Solanaceae sequences. Major tools and datasets of use by the public are candidate markers include simple sequence repeats and single nucleotide polymorphisms, orthologous linkages across the Solanaceae and model dicot species, paralogous relationships within each species, and a large set of functional annotations. Another major tool that we have provided is a suite of genome browsers in which not only Solanaceae sequences are presented in a graphical format with annotation, but also in which we have provided major model dicot genomes with linkages to Solanaceae sequences.
Publications
- No publications reported this period
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Collectively, the Solanaceae are a valuable component of US agriculture. The major Solanaceae crop species share both sequence identity and gene order thereby providing the basis for leveraging genomic resources across taxa. Transcriptome and genome sequencing projects have been initiated for the major crop species; albeit none of the three genome initiatives (potato, tomato, tobacco) will generate a high quality, finished complete genome sequence in the near future. Thus, it is essential that all of the partial Solanaceae transcript and genome sequence be integrated at the family level and linked to other model dicot species to provide contextual information on the putative function of Solanaceae homologs. In this project, we have created a central web portal for accessing sequence data for the Solanaceae (http://solanaceae.plantbiology.msu.edu/). In our Species Overview pages, we provide a central resource for sequence, transcript, expression, publications, and analyses/tools for 11 species in the Solanaceae. We have identified Single Nucleotide Polymorphisms and Simple Sequence Repeats within the Solanaceae transcriptome sequence datasets for use as potential genetic markers. We have identified putative orthologs, paralogs, and lineage-specific genes within the Solanaceae to facilitate intra- and inter-species comparisons. We have annotated 1386 bacterial artificial chromosome clones primarily from potato and tomato as well as 14 other Solanaceae species and made these available on our Solanaceae Genome Browser. We have mapped sequences from the Solanaceae species to the genomes of four dicot species (Arabidopsis, Medicago, GrapeVine, Poplar) to permit leveraging resources from these model species to the Solanaceae. PARTICIPANTS: Individuals: PD: C. Robin Buell, Michigan State University, performed oversight and management to the project. Bioinformaticists: Brett Whitty and Morgan Chaires performed computational analyses on the project. Partners: Michigan State University, East Lansing MI; Collaborators: Sergio Feingold, Argentina; Dave Douches, USDA SolCAP project; Lukas Mueller, SGN project. Training: We have disseminated our knowledge on comparative genomics for the Solanaceae through the project website. TARGET AUDIENCES: Target Audience The target audience is plant biologists, molecular biologists, breeders, and genomics experts. PROJECT MODIFICATIONS: None
Impacts
This project provides tools for translational genomics that are essential to elevate Solanaceae from a morphologically diverse set of important vegetable species with distributed genomics resources to a suite of crop species integrated through the commonality of their genomes. We have provided a suite of tools and analyses for maximizing use of sequence data from the Solanaceae by biologists.
Publications
- No publications reported this period
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