The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL)

The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, The Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the ‘International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation’. The goal of this grassroots initiative, launched in November 2003, is to establish a network of information, resources and scientists to ultimately tackle two of the most significant questions in plant biology and agriculture: (1) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (2) How can a deeper understanding of the genetic basis of plant diversity be harnessed to better meet the needs of society in an environmentally friendly and sustainable manner? The Solanaceae and closely related species such as coffee, which are included in the scope of the SOL project, are ideally suited to address both of these questions. The first step of the SOL project is to use an ordered BAC approach to generate a high quality sequence for the euchromatic portions of the tomato as a reference for the Solanaceae. Due to the high level of macro and micro-synteny in the Solanaceae the BAC-by-BAC tomato sequence will form the framework for shotgun sequencing of other species. The starting point for sequencing the genome is BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers from the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These seed BACs will be used as anchors from which to radiate the tiling path using BAC end sequence data. Annotation will be performed according to SOL project guidelines. All the information generated under the SOL umbrella will be made available in a comprehensive website. The information will be interlinked with the ultimate goal that the comparative biology of the Solanaceae—and beyond—achieves a context that will facilitate a systems biology approach.     

The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond

The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond.     

Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits

With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition.Tomato (Solanum species) fruits constitute one of the most important sources of minerals, vitamins, fibers, and antioxidants in the human diet. Genomic approaches focused on determining the genetic basis of pathway regulation underlying quantitative variation in the production of these nutrients will likely provide information to facilitate the identification of cardinal genes. The cumulative body of data concerning developmental and metabolic shifts coupled with those recently acquired using postgenomic tools has prompted the adoption of this species as a model system for plants bearing fleshy fruits (Mueller et al., 2005). Such a model is required, because although many of these processes might be shared by many different plant species, this should not be straightly assumed, since remarkable metabolic differences have been observed even between closely related species (Fernie and Willmitzer, 2001).The facts that the domesticated species Solanum lycopersicum can be crossed with a number of its wild relatives and that these species have shown tremendous variation in metabolite content both in leaves and fruits (Schauer et al., 2006) render wild germplasm as an important source for metabolic gene discovery (Zamir, 2001). For this reason, extensive germplasm collections, including numerous natural and induced mutants and interspecific populations, have been made publicly available by the Tomato Genetics Resource Center (http://tgrc.ucdavis.edu/). An example of this is the collection of 76 introgression lines (ILs; Eshed and Zamir, 1995) comprising single overlapping introgressions of the Solanum pennellii (accession no. LA716) genome within the S. lycopersicum genome (cv M82). These lines are an excellent source of the stable genetic variation used worldwide by different researchers to map 2,795 quantitative trait loci (QTLs) to date, including those affecting plant biomass, yield, drought tolerance, morphology, gene expression, and metabolism (Lippman et al., 2007). The success of the S. pennellii ILs in establishing new principles for plant breeding and for resolving the molecular basis of complex traits has been demonstrated by the cloning of the first QTLs in this species: FW2.2 (a fruit size gene; Frary et al., 2000) and Brix9-2-5 (a sugar yield gene; Fridman et al., 2000, 2004). The broad phenotypic diversity inherent in this population alongside its simple mapping framework has also led to the identification of heterotic QTLs for biomass production, a major step toward isolating heterosis genes (Lippman et al., 2007). A clone-based physical map of S. pennellii, however, is necessary to fully exploit this population and to produce a unique resource for Solanaceae genomics. Such a map would also provide previous information for comparative analyses, map-based cloning, and validation of the sequence assemblies of the tomato whole genome (Solanaceae Genome Network [SGN]; www.sgn.cornell.edu).The aim of our current research was to perform a large-scale comparative genome analysis of the S. pennellii wild tomato and S. lycopersicum. Five genomic regions (BINs) comprising more than 100 recently identified QTLs associated with fruit carbon primary metabolism (Schauer et al., 2006, 2008) were chosen. These QTLs include fruit color (Liu et al., 2003), volatile content (Tieman et al., 2006), and yield traits linked to metabolite variations found in the fruits (Eshed and Zamir, 1995; Schauer et al., 2006; Semel et al., 2006). The physical map, built by anchoring 374 clones from bacterial artificial chromosome (BAC) and cosmid S. pennellii genomic libraries to the tomato genetic map, revealed a consistent pattern of coaligning regions, thus suggesting that the two genomes can largely be considered as colinear. Targeted sequencing of 1,238,705 bp allowed the annotation of 407 genes and uncovered a high degree of microsynteny between the two species. To a lesser extent, microsynteny was also observed with the Arabidopsis genome. However, this colinearity was somewhat perturbed by differential transposable element (TE) insertion patterns, different intergenic region lengths, and extensive single nucleotide polymorphism (SNP) and insertion-deletion (InDel) polymorphism. The time of divergence between species was estimated to be 2.7 million years ago (MYA). Furthermore, the large data set presented here would constitute a useful tool for QTL fine-mapping and relatively easy screening of target clones in map-based cloning approaches.     

High-Throughput Genomics Enhances Tomato Breeding Efficiency

Tomato (Solanum lycopersicum) is considered a model plant species for a group of economically important crops, such as potato, pepper, eggplant, since it exhibits a reduced genomic size (950 Mb), a short generation time, and routine transformation technologies. Moreover, it shares with the other Solanaceous plants the same haploid chromosome number and a high level of conserved genomic organization. Finally, many genomic and genetic resources are actually available for tomato, and the sequencing of its genome is in progress. These features make tomato an ideal species for theoretical studies and practical applications in the genomics field. The present review describes how structural genomics assist the selection of new varieties resistant to pathogens that cause damage to this crop. Many molecular markers highly linked to resistance genes and cloned resistance genes are available and could be used for a high-throughput screening of multiresistant varieties. Moreover, a new genomics-assisted breeding approach for improving fruit quality is presented and discussed. It relies on the identification of genetic mechanisms controlling the trait of interest through functional genomics tools. Following this approach, polymorphisms in major gene sequences responsible for variability in the expression of the trait under study are then exploited for tracking simultaneously favourable allele combinations in breeding programs using high-throughput genomic technologies. This aims at pyramiding in the genetic background of commercial cultivars alleles that increase their performances. In conclusion, tomato breeding strategies supported by advanced technologies are expected to target increased productivity and lower costs of improved genotypes even for complex traits.Key Words: Solanum lycopersicum, genetic and genomic resources, molecular markers, microarray, resistance to pathogens, fruit quality.     

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Tomato (Solanum lycopersicum) and coffee (Coffea canephora) belong to the sister families Solanaceae and Rubiaceae, respectively. We report herein the mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species. The mapped markers are well distributed across both genomes allowing the first syntenic comparison between species from these two families. The majority (75%) of the synteny blocks are short (<4 cM); however, some extend up to 50 cM. In an effort to further characterize the synteny between these two genomes, we took advantage of the available sequence for the tomato genome to show that tomato chromosome 7 is syntenic to half of the two coffee linkage groups E and F with the putative break point in tomato localized to the boundary of the heterochromatin and euchromatin on the long arm. In addition to the new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae, the comparative maps presented herein provide a translational tool by which coffee researchers may take benefit of DNA sequence and genetic information from tomato and vice versa. It is thus expected that these comparative genome information will help to facilitate and expedite genetic and genomic research in coffee.     

Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family‐specific impact on gene structure and genome organization

Short interspersed nuclear elements (SINEs) are highly abundant non‐autonomous retrotransposons that are widespread in plants. They are short in size, non‐coding, show high sequence diversity, and are therefore mostly not or not correctly annotated in plant genome sequences. Hence, comparative studies on genomic SINE populations are rare. To explore the structural organization and impact of SINEs, we comparatively investigated the genome sequences of the Solanaceae species potato (Solanum tuberosum), tomato (Solanum lycopersicum), wild tomato (Solanum pennellii), and two pepper cultivars (Capsicum annuum). Based on 8.5 Gbp sequence data, we annotated 82 983 SINE copies belonging to 10 families and subfamilies on a base pair level. Solanaceae SINEs are dispersed over all chromosomes with enrichments in distal regions. Depending on the genome assemblies and gene predictions, 30% of all SINE copies are associated with genes, particularly frequent in introns and untranslated regions (UTRs). The close association with genes is family specific. More than 10% of all genes annotated in the Solanaceae species investigated contain at least one SINE insertion, and we found genes harbouring up to 16 SINE copies. We demonstrate the involvement of SINEs in gene and genome evolution including the donation of splice sites, start and stop codons and exons to genes, enlargement of introns and UTRs, generation of tandem‐like duplications and transduction of adjacent sequence regions.     

Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes

Tomato, Solanum lycopersicum (formerly Lycopersicon esculentum), has long been one of the classical model species of plant genetics. More recently, solanaceous species have become a model of evolutionary genomics, with several EST projects and a tomato genome project having been initiated. As a first contribution toward deciphering the genetic information of tomato, we present here the complete sequence of the tomato chloroplast genome (plastome). The size of this circular genome is 155,461 base pairs (bp), with an average AT content of 62.14%. It contains 114 genes and conserved open reading frames (ycfs). Comparison with the previously sequenced plastid DNAs of Nicotiana tabacum and Atropa belladonna reveals patterns of plastid genome evolution in the Solanaceae family and identifies varying degrees of conservation of individual plastid genes. In addition, we discovered several new sites of RNA editing by cytidine-to-uridine conversion. A detailed comparison of editing patterns in the three solanaceous species highlights the dynamics of RNA editing site evolution in chloroplasts. To assess the level of intraspecific plastome variation in tomato, the plastome of a second tomato cultivar was sequenced. Comparison of the two genotypes (IPA-6, bred in South America, and Ailsa Craig, bred in Europe) revealed no nucleotide differences, suggesting that the plastomes of modern tomato cultivars display very little, if any, sequence variation. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Rüdiger Cerff]     

A community-based annotation framework for linking solanaceae genomes with phenomes

The amount of biological data available in the public domain is growing exponentially, and there is an increasing need for infrastructural and human resources to organize, store, and present the data in a proper context. Model organism databases (MODs) invest great efforts to functionally annotate genomes and phenomes by in-house curators. The SOL Genomics Network (SGN; http://www.sgn.cornell.edu) is a clade-oriented database (COD), which provides a more scalable and comparative framework for biological information. SGN has recently spearheaded a new approach by developing community annotation tools to expand its curational capacity. These tools effectively allow some curation to be delegated to qualified researchers, while, at the same time, preserving the in-house curators' full editorial control. Here we describe the background, features, implementation, results, and development road map of SGN's community annotation tools for curating genotypes and phenotypes. Since the inception of this project in late 2006, interest and participation from the Solanaceae research community has been strong and growing continuously to the extent that we plan to expand the framework to accommodate more plant taxa. All data, tools, and code developed at SGN are freely available to download and adapt.     

SNP Discovery and Linkage Map Construction in Cultivated Tomato

Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/.     

番茄生物学研究的相关网络资源

番茄(Solanum lycopersicum)是一种重要的蔬菜作物, 也是研究茄科作物的模式植物。互联网上有丰富的与番茄相关的生物信息学资源, 对其生物学研究带来极大便利。该文介绍了目前网络上与番茄生物学研究相关的资源, 利用这些资源将会加快对番茄遗传学和基因组学及对茄科植物多样性的研究。     

番茄生物学研究的相关网络资源

番茄（Solanum lycopersicum）是一种重要的蔬菜作物, 也是研究茄科作物的模式植物。互联网上有丰富的与番茄相关的生物信息学资源, 对其生物学研究带来极大便利。该文介绍了目前网络上与番茄生物学研究相关的资源, 利用这些资源将会加快对番茄遗传学和基因组学及对茄科植物多样性的研究。     

A snapshot of the Chinese SOL Project

In 2003, the International Solanaceae Project (SOL) was initiated by an international consortium of ten countries including Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States. The first major effort of the SOL aimed to produce a DNA sequence map for euchromatin regions of 12 chromosomes of tomato (Solanum lycopersicum) before 2010. Here we present an update on Chinese effort for sequencing the euchromatin region of chromosome 3.     

A novel tomato mutant,Solanum lycopersicum elongated fruit1 (Slelf1), exhibits an elongated fruit shape caused by increased cell layers in the proximal region of the ovary

Genes controlling fruit morphology offer important insights into patterns and mechanisms determining organ shape and size. In cultivated tomato (Solanum lycopersicum L.), a variety of fruit shapes are displayed, including round-, bell pepper-, pear-, and elongate-shaped forms. In this study, we characterized a tomato mutant possessing elongated fruit morphology by histologically analyzing its fruit structure and genetically analyzing and mapping the genetic locus. The mutant line, Solanum lycopersicum elongated fruit 1 (Slelf1), was selected in a previous study from an ethylmethane sulfonate-mutagenized population generated in the background of Micro-Tom, a dwarf and rapid-growth variety. Histological analysis of the Slelf1 mutant revealed dramatically increased elongation of ovary and fruit. Until 6 days before flowering, ovaries were round and they began to elongate afterward. We also determined pericarp thickness and the number of cell layers in three designated fruit regions. We found that mesocarp thickness, as well as the number of cell layers, was increased in the proximal region of immature green fruits, making this the key sector of fruit elongation. Using 262 F₂ individuals derived from a cross between Slelf1 and the cultivar Ailsa Craig, we constructed a genetic map, simple sequence repeat (SSR), cleaved amplified polymorphism sequence (CAPS), and derived CAPS (dCAPS) markers and mapped to the 12 tomato chromosomes. Genetic mapping placed the candidate gene locus within a 0.2?Mbp interval on the long arm of chromosome 8 and was likely different from previously known loci affecting fruit shape.     

Comparative genome analysis of Solanum lycopersicum and Solanum tuberosum

Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato.     

Effect of Gibberellin and Auxin on Parthenocarpic Fruit Growth Induction in the cv Micro-Tom of Tomato

The effect of applied gibberellin (GA) and auxin on fruit-set and growth has been investigated in tomato (Solanum lycopersicum L.) cv Micro-Tom. It was found that to prevent competition between developing fruits only one fruit per truss should be left on the plant. Unpollinated ovaries responded to GA₃ and to different auxins [indol-3-acetic acid, naphthaleneacetic acid, and 2,4-dichlorophenoxyacetic acid (2,4-D)], 2,4-D being the most efficient. GA₃- and 2,4-D-induced fruits had different internal morphology, with poor locular tissue development in the case of GA, and pseudoembryos development in the case of 2,4-D. Also, GA₃ produced larger cells in the internal region of the mesocarp (IM) associated with higher mean C values, whereas 2,4-D produced more cell layers in the pericarp than pollinated fruits. The smaller size of GA₃- compared with 2,4-D-induced fruits was due to them having fewer cells, only partially compensated by the larger size of IM cells. Simultaneous application of GA₃ and 2,4-D produced parthenocarpic fruits similar to pollinated fruits, but for the absence of seeds, suggesting that both kinds of hormones are involved in the induction of fruit development upon pollination. It is concluded that Micro-Tom constitutes a convenient model system, compared to tall cultivars, to investigate the hormonal regulation of fruit development in tomato.     

Use of Micro-Tom cultivar in a <Emphasis Type="Italic">Bemisia tabaci</Emphasis> biotype B interaction study

Tomatoes of the Micro-Tom cultivar, Solanum lycopersicum L. (Solanaceae), are small, have a short life cycle, high-density growth, high-efficiency protocols for genetic transformation, and hormonal and morphological mutants. These characteristics make this cultivar a good candidate as a helpful tool in resistance studies against the whitefly, Bemisia tabaci (Gennadius 1889) (Hemiptera: Aleyrodidae). The insect behavior in the Micro-Tom cultivar was observed through free-choice and no-choice oviposition preference tests and life cycle in lab conditions, having as reference the Santa Clara cultivar. In these tests, behavioral and biological insect parameters were obtained and the purpose was used to assess the trichome absence effect on oviposition with the hairless mutant. In the studies for oviposition preference, no difference was observed among the three material obtained. A nymphal stage prolongation and a low nymph viability with an adult longevity reduction were observed in relation to the Santa Clara in the Micro-Tom cultivar and hairless mutant. The Micro-Tom cultivar and hairless mutant do not present antixenotic effects to the oviposition. Mutation present in the hairless mutant does not alter the results observed in the ‘Micro-Tom.’ In general, the absence of the trichome did not reduce the Micro-Tom susceptibility to the oviposition. Antibiosis was observed in the Micro-Tom and it was discussed considering its association with salicylic and jasmonic acids, and brassinosteroid levels. These results show that this cultivar is a pest host and suitable for greenhouse and lab tests, in addition to being able to be used as a susceptibility standard for antixenosis.     

Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum

Recent studies have reported that decreased level of DNA cytosine methylation in the global genome was closely related to the initiation of tomato (Solanum lycopersicum) fruit ripening. However, genome-scale analysis of cytosine-5 DNA methyltransferases (C5-MTases) and demethylases in tomato has not been engaged. In this study, 7 C5-MTases and 3 demethylases were identified in tomato genome, which probably contributed to DNA cytosine methylation level in tomato. The 7 C5-MTases were categorized into 4 subgroups, and the 3 demethylases were classified into 2 subgroups based on phylogenetic analyses. Comprehensive analysis of their structure and genomic localization was also performed in this paper. According to online RNA-seq data, 4 S. lycopersicum C5-MTase (SlC5-MTase) genes (SlMET, SlDRM1L1, SlDRM5, SlMET3L) were expressed higher than others, and one DNA demethylase gene (SlDML) was significantly changed during tomato fruit development and ripening. Furthermore, all these five gene expressions at breaker (BK) stage changed with 1-methylcyclopropene (1-MCP) treatment, indicating that they were regulated by ethylene directly or indirectly in tomato fruit. In addition, subcellular localization analysis indicated that SlDRM1L1 and SlDRM5 located in the nucleus might have responsibility for RNA-directed DNA methylation (RdDM). Collectively, this paper provided a framework for gene discovery and functional characterization of C5-MTases and DNA demethylases in other Solanaceae species.