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

The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana. The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases.

We develop a new method for estimating effective population sizes, N e , and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-D32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s ¼ 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is $0.43.

R-band intensity measurements along the light curve of Type Ia supernovae discovered by the Supernova Cosmology Project (SCP) are fitted in brightness to templates allowing a free parameter the time-axis width factor w ≡ s × (1 + 2 z). The data points are then individually aligned in the time-axis, normalized and K-corrected back to the rest frame, after which the nearly 1300 normalized intensity measurements are found to lie on a well-determined common rest-frame B-band curve which we call the "composite curve". The same procedure is applied to 18 low-redshift Calán/Tololo SNe with z < 0.11; these nearly 300 B-band photometry points are found to lie on the composite curve equally well. The SCP search technique produces several measurements before maximum light for each supernova. We demonstrate that the linear stretch factor, s, which parameterizes the light-curve timescale appears independent of z, and applies equally well to the declining and rising parts of the light curve. In fact, the B band template that best fits this composite curve fits the individual supernova photometry data when stretched by a factor s with χ 2 /DoF ≈ 1, thus as well as any parameterization can, given the current data sets. The measurement of the date of explosion, however, is model dependent and not tightly constrained by the current data. We also demonstrate the 1 + z light-curve time-axis broadening expected from cosmological expansion. This argues strongly against alternative explanations, such as tired light, for the redshift of distant objects.