Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness

BackgroundThe Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular cultivated species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. Here we investigate molecular divergence times for Solanaceae using a densely-sampled species-level phylogeny. We also review the fossil record of the family to derive robust calibration points, and estimate a chronogram using an uncorrelated relaxed molecular clock.ResultsOur densely-sampled phylogeny shows strong support for all previously identified clades of Solanaceae and strongly supported relationships between the major clades, particularly within Solanum. The Tomato clade is shown to be sister to section Petota, and the Regmandra clade is the first branching member of the Potato clade. The minimum age estimates for major splits within the family provided here correspond well with results from previous studies, indicating splits between tomato & potato around 8 Million years ago (Ma) with a 95% highest posterior density (HPD) 7–10 Ma, Solanum & Capsicum c. 19 Ma (95% HPD 17–21), and Solanum & Nicotiana c. 24 Ma (95% HPD 23–26).ConclusionsOur large time-calibrated phylogeny provides a significant step towards completing a fully sampled species-level phylogeny for Solanaceae, and provides age estimates for the whole family. The chronogram now includes 40% of known species and all but two monotypic genera, and is one of the best sampled angiosperm family phylogenies both in terms of taxon sampling and resolution published thus far. The increased resolution in the chronogram combined with the large increase in species sampling will provide much needed data for the examination of many biological questions using Solanaceae as a model system.

At that time the biosynthesis and mode of action of ethylene in fruit ripening had already been established, and advances in genetics were revealing links between genes and phenotypes, especially noteworthy was the map-based cloning of genes underlying tomato non-ripening loci such as ripening inhibitor (rin). Since then there have been substantial advances in our understanding of ripening in tomato and many other dry and fleshy fruits. This has been accelerated by the delivery of genome sequences for a wide range of plants including fleshy fruit bearing species and the development of systems biology approaches to understanding regulatory networks.The first paper in the 2002 issue was a seminal work by Sandy Knapp focused on fruit diversity in the Solanaceae and highlighting the phylogenetic relationships between dry and fleshy fruit forms (Knapp, 2002). The current volume describes the progress that has been made in understanding the mechanistic basis of fruit development and ripening and the conservation of regulatory networks controlling these processes, in both dry and fleshy forms across a wide range of taxa. Systems biology approaches have begun to reveal the complexity of the ripening process, while genome sequences have facilitated the identification of genes underlying quantitative trait loci (QTL) and the importance of epigenetics is beginning to become apparent.In the first paper in this special issue, Sofia Kourmpetli and Sinéad Drea from the University of Leicester in the UK review the regulatory networks involved in the development and maturation of two, at first sight, very different dry fruits, the poppy capsule and the cereal grain. They highlight the importance of MADS-box genes including FRUITFULL (FUL) and SHATTERPROOF (SHP), and set these events in the context of a phylogenetic framework. Cristina Ferrándiz and Chloé Fourquin from Instituto de Biología Molecular y Celular de Plantas in Valencia, Spain, then review the role of FUL and SHP in Arabidopsis and provide a comprehensive discussion of their role in many other species including Brassicas, legumes and also in fleshy fruits (Ferrándiz and Fourquin, 2014). Dehiscence in dry fruits and ripening, and even the extent of lignification in fleshy fruits, is linked to the complex relationship between FUL and SHP expression, and their review concludes that there are conserved roles of FUL and SHP in late fruit development both in fleshy and dry fruits. These ideas were hinted at in the 2002 Special Issue and strong supporting evidence is now presented consistent with dehiscence and ripening sharing a common origin and being parallel, rather than completely different processes. María Dolores Gómez and colleagues, also from Valencia, explore and develop for us further ideas about the similarities and differences between the mechanistic basis of 'ripening' and 'over-ripening' in dry and fleshy fruits including comparing the transcriptomes of senescent and ripening Arabidopsis siliques and tomato berries (Gómez et al., 2014).Molecular networks cont...

OBITUARY Heinrich Rohrer, pioneer of scanning tunnelling microscopy, remembered p.30 GENES US Supreme Court patent rulings set a higher bar for innovation p.29 ART Exhibition revels in the power of unconstrained thought p.28 SPACE An elegy for the disappearing dark, banished by science p.26 Feeding the future We must mine the biodiversity in seed banks to help to overcome food shortages, urge Susan McCouch and colleagues. The International Center for Tropical Agriculture in Colombia holds 65,000 crop samples from 141 countries.

Phylogenetic relationships in the genus Nicotiana were investigated using parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA). In addition, origins of some amphidiploid taxa in Nicotiana were investigated using the techniques of genomic in situ hybridization (GISH), and the results of both sets of analyses were used to evaluate previous hypotheses about the origins of these taxa. Phylogenetic analyses of the ITS nrDNA data were performed on the entire genus (66 of 77 naturally occurring species, plus three artificial hybrids), comprising both diploid and polyploid taxa, and on the diploid taxa only (35 species) to examine the effects of amphidiploids on estimates of relationships. All taxa, regardless of ploidy, produced clean, single copies of the ITS region, even though some taxa are hybrids. Results are compared with a published plastid (matK) phylogeny using fewer, but many of the same, taxa. The patterns of relationships in Nicotiana, as seen in both analyses, are largely congruent with each other and previous evolutionary ideas based on morphology and cytology, but some important differences are apparent. None of the currently recognized subgenera of Nicotiana is monophyletic and, although most of the currently recognized sections are coherent, others are clearly polyphyletic. Relying solely upon ITS nrDNA analysis to reveal phylogenetic patterns in a complex genus such as Nicotiana is insufficient, and it is clear that conventional analysis of single data sets, such as ITS, is likely to be misleading in at least some respects about evolutionary history. ITS sequences of natural and well-documented amphidiploids are similar or identical to one of their two parents-usually, but not always, the maternal parent-and are not in any sense themselves 'hybrid'. Knowing how ITS evolves in artificial amphidiploids gives insight into what ITS analysis might reveal about naturally occurring amphidiploids of unknown origin, and it is in this perspective that analysis of ITS sequences is highly informative.