tomato 
 ( solanum lycopersicum l. , formerly lycopersicon esculentum miller ) is an 
 economically important crop worldwide , and a preeminent model system for 
 genetic studies in plants .
it is also the most intensively investigated solanaceous 
 species , with simple diploid genetics , a short generation time , routine 
 transformation technology , and availability of rich genetic and genomic 
 resources .
it has a diploid genome with 12  chromosome pairs and a genome size 
 of 950  mb   encoding approximately 35,000 genes that are largely sequestered 
 in contiguous euchromatic regions .
several resources are available for 
 genetic / genomic research in tomato including the following : ( i ) tomato wild 
 species and mutant collections ; ( ii ) marker collections ; ( iii ) f2 synteny mapping population and permanent recombinant inbred ( ri ) mapping 
 populations ; ( iv ) bac libraries and an advanced physical map ; ( v ) tilling 
 populations ; and ( vi ) tomato microarrays , gene silenced tomato lines , and vigs 
 libraries ( for transient silencing ) . till recently ,
tomato genomics has largely 
 relied on molecular marker analysis and functional analysis of gene - sets .
however , 
 for a better understanding of structural and functional aspects of its genome , 
 following latest high - throughput technologies are also being utilized : ( i ) rna transcription and protein analysis , ( ii ) 
 screening of posttranslational modifications and protein - protein interactions , and 
 ( iii ) discovery of metabolic networks .
the information generated by large - scale 
 genome sequencing can lead a major revolution in the understanding of tomato 
 biology .
the international solanaceae genome project 
 ( sol ) was established to develop a network of knowledge on the solanaceae 
 family and to coordinate the research efforts of different groups from around 
 the world .
the solanaceae genomics 
 network website ( sgn;http://www.sgn.cornell.edu ) was created 
 to facilitate distribution of genomic information for tomato in particular and 
 for solanaceous species in general in a comparative genomic context .
the 
 challenge facing sol in the coming years is to develop methodologies that will 
 enable genomic information to be associated with phenotypes of interest for crop 
 improvement .
the framework for organizing these data is the highly conserved 
 genetic map of the solanaceae that will allow the information basis to be 
 extended beyond individual species .
progress in tomato research will depend on our 
 ability to tie together the independent components into higher - order complexity 
 with multiple dimensions .
multidisciplinary research efforts , involving the 
 increased input of chemistry , physics , statistics , mathematics , and computing 
 sciences , are becoming increasingly crucial for the success of such approach .
beginning in the 1980s , different types of 
 molecular markers have been developed in tomato . among crop species ,
tomato is 
 one of the richest in the number and type of these genetic markers , including restriction 
 fragment length polymorphisms ( rflps ) , simple sequence repeats ( ssrs ) , cleaved amplified 
 polymorphic sequence ( caps ) , amplified fragment length polymorphisms ( aflps ) , 
 and single nucleotide polymorphism ( snp ) .
chronologically , rflps were the 
 first markers developed . currently , more than 1000 rflps have been mapped on 
 the 12 tomato chromosomes .
a subset of rflp markers has been converted into 
 pcr - based markers through sequencing of their ends .
these sequences are 
 available from the sgn database , thus allowing specific primers for pcr 
 reaction to be designed .
other pcr - based markers were developed both as random 
 markers , such as random amplified polymorphic dna ( rapd ) , aflps , and 
 locus - specific markers , such as ssrs , caps , and conserved ortholog sets ( coss ) ; 
 and many of them have been mapped onto the high - density tomato genetic map . given the huge number of markers that have been 
 set up for tomato using different methods , a database collecting the different 
 datasets is available at the sgn website .
indeed , all information for more than 
 15,000 markers is collected in the sgn , where a specific tool for 
markers can be searched by name , 
 chromosome position , mapping population , and bac associations ( if they have 
 been associated with bac from the tomato sequencing project by hybridization 
 with overgo probes or computationally by blast comparisons ) .
some of them have 
 also been grouped into collections for organizational purposes or because they 
 are part of a particular project .
so , it is possible to select either cos 
 ( markers that have been mapped in both tomato and arabidopsis ) or cosii markers 
 ( markers that have been mapped in several asterid species , including several 
 solanaceous species ) [ 7 , 8 ] .
other groups comprise known function genes 
 ( kfg ) , or est - derived ( tm ) markers .
recently , large - scale sequencing 
 work in tomato has been generating sequences of whole bac and cloned genes , 
 ests collected from different cdna libraries , and the sequences of full - length 
 cdnas .
the cataloguing of these sequences in public databases is providing 
 useful information to develop markers with high resolving power , such as snps 
 and indels , thus initiating an era of in 
 silico tomato marker discovery .
the tomato ssrs are an example of 
 genetic markers that can be mined from existing sequence data
, by screening the embl and genbank databases , identified 36 primer pairs , 
 which detected polymorphisms at or close to coding regions . in recent studies , 
 as many as 2627 ssrs were mined from an est dataset by screening the 26,363 tomato est unigene dataset and 57,222 
 full - length cdna sequences that were available in mibase 
 ( http://www.accelrys.com/products/gcg ) . 

most of these ssrs ( around 80% ) were novel ssrs , since they did not match any 
 of the the mapped markers , thus being candidates for novel microsatellite markers 
 .
in addition , more than 250,000 ests derived from cdna libraries are 
 currently catalogued on the sgn website .
all these sequences are potentially 
 source of new markers , such as ssrs and snps , useful for tomato genome 
 analysis . in fact , besides ssrs , snps can also be mined from sequence data ; 
 and an efficient in silico snps 
 discovery is feasible for tomato due to the availability of est in public 
 databases . moreover , in the framework of the tomato sequencing project , 
 around 400,000 bac ends are being sequenced that could also be mined to search 
 snps among solanum genotypes ( ercolano 
 et al .
these will 
 allow useful pcr marker to be derived that also fall in intron regions , thus 
 complementing the detection of polymorphism in the coding regions represented 
 by the ests .
recently , oligonucleotide - based arrays have been used to identify dna sequence 
 polymorphisms in different species , since they allow high - throughput 
 development of markers .
total genomic dna hybridization methods are also being 
 exploited in tomato with the aim of identifying markers such as single feature polymorphisms 
 ( sfps ) .
for instance , a 15.27  k gene nimblegen tomato array was used by sim et 
 al .   for a study of polymorphism between s. lycopersicum and its closely related wild species .
genetic mapping of morphological traits in tomato started at the beginning of last century , and by 1973 a total of 257 
 morphological and disease resistance markers had been mapped . by the 
 1990s ,
tomato had become one of the first plants for which rflps were used to generate a high - density linkage map .
later several genetic maps using pcr - based markers were developed and integrated with the rflp maps , as reviewed by labate et al . .
the first pcr - based reference genetic map covering the entire tomato genome was reported by frary et al .   for a population derived from the cross s. lycopersicum
 s. pennellii the solanaceae is the first family of flowering plants for which comparative mapping was conducted [ 17 , 18 ] . as a result , several genetic maps not only for tomato genome , but also for the genomes of other solanaceous crops are now available at the sgn site . 

comparative genome analysis showed that tomato and potato genomes differ in only five paracentric inversions , whereas the tomato and pepper genomes differ in numerous rearrangements including several 
 translocations as well as both pericentric and paracentric inversions [ 19 , 20 ] . 

more recently , doganlar et al .   have shown that eggplant and tomato genomes 
 are differentiated by 28 rearrangements , which could be explained by 23 
 paracentric inversions and five translocations .
these data suggest that paracentric 
 inversions have been the primary mechanism for chromosome evolution in the 
 solanaceae .
comparative genomics research is presently gaining momentum in solanaceae due to availability of sequencing data 
 for several species .
this research activity received further support due to the availability of whole genome sequence of a. thaliana , which facilitated the development of pcr - based cos markers using genes shared between distantly related plant taxa [ 7 , 8 ] .
for instance ,   in an effort to determine the level of synteny between arabidopsis genome and the genomes of tomato and other solanceous species , cosii markers are being mapped not only on tomato genome , but also on the genomes of other major solanaceous species including eggplant , pepper , and nicotiana ( http://www.sgn.cornell.edu/markers/cosii_markers.pl ) .
also , in order to test 
 the efficacy of cosii markers for comparative mapping across large phylogenetic 
 distances , a subset of cosii markers is being mapped on the genomes of both 
 tomato and diploid coffee ( coffea 
 canephora ) .
besides genetic linkage maps , 
 cytological and cytogenetic maps are also available for tomato .
for example , 
 sherman and stack   developed a physical map that was used to quantify the 
 distribution of crossovers along each chromosome .
physical maps were also developed 
 by in situ hybridisation 
 techniques and allowed a comparison of linear order and distances between markers 
 on genetic linkage maps and physical maps [ 2325 ] .
the results obtained by peterson et al . 
 have shown that the linear order of markers is not always conserved between 
 genetic and cytological positions .
the availability of 
 mapped markers and of fished bac allowed the construction of a high - density 
 integrated genetic and physical map , whose definition is still in progress , and 
 which is the foundation for the tomato genome sequencing project .
overgo 
 analysis has been used to match bac to probes based on markers from the s. lycopersicon  s. pennellii map .
this analysis found 600 markers that unambiguously anchor over 5000 bacs to the genetic map .
actually , at sgn site there are more than 10  000 bacs , which are anchored to 
 the genetic maps .
the high - density rflp linkage map 
 developed for tomato facilitated extensive mapping of qualitative traits such 
 as various disease resistance genes , for example , [ 27 , 28 ] .
this allowed tomato 
 breeders to use marker - assisted selection ( mas ) for variety improvement . 
 furthermore , tomato was the first species for which a whole genome molecular 
 linkage map was used to identify quantitative trait loci ( qtl ) , leading to 
 an understanding of the genetic basis of numerous quantitative traits including 
 morphology , yield , fruit quality , fruit primary and secondary metabolites , as 
 well as resistance to a variety of abiotic and biotic stresses   .
the qtl mapping studies conducted by de vicente and 
 tanksley   and by eshed and zamir   using mapping populations derived 
 from interspecific tomato crosses provided stronger evidence that despite the 
 inferior phenotype , unadapted germplasm could also be used as a source of 
 complementary positive alleles that can result in favorable transgressive 
 phenotypes once incorporated in the cultivated background .
the above results 
 indicated that new molecular breeding strategies need to be devised in order to 
 allow more efficient use of the genetic potential stored in seed banks and 
 exotic germplasm .
advanced backcross qtl mapping 
 method  was proposed by tanksley and nelson   with the purpose of combining 
 the process of qtl analysis with variety development , by simultaneously 
 identifying and transferring favorable qtl alleles from unadapted to 
 cultivated germplasm .
the ab - qtl strategy was initially developed and tested in 
 tomato , and since then , it has been adapted for use in other crops 
 including rice , maize , wheat , pepper , barley , and bean .
so far five ab - qtl 
 studies have been conducted in tomato involving crosses with five wild solanum species and in all cases 
 favorable wild qtl alleles have been detected for more than 45% of the 
 evaluated traits .
these data suggest that continued sampling of exotic 
 germplasm should guarantee the discovery of new and useful qtl alleles .
another 
 advantage of the ab - qtl method is that once favorable qtl alleles are detected 
 in segregating populations ( i.e. , bc2 or bc3 ) , few additional 
 marker - assisted generations are required to develop near isogenic lines ( nils ) 
 or introgression lines ( ils ) that can be phenotyped in replicated trials in 
 order to confirm the qtl effect and subsequently be used for variety 
 development .
numerous qtl - nils or ils have been developed starting from the 
 tomato ab - qtl mapping populations , and several of them have been characterised 
 for numerous quantitative traits , for example , [ 35 , 36 ] . since exotic germplasm is an important source of 
 favorable alleles for the improvement of quantitative traits , introgression 
 lines ( ils ) developed in tomato have a special significance .
this also supports 
 the proposal by zamir   for investment in the development of  exotic 
 libraries . 
each such library consists of a set of ils , each il carrying a 
 single marker - defined chromosome segment derived from a donor exotic parent in 
 an otherwise homogeneous elite genetic background .
the alien segment in each il 
 generally also carries a specific gene , preferably in homozygous condition .
a set 
 of overlapping ils would together represent the entire genome of the donor 
 parent and several such sets of ils constitute a permanent genetic resource , 
 since they can be maintained by self - pollination . in tomato ,
the first exotic library 
 ensuring whole genome coverage was developed by eshed and zamir   from the 
 cross between the wild green - fruited species s. pennellii ( acc .
presently , 
 this library consists of 76 rflp - defined ils which partition the entire genetic 
 map into 107 bins defined by single or overlapping segments . over the past 

15 years , the s. pennellii ils and 
 their hybrids have been phenotyped for more than one hundred traits . for 20 
 different characters , such as   yield , 
 fruit morphology , and biochemical traits ,
repeated measurements are 
 available , and the resulting data are presented , in silico , in a search engine 
 called  real time qtl    ( http://zamir.sgn.cornell.edu/qtl/html/home.htm ) .
the studies conducted on the s. pennellii il library have highlighted the higher qtl mapping power of  exotic libraries  compared with 
 conventional segregating populations .
moreover , ils have shown to be a powerful 
 genetic tool to study the epistatic interactions among qtls , to obtain 
 more precise estimates of the magnitude of qtl x genetic background interaction 
 [ 31 , 36 , 41 ] , and of qtl x environment 
 interaction [ 34 , 36 , 38 , 41 ] .
the high - resolution 
 mapping approach applied to s. pennellii ils has led to the map - based cloning of the first two qtls ever cloned : the 
 fruit weight qtl , fw2.2 , and the sugar yield qtl , brix9 - 2 - 5 .
more recently , the s. pennellii  exotic library  is now being used to identify the genes that influence heterosis [ 44 , 45 ] .
furthermore , 
 mas pyramiding of valuable wild qtls in the genetic background of cultivated tomato has demonstrated to be a successful approach for developing breeding lines that can significantly outperform leading commercial hybrids under both 
 wet and dry field conditions .
the outcome of the application of the il 
 breeding concept has been the development of a new processing tomato hybrid thatis currently the leading variety in california 
 ( http://www.ptab.org/ranking9.htm ) 
 ( d. zamir , personal communication ) .
the advantages of the il 
 approach have motivated the public and private sectors to invest in the 
 development of new library resources starting from interspecific crosses with 
 different wild species of tomato including s. 
 habrochaites , s. pimpinellifolium , s. lycopersicoides ,   and s. chmielewskii [ 35 , 4649 ] . to enhance the rate of 
 progress of introgression breeding in tomato , within the framework of a 
 currently running eu project ( eu - sol ) 
 ( http://www.eu-sol.net ) , a genetic 
 infrastructure of  exotic libraries  is being further refined from a diverse 
 selection of accessions .
moreover , the il populations are being anchored to a 
 common pcr marker - based framework , mostly consisting of cosii markers , which 
 will facilitate qtl identification , mapping , cloning of the underlying genes , 
 and the use of the novel variation in marker - assisted breeding .
the 
 tomato genome is being sequenced as the cornerstone of an international 
 solanaceae genome initiative , a project that aims at developing the family 
 solanaceae as a model for systems biology for understanding plant adaptation 
 and diversification ( see international solanaceae genome initiative white paper 
 ( http://sgn.cornell.edu/solanaceae-project ) ) . 
 a sequencing strategy on a bac by bac basis of approximately 220  mb euchromatin 
 was proposed .
the tomato genome comprises approximately 950  mb of dna  more than 75% of which is heterochromatin and 
 largely devoid of genes .
most genes are found in long contiguous stretches 
 of gene dense euchromatin located on the distal portions of each chromosome 
 arm .
the starting points for sequencing the genome are approximately 1500 
  seed  bac clones individually anchored to the tomato map by means of overgo 
 markers . since most of the genetic markers anchoring the bac correspond to 
 genes ( or ests ) , the bac are likely to be biased towards the euchromatic 
 portion of the genome .
the division of sequencing activities between 
 countries was effected on a chromosome basis ( see figure 1 ) .
additional funds to complete this task were provided for european countries by 
 the eu - sol project . in order to facilitate the sequencing task , 
 marker analysis strategies , cytogenetic protocols , and a number of 
 bionformatics and molecular tools
most of 
 the genome sequencing resources , such as bac libraries ( le_hba hindiii library , sl_mboi , and sl_ecori , based on the heinz 1706 genotype ) 
 and web repositories , were provided by different partners .
seed bac and contigs 
 were mapped to each chromosome at cornell university by means of overgo probes . 

a fingerprint map of approximately 10x genome equivalents from the le_hba 
 library has been constructed at the university of arizona through funding from 
 the national science foundation ( http://www.genome.arizona.edu/fpc/tomato ) .
recently , a sanger initiative was focussed on the generation of additional 
 fingerprint data from the mboi library in order to allow comparison and integration of the two datasets . 

fluorescent in situ hybridization ( fish ) was provided to help guide the 
 extension of the tiling path through the euchromatic arms of each chromosome 
 and to determine the location of heterochromatin regions [ 22 , 50 ] .
validation 
 of single bac assigned to each individual chromosome arm was also performed in 
 different participant countries . moreover , a 3d pooling library to perform new 
 bac screening was developed in japan . starting in 2005 , during 
 the last two years of tomato sequencing activity , the participant countries set 
 up their own sequencing pipelines and started to construct the sequence 
 scaffold of assigned chromosomes . before 
 starting the sequencing work according to mapping information available at sgn
, 
 seed bac were selected using different strategies ( il mapping , internal 
 sequencing strategy , fish localization ) . 

after a low - coverage sequencing of each seed bac , the construction of a 
 minimal tiling path of bac clones was performed by blasting the sequence of 
 each  seed  bac against the bac - end stc database to identify bac with minimal 
 overlap in either directions .
the bac - end database consisting of 200,000 clones 
 ( from ecori , hindiii , and mboi 
 libraries ) was used both to confirm and extend the euchromatin minimal tiling 
 path ( e - mtp ) .
each bac - end sequence was 
 subjected to automated annotation to determine the proportion of ends that are 
 likely to correspond to genic regions . to improve this process , different 
 strategies have been developed . in the netherlands ,
bac walking was supported 
 using a sequence - tagged connector approach based on aflp fingerprinting as 
 outlined in peters et al . .
in japan , selected bac mixture ( sbm ) shotgun 
 sequencing has been set up . in this method ,
bac clones whose end sequences do 
 not contain repeat sequences are selected : then the selected bacs are mixed and 
 shotgun sequencing is performed . in our own laboratory , the use of 
 combined bioinformatics tools and molecular data to select a minimum tiling 
 path has been proven to reduce the overlap between adjacent clones .
bacends 
 extension v 0.1  , which is complementary to the sgn online 
 blast interface .
following selection based on bioinformatics 
 analysis , and using the il mapping strategy , chromosome location of the 
 selected extending bac was experimentally confirmed . also , the detection of 
 snps between s. lycopersicon and s. pennellii in both the resequenced 
 anchor marker region and the bac - ends allowed positioning of each extending bac 
 on chromosome 12 ( see figure 2 ) . despite a nonuniform distribution of seed bac 
 on chromosome 12 ,
currently , sixty - five bacs are in different sequencing phases , and 20 
 of them will be available on public databases by the end of 2007 . for 15 seed bac
, 
 at least one round of extension was performed ; in some cases , where two or three 
 rounds of extension were performed , overlapping bacs were merged in sequence islands 
 of > 300  kb .
the contig of approximately 500  kb between markers t1045 and 
 t1211 was also filled up .
interestingly , the ratio of physical and genetic 
 distance in this region is 250  kb / cm . in all , a draft sequence has been constructed 
 for approximately 24% of the tomato euchromatic genome space , including all the 
 twelve chromosomes .
progress can be viewed through the development of the 
 tpf and agp files , available from the sgn repository .
the tpf indicates the 
 expected relative positions of the bac and the agp provides assembly 
 information .
the best coverage is on chromosome 2 , where the sequencing of 141 bac 
 is finished .
large portions of chromosomes 4 ( with 77 bac already sequenced ) and 
 chromosome 8 ( with 91 bac already sequenced ) have also been sequenced . in all , 
 more than 800 bac are in different phases of sequencing , and sequences 
 belonging to more than 500 bac accounting for approximately 21% of total
bac have 
 already been submitted to the sgn website . assuming that work on the tomato genome project 
 will continue at the current pace , high - quality sequencing of the euchromatic 
 space
should be completed within the next one or two years ( by 2008 or 2009 ) . 
 since the euchromatic portion of the genome
is estimated to be approximately 
 220  mb , the average physical distance between two adjacent seed bac should be 
 as little as 200  kb
. however , the available map has insufficient density and resolution 
 to provide a template for complete sequencing , since there are large chromosome 
 regions , which are not yet targeted with markers .
therefore , in order to 
 complement the ongoing sequencing project , several new strategies have been undertaken . for 
 instance , selection of additional seed bac with different verification methods 
 ( e.g. , il mapping , fish , etc . ) has been proposed .
the recent release of markers 
 from syngenta to the sgn repository also allowed the identification of new 
 candidate seed bac , which are distributed throughout the full genome .
this may prove 
 useful for filling in gene spaces at a later stage of the project .
whole genome 
 shotgun sequencing and the availability of new generation sequencing 
 technologies , including 454/roche s sequencer flx , solexa s sequencing system , 
 and abi s solid , may also prove useful in completing the whole genome 
 sequencing of the tomato genome .
in order to understand 
 the function of specific genes and their role in metabolic pathways , as also to 
 identify the key steps in their coregulation mechanisms , several approaches 
 have been exploited , including mutagenesis , genetic transformation , and 
 transcriptome analysis .
indeed , together with barley , arabidopsis , and maize , tomato was the focus of early , extensive 
 mutagenesis programs . in a paper published in 1964 , hans stubbe reviewed over 
 250 tomato mutants   arising from the seminal work of the gatersleben group . 
 to date , over 600 characterized monogenic mutations are available in a variety 
 of genetic backgrounds at the tomato genetics resource center 
 ( http://tgrc.ucdavis.edu ) .
more recently , 
 an extensive mutant population consisting of 6000 ems - induced and 7000 fast neutron - induced 
 mutant lines has been obtained ( 54 ) . this population is probably saturating . 

for instance , extensive allelic tests confirmed that all the wiry mutants with 3 to 7 alleles present 
 in tgrc are represented in the population .
two new wiry loci have also been described in the collection , each with 10 
 alleles .
insertional mutagenesis systems 
 exploiting exogenous transposon systems have also been described in tomato [ 5557 ] .
nevertheless , these systems , some of which utilize the micro - tom 
 cultivar , have not yielded saturating mutant collections and have thus not been 
 utilized extensively .
highly efficient protocols for transformation of 
 micro - tom have been described , which may serve as a tool for extensive 
 t - dna mutagenesis programs also .
in addition to the above , 
 a more recent strategy called targeting induced local lesions in genomes ( tilling ) was described by 
 mccallum et al .   for targeting local mutations in the genome .
this is , a 
 pcr - based strategy that provides an allelic series of induced point mutations 
 in genes of interest . as such
, it can be applied to most organisms , even to 
 those for which an efficient transformation system is not available .
tilling 
 has been used for high - throughput isolation of mutants in arabidopsis   as 
 well as in several crop plants .
tilling platforms for tomato are under 
 development in several countries , including the us , france , italy , and india . 

the franco - italian effort is coordinated by the eu - sol project 
 ( http://www.eu-sol.net ) . 
  
strategies for gene 
 silencing have also been widely used as a tool for functional genomics research 
 in tomato .
indeed , tomato fruit ripening was one of the early systems in which 
 both sense and antisense silencing were found to be effective [ 62 , 63 ] . more 
 recently , rna interference ( rnai ) and virus - induced gene silencing ( vigs ) have also 
 been successfully used as functional genomics tools in tomato .
interestingly , the use of rnai remains 
 confined in the fruit , thus making 
 the fruit - specific silencing of genes possible .
similarly , vigs has been 
 described in tomato roots   and fruits   although the extent to which 
 silencing remains confined to these organs has not been extensively investigated .
several 
 viral vectors have been used , including tobacco rattle virus ( trv ) , tomato 
 yellow leaf curl china virus isolate , and potato virus x . of these
, trv displays the widest host range , allowing silencing in several solanum species , as well as in non - solanaceous species like opium poppy   and arabidopsis .
transient expression of 
 exogenous genes has also been achieved through several transient transformation 
 techniques , such as particle bombardment or agroinfiltration .
recently , an 
 agroinjection technique was developed for tomato fruits , which allow the 
 functional analysis of several genes in fruits in a short time .
this technique 
 has been used both for expression of exogenous genes and for trv - induced gene 
 silencing .
finally , transcriptional 
 profiling is being widely explored since the extensive est collection available 
 in tomato   has allowed designing of several microarray platforms : the most 
 widely used to date has been tom1 , a cdna - based microarray containing probes 
 for approximately 8000 independent genes ; and tom2 , a long oligonucleotide - based microarray 
 containing probes for approximately 11000 independent genes .
both these microarrays 
 are already available from bti 
 ( http://bti.cornell.edu/cgep/cgep.html ) 
 and soon tom2 will also be available from the eu - sol project 

 ( http://www.eu-sol.net ) .
the third array 
 is an affymetrix genechip , which contains 
 probe sets for approximately 9000 independent genes 

 ( http://www.affymetrix.com/products/arrays/specific/tomato.affx ) . 

as the tomato genome project progresses , a comprehensive , public tomato microarray 
 platform will become indispensable .
in order to address key questions 
 arising from the sol initiative , an overwhelming amount of data from 
 different  omics  approaches is being generated and can be utilized 
 for genomics research .
therefore , bioinformatics approaches assume major 
 importance in order to convert raw data into biologically meaningful 
 information . the sol network is planning a bioinformatics infrastructure that 
 should support integration of information from solanaceae research into a 
  one - stop shop  on the web .
this will ultimately allow solanaceae biology to be 
 approached from a systems biology perspective .
the bioinformatics centers in 
 the sol network are all involved in building this infrastructure .
it will rely 
 on web service approaches   to implement a virtual online center of 
 information dedicated to solanaceae .
the preliminary effort 
 of the bioinformatician in the sol network is mainly focussed on setting up a 
 distributed annotation pipeline to provide a high - quality , information - enriched 
 tomato genome . for this purpose ,
the international tomato annotation group ( itag ) 
 has been constituted , which is a collaborative effort in annotating the tomato 
 genome .
these groups 
 of scientists are organizing data and sharing methodologies to provide a 
 reliable tomato genome annotation .
the itag annotation pipeline 

 ( http://www.sgn.cornell.edu/sequencing/itag/status_html.pl ) 
 is currently being 
 developed through work on batches of sequences , which are generated at the sgn 
 by grouping bac which are being submitted by each sequencing center .
analyses , 
 such as repeat masking , est alignment and gene predictions , are performed on 
 the bac .
these data are fed into the eugene combiner software   for homology 
 searches using protein or genomic sequences from other species .
the resulting 
 predicted genes are then functionally annotated based on homology searches , protein 
 domain identifications , and gene ontology assignments .
each consortium member 
 takes on different tasks according to a predefined job distribution and in 
 accordance with its specific expertise .
the preliminary effort 
 of a genome annotation exercise requires a definition of reliable gene models 
 from tomato to support the training of gene predictors .
the definition of a 
 tomato - specific set of reference gene models is a necessary step towards 
 reliable predictions and a preliminary task of the itag .
est / cdna sequences can 
 be fully exploited if they are first clustered and assembled into high - quality 
 consensus and are then properly aligned against genomic sequences .
the 
 organization of tomato and other solanaceae est collections is a prerequisite 
 to provide a preliminary annotation of the tomato genome , which is supported by 
 experimental evidence .
several 
 specific est repositories from s. 
 lycopersicum are available worldwide ( table 1 ) .
the tigr tomato gene index ( legi ) is a collection of virtual 
 tentative consensus ( tc ) sequences constructed by clustering and assembling 
 213,974 ests and 2,043 ets ( release 11 ) generated in several 
 laboratories , including the tigr institute , cornell university , and the boyce 
 thompson institute.the sol 
 genomics network ( sgn ) , a website dedicated to the biology of 
 the solanaceae , organizes and distributes ests ( ~239,593 ) , sequenced from 35 
 different cdna libraries from s. 
 lycopersicum ( 32 ) , s. pennellii ( 2 ) , s. habrochaites ( 1 ) , and the 
 corresponding  combined  consensus sequences .
other est resources are as follows : ( i ) the tomato stress est database ( tsed ) , which contains ests from more 
 than ten stress - treated substractive cdna libraries from s. lycopersicum ; ( ii ) the 
 micro - tom database ( mibase ) 
 , which distributes unigenes obtained by assembling 35,824 micro - tom ( a 
 miniature and dwarf tomato cultivar ) ests from full - length cdna libraries and 
 150,581 ests from other tomato lines ; ( iii ) the plantgdb , which collects 
 plantgdb - assembled unique transcripts ( put ) from many different species 
 including those of s. lycopersicum generated 
 from est sequences available at the ncbi dbest database .
cab - developed tomatest , a secondary database of est / cdna sequences , 
 today contains 112 libraries from all the tomato 
 species available at dbest .
tomatest has been designed to provide a workbench for mining the 
 complexity of est sequences information content from multiple tomato species . 

this will then allow expression pattern analysis and gene discovery in the 
 framework of the s. lycopersicum genome project .
the cab group within the eu - sol project ( http://www.eu-sol.net ) is committed to 
 collect all est data from solanaceae species available in dbest ( table 1 ) and 
 to provide est alignments to the tomato genome draft sequences under production .
also ests from two species of the coffea genus ( rubiaceae ) were considered in the cab collection , since coffee and tomato share common gene repertoires .
a specific tool has been designed to remove the overrepresented est sequences from each of the 16 species collections in order to clip the original datasets and produce nonredundant 
 sets of sequences .
these est collections are independently processed by the parpest pipeline   to generate tentative consensus sequences ( tcs ) .
the definition of gene models based on est / cdna data is a complex effort .
proposed a methodology based on the analysis of spliced alignments of est and tentative consensus sequences to automatically define a reliable dataset of gene models in tomato .
suitable methodologies are used for est clustering and assembling , and for est / tc to genome mapping ; and resulting conflicts and ambiguities are independently 
 classified . in the current update of the tomato genome , 582 tcs of s. lycopersicum have been selected as they are consistently supported by est evidence . among these 
 tcs , 70 cover at least 95% of the length of the most similar protein sequence ; 
 168 cover at least 50% ; 257 cover less than 50% of the matching protein , and 
 the remaining 87 show no significant similarity to known proteins .
considering tcs from other tomato 
 species among those mapping to the s. lycopersicum bac , additional 21 loci 
 are located .
the number accordingly increases to 251 loci if the potato tc sequences are also considered . only the tcs covering 95% of the length of the matching protein
they account for a total of 108 gene models . in order to contribute to the tomato genome annotation and to accomplish the requirements 
 of an efficient data integration , the cab group developed isol@ ( chiusano et al .
this effort is conceived to support the analysis of the 
 genome organization and its functionality in the light of evolutionary 
 approaches over the entire solanaceae family .
isol@ is currently organized into two main levels : the genome level and the expression level .
the founding elements of the expression level are the solanaceae est collections and the oligonucleotide probe sets , which have been 
 generated for the production of the tomato expression microarrays 
 ( http://www.affymetrix.com/products/arrays/specific/tomato.affx ) .
a nonstop crosstalk between the levels is based on data source sharing and on integration of the information , which belongs to the respective under parts
. 
 each level can be independently accessed through specific web interfaces which allow user - driven data investigation ( http://biosrv.cab.unina.it/isola/isola.html ) . in order to provide a preliminary annotation of the bac sequences while waiting for the whole genome annotation
that will be 
 provided by the itag , the cab group has set up an automated annotation pipeline in order to ensure daily retrieval of new s. 
 lycopersicum bac sequences from genbank , which are used to feed the genome annotation process .
the bac annotation 
 process aims at identifying genes and other genetic elements on the draft genome sequence . the protein coding 
gene finding  process is exclusively based on spliced - alignments of expressed sequence tags ( ests ) to 
 the s. lycopersicum genomic sequences that are also provided to the distributed pipeline , which was set up within the itag effort .
to accomplish this task , ests from the different plant source collection at cab ( solanaceae 
 and rubiaceae species ) , and the corresponding tcs , created by assembling ests in a cluster , are both used .
noncoding rnas ( ncrnas ) from the rfam collection   are also aligned to the genomic sequences .
the tigr solanaceae repeats database   is the resource selected for the identification of repetitive sequences in the s. lycopersicum genome .
the italian platform also includes 
 alignments of all the rna sequences from arabidopsis to the tomato genomic sequences in order to identify genes that are conserved between the two species .
the collection , as of july 2007 , comprises 186 bac 
 sequences which have been uploaded from all the sequencing centers to the 
 genbank database .
the bac sequences collected and annotated are released to the scientific 
 community through the gbrowse   web application at cab 
 ( http://biosrv.cab.unina.it/gbrowse ) .
tracks showing annotations and other 
 features are displayed and cross - linked with other local or external databases 
 which can be explored through web interfaces .
this above effort aims at 
 producing a computational workbench for the analysis of the organization , the 
 functionality , and the evolution of genomes in the solanaceae family . in 
 addition , it provides experimental biologists with a preliminary annotation of 
 tomato genome data , and represents a reference point while sequencing the 
 tomato genome . indeed , the 
 crosstalk between the sequencing data and the computationally defined tcs may 
 support bac extension   and a 
 preliminary evaluation of the gene content of each bac under sequencing .
in the  -omics  age , strategies for 
 integrated genomics that include dna sequence mining , expression profiling 
 data , and functional and molecular diversity analyses of candidate genes , 
 combined with the use of introgression lines , can increase the efficiency in 
 discovery , candidate gene identification , and cloning of target qtls . 
 given the large amount of data that is being generated and will be generated in 
 future ,
a current bioinformatics challenge is to develop user - friendly 
 bioinformatics management systems that will allow description of the genetic 
 components of subtle qtls and their integration with genome information including 
 gene content , expression , and function .
the development of tomato into a 
 model solanaceous plant , with a large collection of genetic and genomic tools 
 and a high - quality reference genome sequence , and the high throughput 
 sequencing of 100 additional solanaceae genomes ( sol-100 project ) will 
 facilitate the understanding of the incredible ecological and morphological 
 adaptation exhibited by the solanaceae family .
 tomato ( solanum lycopersicum l. ) is the most intensively investigated solanaceous species both in genetic and genomics studies . 
 it is a diploid species with a haploid set of 12 chromosomes and a small genome ( 950  mb ) . 
 based on the detailed knowledge on tomato structural genomics , the sequencing of the euchromatic regions started in the year 2005 as a common effort of different countries . 
 
 the manuscript focuses on markers used for tomato , on mapping efforts mainly based on exploitation of natural biodiversity , and it gives an updated report on the international sequencing activities . 
 the principal tools developed to explore the function of tomato genes are also summarized , including mutagenesis , genetic transformation , and transcriptome analysis . 
 the current progress in bioinformatic strategies available to manage the overwhelming amount of data generated from different tomato  omics  
 approaches is reported , and emphasis is given to the effort of producing a computational workbench for the analysis of the organization , as well as the functionality and evolution of the solanaceae family . 
 
1. INTRODUCTION
2. STRUCTURAL GENOMICS
3. STRATEGIES FOR TOMATOGENOME SEQUENCING
4. FUNCTIONAL GENOMICS
5. BIOINFORMATICS
6. PERSPECTIVES