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.     

Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom

Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu ) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom.Key Words: Expressed sequence tag, full-length cDNA, genome sequence, mutant resource, Micro-Tom, JSOL, Solanum lycopersicum, tomato.     

Molecular identification of the economically important Solanum subgenus Leptostemonum (Solanaceae) using DNA barcodes

Journal of Plant Biochemistry and Biotechnology - Solanum is the largest and most diverse genus of the Solanaceae family. The genus includes around 1,400 species, and almost a third belong to...     

Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae

The Solanaceae contains many species of agricultural importance. Several of these are cultivated for their fruits, such as the tomato, the pepper and the aubergine. The family is very diverse in fruit type with capsules, drupes, pyrenes, berries, and several sorts of dehiscent non-capsular fruits occurring in the 90+ genera. In this paper, recent work on fruit type evolution in angiosperms is reviewed in relation to dispersal agents and habitat ecology. Defining fruit types in the Solanaceae in a simple five state system, then mapping them onto a previously published molecular phylogeny based on chloroplast DNA allows discussion of the evolution of these fruit types in a phylogenetic framework. Capsules are plesiomorphic in the family, and although berries are a synapomorphy (shared derived character) for a large clade including the genus Solanum (tomatoes and aubergines), they have arisen several times in the family as a whole. Problems with homology of drupes and pyrenes are discussed, and areas for future investigation of fruit structure homology identified. The distribution of fruit types in the large and diverse genus Solanum is also discussed in the light of monophyletic groups identified using chloroplast gene sequences. This variety is related to recent advances in the understanding of the molecular biology of fruit development. Finally, several key areas of future comparative, phylogenetic investigation into fruit type evolution in the family are highlighted.     

Different aggregation approaches in the chironomid community and the threshold of acceptable information loss

Due to the problem of identification, Chironomidae larvae, although very abundant, are often avoided or not properly used in bioassessment programs. The aim of this work was to test how different aggregation processes—taxonomic resolution and the random aggregation approach (best practicable aggregation of species—BestAgg) affect the analysis of chironomid communities regarding any information loss. The self-organizing map method, together with classification strength analysis and Spearman’s rank correlation, revealed that the genus-level and BestAgg-abundance matrix most accurately approximated the species-level community pattern. The subfamily-level dataset was ineffective at presenting the chironomid community structure, with a substantially lower concordance with the species-level dataset. The biologic environmental gradients analyses presented the same set of important environmental variables for the species-level, genus-level, and BestAgg-abundance matrix. The indicator values analysis showed that indicator genera provide information very close to that gained from species indicators. According to our results, the numeric relationship between species and higher taxa influences taxonomic scaling, limiting Chironomidae family aggregation, with acceptable information loss only up to genus level. In addition, the BestAgg approach, with the maximum level of aggregation, properly assesses the community structure and consequently describes environmental conditions.     

Analysis of unigene derived microsatellite markers in family solanaceae

The family Solanaceae is the source of several economically important plants. The aim of this study was to trace and characterize simple sequence repeat (SSR) markers from unigene sequences of Solanum lycopersicum, an important member of family Solanaceae. 18,228 unigene sequences of Solanum lycopersicum was taken in order to develop SSR markers and analyzed for the in-silico design of PCR primers. A total of 12,090 (66.32 %) unigenes containing 17,524 SSRs (microsatellites) were identified. The average frequency of microsatellites in unigenes was one in every 1.3 kb of sequence. The analysis revealed that trinucleotide motifs, coding for Glutamic acid (GAA) and AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking sequences of the SSRs generated 877 primers with forward and reverse strands. Functional categorization of SSRs containing unigenes was done through gene ontology terms like Biological process, Cellular component and Molecular function.     

Two new species of Acizzia Crawford (Hemiptera: Psyllidae) from the Solanaceae with a potential new economic pest of eggplant, Solanum melongena

Two new species of Acizzia Heslop-Harrison (Hemiptera: Psyllidae) from the plant family Solanaceae in eastern Australia are described. Acizzia solanicola sp. n. can damage eggplant, Solanum melongena (Solanaceae), in commercial crops and gardens in eastern Australia. It is a new, potentially serious commercial pest species, of which the nymphs induce malformation of leaves, produce copious amounts of viscous waste and cause leaf wilting, premature leaf senescence and crop loss. These psyllids have a unique and characteristic method of disposing of honeydew and this is illustrated for the first time. Acizzia alternata sp. n. is recorded from the weed, wild tobacco bush, Solanum mauritianum , but appears to cause little damage. These comprise the first record of a pest psyllid on eggplant and the first record of Acizzia from the Solanaceae. The parasitoid, Psyllaephagus sp. (Hymenoptera: Encyrtidae), is recorded parasitising nymphs of A. solanicola sp. n., and is here proposed as a potential biological control agent against it.     

植物DNA条形码与生物多样性数据共享平台构建

DNA条形码基于较短的DNA序列实现物种的快速、准确鉴定, 不仅加快了全球生物物种的鉴定和分类步伐, 也为生物多样性的管理、保护和可持续利用提供了新思路和研究方法。植物DNA条形码标准数据库的不断完善, 将使植物多样性信息的快速获取成为可能; 将不同类型数据资源整合、共享和利用, 构建植物DNA条形码数据共享平台, 是满足公众对物种准确鉴定和快速认知的重要支撑。本文介绍了近年来植物DNA条形码的研究进展; 植物DNA条形码参考数据库的研发现状和存在的问题。结合上述问题, 围绕“大数据”时代背景, 对如何管理和使用好海量的植物信息, 如何构建数据共享平台提出了一些设想: (1)数据共享平台的元数据应尽可能翔实、丰富、准确和多关联; (2)数据标准应统一规范; (3)查询入口方便、迅速、多样, 易于管理, 便于实现更大程度的数据共享和全球化的合作交流。     

Evolutionary meta-analysis of solanaceous resistance gene and solanum resistance gene analog sequences and a practical framework for cross-species comparisons

Cross-species comparative genomics approaches have been employed to map and clone many important disease resistance (R) genes from Solanum species-especially wild relatives of potato and tomato. These efforts will increase with the recent release of potato genome sequence and the impending release of tomato genome sequence. Most R genes belong to the prominent nucleotide binding site-leucine rich repeat (NBS-LRR) class and conserved NBS-LRR protein motifs enable survey of the R gene space of a plant genome by generation of resistance gene analogs (RGA), polymerase chain reaction fragments derived from R genes. We generated a collection of 97 RGA from the disease-resistant wild potato S. bulbocastanum, complementing smaller collections from other Solanum species. To further comparative genomics approaches, we combined all known Solanum RGA and cloned solanaceous NBS-LRR gene sequences, nearly 800 sequences in total, into a single meta-analysis. We defined R gene diversity bins that reflect both evolutionary relationships and DNA cross-hybridization results. The resulting framework is amendable and expandable, providing the research community with a common vocabulary for present and future study of R gene lineages. Through a series of sequence and hybridization experiments, we demonstrate that all tested R gene lineages are of ancient origin, are shared between Solanum species, and can be successfully accessed via comparative genomics approaches.     

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.     

Multivariate analyses of morphological characters of Leptolaena Thouars s.l. subgenera Mediusella and Xerochlamys (Sarcolaenaceae)

Leptolaena Thouars is one of the first described genera within Sarcolaenaceae, but represents the last great species-level taxonomic challenge in this endemic Malagasy plant family. As currently circumscribed, this genus comprises three subgenera, two of which, Mediusella Cavaco and Xerochlamys (Baker) Cavaco, exhibit patterns of morphological variation that have been understood differently and have led to an unstable taxonomy, such that a consensus on the delimitation of species has yet to be reached. Principal component analysis of morphological characters was performed on 211 herbarium specimens in order to evaluate the morphological variation within the two subgenera and to clarify historically problematical species boundaries. The results showed that ten entities could be distinguished on the basis of vegetative, floral, and fruit characters, and that they provide a robust basis for proposing a new species-level taxonomic framework.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 559–574.     

Nitrogen-containing compounds from Solanum lyratum Thunb

The medicinal plant Solanum lyratum Thunb（Solanaceae）is distributed widely in China. The present phytochemical investigation on S. lyratum led to the isolation of ten known Nitrogen-containing compounds. Compounds 1, 2, 3, 6, 9 were isolated for the first time from this plant and compounds 8,10 were obtained for the first time from Solanum. Compound 10 was isolated from Solanaceae family and obtained outside from Loganiaceae family for the first time. This has important chemotaxonomic significance on solanaceae.     

Chasing the dream: plant EST microarrays

DNA microarray technology is poised to make an important contribution to the field of plant biology. Stimulated by recent funding programs, expressed sequence tag sequencing and microarray production either has begun or is being contemplated for most economically important plant species. Although the DNA microarray technology is still being refined, the basic methods are well established. The real challenges lie in data analysis and data management. To fully realize the value of this technology, centralized databases that are capable of storing microarray expression data and managing information from a variety of sources will be needed. These information resources are under development and will help usher in a new era in plant functional genomics.     

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]     

Screening of non-tuber bearing Solanaceae for resistance to and induction of juvenile hatch of potato cyst nematodes and their potential for trap cropping

Ninety accessions of non‐tuber bearing Solanaceae were screened for (i) resistance to and (ii) stimulatory effect on juvenile hatch of potato cyst nematodes, and (iii) their growth under temperate climatic conditions. All plant species belonging to the genus Solanum tested induced hatching but this effect was most pronounced for plant species of the Solanum nigrum complex. Hatching of juveniles was hardly or not stimulated by other plant genera of the Solanaceae. Solanum sisymbriifolium combined a high hatching effect with complete resistance to both Globodera rosiochiensis and G pallida. Two S. nigrum varieties showed full resistance to G rostochiensis and a high level of resistance to G pallida. Moreover, S. sisymbriifolium and the two varieties of S. nigrum performed very well under Dutch field conditions and, therefore, they are suggested as candidate trap crops for the control of potato cyst nematodes.     

Unilateral incompatibility in Capsicum (Solanaceae): occurrence and taxonomic distribution

BACKGROUND AND AIMS: Unilateral incompatibility (UI) occurs when pollinations between species are successful in one direction but not in the other. Self-incompatible (SI) species frequently show UI with genetically related, self-compatible (SC) species, as pollen of SI species is compatible on the SC pistil, but not vice versa. Many examples of unilateral incompatibility, and all those which have been studied most intensively, are found in the Solanaceae, particularly Lycopersicon, Solanum, Nicotiana and Petunia. The genus Capsicum is evolutionarily somewhat distant from Lycopersicon and Solanum and even further removed from Nicotiana and Petunia. Unilateral incompatibility has also been reported in Capsicum; however, this is the first comprehensive study of crosses between all readily available species in the genus. METHODS: All readily available (wild and domesticated) species in the genus are used as plant material, including the three genera from the Capsicum pubescens complex plus eight other species. Pollinations were made on pot-grown plants in a glasshouse. The number of pistils pollinated per cross varied (from five to 40 pistils per plant), depending on the numbers of flowers available. Pistils were collected 24 h after pollination and fixed for 3-24 h. After staining, pistils were mounted in a drop of stain, squashed gently under a cover slip and examined microscopically under ultra-violet light for pollen tube growth. KEY RESULTS: Unilateral incompatibility is confirmed in the C. pubescens complex. Its direction conforms to that predominant in the Solanaceae and other families, i.e. pistils of self-incompatible species, or self-compatible taxa closely related to self-incompatible species, inhibit pollen tubes of self-compatible species. CONCLUSIONS: Unilateral incompatibility in Capsicum does not seem to have arisen to prevent introgression of self-compatibility into self-incompatible taxa, but as a by-product of divergence of the C. pubescens complex from the remainder of the genus.     

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。