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.

A key problem of the post-genomic era is the linking of the phenome to the genome, and SGN allows to track and help discover new such linkages.

Data 
Solanaceae and other Genomes
SGN is a home for Solanaceae and closely related genomes, such as selected Rubiaceae genomes (e.g., Coffea). The tomato, potato, pepper, and eggplant genome are examples of genomes that are currently available. If you would like to include a Solanaceae genome that you sequenced in SGN, please contact us.
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.
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 Alignment Analyzer and browser for phylogenetic trees. The VIGS tool can help predict the properties of VIGS (Viral Induced Gene Silencing) constructs.

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.

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

SGN community-driven gene and phenotype database 
  • We have developed simple web interfaces for the SGN user-community to submit, annotate, and curate the Solanaceae locus and phenotype databases. Our goal is to share biological information, and have the experts in their field review existing data and submit information about their favorite genes and phenotypes.
  • Please read more about the phenome database and how to submit information to SGN.
Lab members 
Staff 
Lukas Mueller Lukas Mueller Director
Naama Menda Naama Menda Postdoc Isaak Y Tecle Isaak Y Tecle Bioinformatics Consultant Tom York Tom York Postdoc
Susan Strickler Susan Strickler Postdoc Noe Fernandez-Pozo Noe Fernandez-Pozo Postdoc Hartmut Foerster Hartmut Foerster MetaCyc curator
Surya Saha Surya Saha Postdoc Guillaume Bauchet Guillaume Bauchet Postdoc Bryan Ellerbrock Bryan Ellerbrock Bioinformatics
Nicolas Morales Nicolas Morales Programmer Alex Agbonna Alex Agbonna Bioinformatics Prashant Hosmani Prashant Hosmani Postdoc
Mirella Flores Mirella Flores Postdoc
Interns 
View more staff & intern photos
Emeritus Staff 
Bioinformatics Analysts
  • Aimin Yan
  • Jeremy Edwards
  • Aureliano Bombarely
  • Anuradha Pujar
  • Robert Buels
  • Joseph Gosselin
  • Jonathan Leto
  • Adri Mills
  • Beth Skwarecki
  • Dean Eckstrom
  • Chris Carpita
  • Marty Kreuter
  • Chenwei Lin
  • John Binns
  • Teri Solow
  • Nicholas Taylor
  • Dan Ilut
  • Robert Ahrens
  • Mark Wright
Interns
  • Allison Izsak (2015)
  • Jonathan Gomes Selman (2015)
  • Ivana Rodriguez (2015)
  • Angela Zhang (2014)
  • Javon Mullings (2014)
  • Matthew Crum (2013)
  • Amelia Lovelace (2013)
  • Akhil Saji (2013)
  • Kevin Nguyen (2013)
  • Andrew Dunford (2012)
  • Paul Van Eck (2012)
  • Kristin Blacklock (2012)
  • Jessica Jeffrey (2011)
  • Dil Begum (2011)
  • Samuel Moijueh (2011)
  • Benjamin Gordon (2011)
  • Jean Lee (2010)
  • Dean Bobo (2010)
  • Carolyn Ochoa (2010)
  • Mallory Freeberg
  • Carolyn Ochoa
  • Johnathon Schulz
  • Tim Jacobs
  • Sasha Naydich
  • Jessica Reuter
  • Matthew Crumb
  • Bob Albright
  • Emily Hart
  • Scott Bland
  • Amarachukwu Enemuo
 
  • Benjamin Cole
  • Caroline Nyenke
  • Tyler Simmons
  • Evan Herbst
  • Emil Keyder
  • Aseem Kohli
  • Igor Dolgalev
  • Miriam Wallace
  • Jay Gadgil
  • Jennifer Lee
Selected Publications 
  • Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA. The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. (2015) Nucleic Acids Res. Volume 43 (Database issue):D1036-41.
  • Fernandez-Pozo N, Rosli H.G., Martin G.B., Mueller L.A. The SGN VIGS Tool: User-Friendly Software to Design Virus-Induced Gene Silencing (VIGS) Constructs for Functional Genomics (2015) Molecular Plant, Volume 8, Issue 3, 486-488
  • The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution (2012) Nature 485, 635-641.
  • Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2010). The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucl. Acids Res. Oct 08, 2010. doi: 10.1093/nar/gkq866.
  • Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA (2010). solQTL: A Tool for QTL analysis, Visualization and Linking to Genomes at SGN Database. BMC Bioinformatics 2010, 11:525.
  • Mueller LA, et al., (2009). A snapshot of the emerging tomato genome sequence. Plant Gen. March 2009 2:78-92; doi:10.3835/plantgenome2008.08.0005.
  • Menda N, Buels RM, Tecle I, Mueller LA (2008). A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol. 2008 Aug;147(4):1788-99 (PMID: 18539779).
  • 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 (2006). 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 (2005). 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.
Funding 
SGN gratefully acknowledges funding from the following funding sources:

National Science Foundation (USA)
  • #0820612 Tomato Chromosome 1 and 10 Sequencing, Coordination and Bioinformatics for the International Solanaceae Genome Initiative
  • #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
  • SolCAP - Solanaceae Coordinated Agricultural Project
 Nestle Corporation
  • SGN gratefully acknowledges a grant from the Nestle Corporation for generation, analysis and integration of Coffea canephora data.




BARD
  • BARD, grant #FI-370-2005 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.

Some data on SGN was obtained from EU-SOL projects. Special thanks to our colleagues at EU-SOL.