Compendium for Quick Access to SGN

The home page of SGN contains and links to information relevant to the Solanaceae genomics research community. This information includes information about the International Solanaceae Genomics Project, a picture of a Solanaceae mutant, two recent publications about Solanaceae genomics, SGN related sites, and miscalaneous community highlights.

There is a searchable and browsable directory of researchers in the search section under the directory tab.

A number of link lists are available in the links section.

EST information can be retrieved from SGN database in the search section under the Libraries/EST tab.

The information about the libraries from which the ESTs were sequenced is also available from SGN database. Text searching retrieves a list with library names, organism, tissue and development stage. Clicking on the library short name retrieves its information pages including experimental details, the number of clones and sequences from that library, and contact information.

Valid search terms in EST search are SGN identifier for est, clone, or chromatogram, clone name, identifier from sequencing facility and microarray spot identifier.The latter are identifiers of sequences used on the tomato array for which data can be retrieved from the TED site. In addition, identifiers, accessions and dbEST numbers from Genbank may be used. Examples are given for most identifier types.

The retrieved information contains the sequence, which can be loaded to BLAST with one click and it can be translated into amino acid sequence. Also it lists the unigenes (various builds) that contain this EST linked to the concomitant unigene entry in SGN database. Furthermore it contains clone information, chromatogram information with links to download or view the chomatogram image, and processing and data recovery information.

There are diffences between Solanceae ESTs in SGN and Genbank. SGN database contains tomato and potato ESTs generated in NSF funded genome projects. Also, a set of tomato RFLP marker sequences and a collection of petunia and eggplant ESTs are stored in SGN's database. All sequence data have the chromatogram stored. EST sequences of which the chromatogram has been lost are not stored, which exludes a lot of data from Genbank. SGN has some data of resequenced ESTs that has not yet been submitted to Genbank. So note that SGN may retrieve a more recent version of EST sequences than those recoreded by Genbank.

The unigenes (contigs build from the EST sequences) can be retrieved from SGN database in the search section under the unigene tab.

Valid search terms are SGN unigene identifier, unigene build (select species and build number and give cluster and contig number), or TIGR gene index number (at present only for tomato unigenes).

The retrieved information contains the sequence, which can be loaded to BLAST with one click and it can be translated into aminoacid sequence. Also it contains an image of the build from the member EST sequences with clickable est identifiers and clone identifiers. In case ESTs of this unigene build are used on a microarray a list is given with clone and EST identifiers(clickable), chip name, spot id and a link to the spot info entry in the Tomato Expression Database.

The retrieved information contains, in case available, also the unigenes' annotations. There are manual annotations and BLAST annotations. Manual annotation gives a defenition of the (putative) function and Gene Ontology annotation. BLAST annotation have been generated automatically by searching for sequence similarity of the unigene with genbank using BLASTX. For each unigene the matches with an e-value above a certain treshold are determined and information from genbank of the best matching 100 sequenceshave been stored in SGN database. The information of the top 100 best hits saved with the unigene record in SGN database contains the Genbank accession numbers, score, e-value, identity percentage, span, frame gene locus, defenition and species name.

You can perform a search on annotation. In this search option the annotation of the unigenes are searched with a full text search option which yields a list ranked by text match relevance. Annotation search is available in the search section page under the annotation tab.

There are two options for annotation search. By choosing manual annotation search you search for text matches in the annotations of the unigenes themselves. Note that only a part of the unigenes has been annotated manually. Alternatively, you can search in the unigene blast annotation search. Then you search in the annotations of sequences from Genbank that were found with BLASTX to match with the unigene sequence. For each unigene the best hits (e-value above a certain treshold level and up to a maximum of 100 sequences) have been stored in SGN database.

The information about markers can be retrieved from SGN database either directly in the search section under the marker tab or via the Maps & Markers section of SGN (see below).

Direct searching requires entering a marker identifier. On the maps you can just click on a marker identifier on the map with its marker position indicators.

The retrieved information shows a list of the occurrences of that marker with the names of the maps on which this marker is present, offset (location), confidence levels, a description of the type of marker and the BACs to which this marker has been mapped. The BAC identifiers can be clicked to retrieve a list of BAC contigs and singletons present in this BAC association group.

In case more information about this marker is available from SGN database there is a link in the section headed 'SGN database information'. For RFLP markers this link retrieves library information and sequence. For microsatellites it retrieves the repeat motive and number, the contig where this repeat is present and the primer sequences and PCR product length to detect it. And for COS markers it retrieves the EST identifier, orthoglogy with Arabidopsis thaliana, GenBank protein hit and assigned MIPS functional category.

A number of maps of tomato, potato and eggplant are available from the maps & markers section.

The maps include markers of different types namely RFLP-, isozyme-, morphological-, microsatellite-, EST-by-clone- and COS-markers. The maps are derived from F2 populations from crosses between varieties. RFLP markers are molecular markers detected by Restriction Fragment Length Polymorphism. Isozyme markers and morhpological markers are classical map markers. A microsatellite, also called Single Sequence Repeat (SSR), can be used as molecular marker in case it is polymorphic. A list of all SSR markers detected in the EST collection is available. EST-by-clone markers are Expressed Sequence Tags that are labelled by a specific clone. The Conserved Ortholog Set (COS) markers is a set of highly conserved, single copy genes identified from the collection of tomato ESTs which are also found in Arabidopsis. A list of this set is available. This marker set can be used for comparative mapping between the tomato and arabidopsis genomes in search for syntheny between these species.

The information retrieved when you click on a clickable (not all are) marker in a map shows a list of occurrences with offset (location) and confidence level. Also, the marker type is indicated and there is a link to the markers' entry in SGN database. Furthermore, it mentions whether this marker was used in the physical mapping process of BACs with a list of the identifiers of the BAC clones with which this marker matched. These identifiers link to the concomitant BAC entry in SGN database.

Most of the maps are dynamic maps. These are generated dynamically by MapVieuwer using a database of markers with their map occurences, location and confidence. The MapVieuwer software allows for navigation and zooming over the map.

Besides the dynamic maps there are also two static maps are available in the map section : the tomato-arabidopsis syntheny map and the interogression lines map. Static maps are not generated from a database, but consist of a number of image files of chromosome sections with marker postions indicated.

The tomato-arabidopsis syntheny map shows images of chromosome sections consisting of three panels. The first panel is the tomato molecular marker map published by Tanksley et al. (1992).The second is the COS marker map currently in preparation. Common markers are connected. The markers from both maps are listed again in the third panel, with the ones that occur in the database made clickable.

The interogression line map shows the set of Lycopersicon pennellii-derived introgression lines (ILs) that together cover the entire genome in the background of L. esculentum Var. M82. Those lines are avialable for the research community by ordering seeds.

The mapping of a library of BACs from tomato generated by the University of Arizona is available from the maps & markers section as well. The physical map shows the position of mapped BAC association groups, i.e. BAC contigs and singletons, on the current high density marker map.

The BACS have been mapped by overgo hybridization. Overgos (overlapping oligonucleotide) probes were generated from a total of 1535 sequenced, mapped markers from the current high density tomato map. Thus far, 384 overgo probes have been hybridized to the BAC library. Unambiguous BAC matches for 180 genetic markers have been identified, taking into account that other BAC members of a fingerprinted contig should not match to markers more than 5 cM appart form the marker to which the matching BAC has been anchored.

The map is build dynamically with Mapviewer which indicates the position of BACs by blocks next to the molecular marker map. Red blocks indicate BAC singletons, brown blocks BAC contigs and green blocks BAC groups. The BAC association group information that you retrieve by clicking on a block lists the BAC singletons and contigs of that particular BAC association group. The BACs that are anchored to that mapping position are listed with the probe marker to which it is anchored, the location (chromosome number and offset in centiMorgan), and the confidence level of the mapping of the marker. In case the anchored BAC is part of a FingerPrinted Contig (FPC), the contig id and its number of BAC members are indicated as well.

Linked from the phenotypes section is 'Genes that make the tomato', a mutant database with data from the Zamir Laboratory. The tomato mutant database contains 3500 phenotyped monogenic mutants from a large mutagenesis project in three seasons. Mutants have been characterized by a phenotype catalogue. Also, photos are stored in the database. The database can be searched by phenotypes and traits. Background information about the mutagenesis method and cultivation is provided as well.

Also linked from the phenotypes section is 'Real Time QTL' This QTL analysis site provides a large QTL dataset accessible with a dynamic interface. This dynamic site allows the user to explore a large QTL dataset in various ways.

The dynamic interface of this site allow the user to explore in silico genetic component of tomato quantitative trait loci (QTL). The large data set is derived from the populations of Introgression Lines (IL) from crosses of a wild tomato species with the variety M82. The dataset includes 20 traits from 8 experiments. The global dataset contains all phenotypes in a single analysis. All statistics is done using JMP and Excel and displayed graphically. QTL's are linked to SGN map intervals and in a few cases to gene sequences.

There is a illustrative tutorial in the form of a powerpoint movie showing how to use this Real time QTL tool.

Linked from the expression section is the Tomato Expression Database TED. TED is also part of the Tomato Genome Project. Currently TED contains ~2700 ESTs. The array spot information in the datawarehouse and clone information in the expression database link to SGN database.

Also linked from the expression section is the tomato microarray page of the Center for Gene Expression Profiling (CGEP) from the Boyce Thompson Institute where microarray experiments are conducted.

Tomato Physical Mapping Project pages of the Arizona Genomics Institute. In SGN's maps & markers section on the infomation page about the physical mapping there is a link to this FPC pages for the BAC collection. In the physical mapping project a BAC FingerPrinted Contig map is constructed from library of tomato with a coverage of 11x. The purpose is to develop a tomato physical map anchored to the genetic map and toidentify the tomato BAC minimum tiling path for positional cloning and whole genome sequencing.