About the SOL Genomics Network

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About the SOL Genomics Network

The SOL Genomics Network (SGN) is a clade oriented database dedicated to the biology of the Solanaceae family which includes a large number of closely related and many agronomically important species such as tomato, potato, tobacco, eggplant, pepper, and the ornamental Petunia hybrida.

SGN is part of the International Solanaceae Initiative (SOL), which has the long-term goal of creating a network of resources and information to address key questions in plant adaptation and diversification.

Data

ESTs

SGN houses EST collections for tomato, potato, pepper, eggplant and petunia and corresponding unigene builds. EST sequence data and cDNA clone resources greatly facilitate cloning strategies based on sequence similarity, the study of syntenic relationships between species in comparative mapping projects, and are essential for microarray technology.

Unigenes

SGN assembles and publishes unigene builds from these EST sequences. For more information, see Unigene Methods.

Maps and Markers

SGN has genetic maps and a searchable catalog of markers for tomato, potato, pepper, and eggplant.

Tomato Sequencing

SGN is the bioinformatics hub for the ongoing international project to fully sequence the euchromatic portion of the tomato genome. In this role, we house:

a searchable catalog of tomato BACS
more than 400,000 BAC end sequences from these BACs
all BAC sequences used to assemble the tomato genome
a Genome Browser for the tomato genome

Tools

SGN makes available a wide range of web-based bioinformatics tools for use by anyone, listed here. Some of our most popular tools include BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an innovative Intron detection tool, an advanced Alignment Analyzer and browser for phylogenetic trees.

The data in SGN have been submitted by many different research groups around the world which are acknowledged on the corresponding pages on SGN. If you have data you would like to submit for display on SGN, please use the contact us web form, or email us at sgn-feedback@sgn.cornell.edu.

For more information about SGN datasets, see the SGN Data Overview. Entire datasets can also be downloaded from our FTP site.

SGN Tools and Processing

We attempt to process all EST sequences directly from sequencing chromatograms using a custom pipeline developed at SGN. The sequences are assembled into unigenes using standard clustering software and in-house tools. A higher level of sequence quality is obtained when sequences are uniformly base-called and quality trimmed. Other software developed at SGN include the interactive comparative map viewer for genetic and physical maps, the Tree Browser and the Alignment Analyzer.
Unigene Methods including assembly process, builds, cluster, and validation

Funding

SGN gratefully acknowledges funding from the following funding sources:

	National Science Foundation (USA) #9872617 - Development of Tools for Tomato Functional Genomics #9975866 - Tools for Potato Structural and Functional Genomics #0116076 - Exploitation of Tomato as a Model for Comparative and Functional Genomics #0421634 - Sequence and Annotation of the Euchromatin of Tomato. #0606595 - Characterization of the Tomato Secretome Using Integrated Functional and Computational Strategies
	USDA USDA CSREES, grant #2007-02777
	Nestle Corporation SGN gratefully acknowledges a grant from the Nestle Corporation for generation, analysis and integration of Coffea canephora data.
	BARD BARD, grant #FI3702005 Bioinformatic links of simple and complex phenotypes with Solanaceae genomes.

Acknowledgments

Special thanks to the Cornell Biological Services Unit for making their compute clusters available for some of our analyses.

Selected Publications

Mueller LA, Mills AA, Skwarecki B, Buels RM, Menda N, Tanksley SD (2008). The SGN comparative map viewer. Bioinformatics. 2008 Feb 1;24(3):422-3.
Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD. (2005) The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond. Plant Physiol 138(3):1310-7.
Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics. 2006 Nov;174(3):1407-20.
Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Petiard V, Tanksley SD. Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet. 2005 Dec;112(1):114-30.

Staff

Senior Staff

Lukas Mueller Director	Naama Menda Postdoctoral Fellow	Anuradha Pujar Postdoctoral Fellow
Isaak Tecle Postdoctoral Fellow	Tom York Postdoctoral Fellow	Aureliano Bombarely Postdoctoral Fellow