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

Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.

Hepatic steatosis is a multifactorial condition that is often observed in obese patients and is a prelude to non-alcoholic fatty liver disease. Here, we combine shotgun sequencing of fecal metagenomes with molecular phenomics (hepatic transcriptome and plasma and urine metabolomes) in two well-characterized cohorts of morbidly obese women recruited to the FLORINASH study. We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. Patients with steatosis have low microbial gene richness and increased genetic potential for the processing of dietary lipids and endotoxin biosynthesis (notably from Proteobacteria), hepatic inflammation and dysregulation of aromatic and branched-chain amino acid metabolism. We demonstrated that fecal microbiota transplants and chronic treatment with phenylacetic acid, a microbial product of aromatic amino acid metabolism, successfully trigger steatosis and branched-chain amino acid metabolism. Molecular phenomic signatures were predictive (area under the curve = 87%) and consistent with the gut microbiome having an effect on the steatosis phenome (>75% shared variation) and, therefore, actionable via microbiome-based therapies.

(2010) Identification of genes selectively disallowed in the pancreatic islet, Islets, 2:2, 89-95,

Previously, a complete genome analysis of Neisseria meningitidis strain MC58 revealed the largest repertoire of putative phase-variable genes described in any species to date. Initial comparisons with two incomplete Neisseria spp. genome sequences available at that time revealed differences in the repeats associated with these genes in the form of polymorphisms, the absence of the potentially unstable elements in some alleles, and in the repertoire of the genes that were present. Analyses of the complete genomes of N. meningitidis strain Z2491 and Neisseria gonorrhoeae strain FA1090 have been performed and are combined with a comprehensive comparative analysis between the three available complete genome sequences. This has increased the sensitivity of these searches and provided additional contextual information that facilitates the interpretation of the functional consequences of repeat instability. This analysis identified : (i) 68 phase-variable gene candidates in N. meningitidis strain Z2491, rather than the 27 previously reported ; (ii) 83 candidates in N. gonorrhoeae strain FA1090 ; and (iii) 82 candidates in N. meningitidis strain MC58, including an additional 19 identified through cross-comparisons with the other two strains. In addition to the 18 members of the opa gene family, a repertoire of 119 putative phase-variable genes is described, indicating a huge potential for diversification mediated by this mechanism of gene switching in these species that is central to their interactions with the host and environmental transitions. Eighty-two of these are either known (14) or strong (68) candidates for phase variation, which together with the opa genes make a total of 100 identified genes. The repertoires of the genes identified in this analysis diverge from the different species groupings, indicating horizontal exchange that significantly affects the species and strain complements of these genes.Keywords : phase variation, Neisseria gonorrhoeae, Neisseria meningitidis, repeat, genome analysis INTRODUCTIONThe pathogenic Neisseria spp. Neisseria meningitidis and Neisseria gonorrhoeae are causative agents of meningitis and septicaemia, and gonorrhoea respectively. These populations are characterized by genetic diversity at several levels. over time to the rest of the population (Bowler et al., 1994 ;Feil et al., 1995 ;Saunders et al., 1999). There is extensive allelic diversity in some genes, particularly those under antigenic selection pressures (Malorny et al., 1998). There are genes within a strain that undergo recombination between expressed and silent cassettes to generate diversity within clonal populations (Haas & Meyer, 1987). Finally, there are genes that are switched on and off by phase variation that can provide a large repertoire of phenotypes from within a clonal population, which can provide adaptation to changing environmental conditions (Sparling et al., 1986 ; Stern A. BUTCHER and N. J. SAUNDERS et al., 1986 ;Meyer & van Putten, 1989 ;Yang & Gotschlich, 1996 ;Saunders et al., 2000). In N...

The genome of tomato (Solanum lycopersicum L.) 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 the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high‐quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole‐genome shotgun techniques will be combined with the BAC‐by‐BAC approach to cover the entire tomato genome. The high‐quality reference euchromatic tomato sequence is expected to be near completion by 2010.

Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Twodimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to <1 min per protein by using the same technology. Finally, we show that absolute quantification of protein levels is relatively straightforward to achieve and discuss the potential of an all-optical high-throughput proteomic platform based on two-dimensional infrared spectroscopic measurements.2DIR ͉ amino acid ͉ bioinformatics ͉ vibrational T he potential of proteomic tools ranges from biomarker discovery and clinical diagnostics to the provision of data for systems biology and fundamental biological research (1-6). This broad range of applications is one of the drivers for the development of protein analysis tools with greater capability. Optical spectroscopies appear to have significant potential for protein analysis (7-9), but conventional approaches suffer from overcongested spectra, which makes feature assignment and quantification highly problematic. Multidimensional coherent infrared spectroscopic techniques, commonly referred to as twodimensional infrared (2DIR) spectroscopies, might be expected to be able to relieve the congestion of infrared spectra sufficiently to allow such assignment and quantification to take place. Indeed, we recently demonstrated how picosecond electronvibration-vibration (EVV) four-wave mixing experiments can decongest 2DIR spectra to an even greater extent (10, 11), and showed how such an EVV approach can be applied to the analysis of peptides (12). In this article we take the approach further to show that it can be used to differentiate and identify proteins and to measure absolute protein quantities. We also demonstrate that the sensitivity and throughput of our EVV 2DIR apparatus is sufficient for this method to be considered for use as a real proteomic tool.Although our previous work showed that it is possible to quantify relative amino acid levels for short peptides (12), there is always the possibility that primary, secondary, or tertiary structural effects would prevent such measurements on proteins.In this article we demonstrate that these structural sensitivities are not limiting factors either for differentiation/identification or for absolute quantification of protein levels.The key proposition of this article is that protein identification can be performed by using spectroscopically determined amino acid content, relative to an internal reference. Amino acid composition analysis is an approach that has been used to determine protein relatedness (13) and protein structural classes (14, 15). Although it is known that c...

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