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

Detection and phylogenetic identification of labeled prokaryotic cells on mineral surfaces using Scanning X-ray Microscopy

International audiencehe involvement of intraterrestrial microbes in geochemical cycles is now well recognized. However, owing to the small number of appropriate methods for probing these ecosystems, the exploration of their metabolic diversity, energy sources, and biogeochemical transformations remains limited. Here we demonstrate the ability of scanning X-ray microscopy using synchrotron radiation to localize and characterize the phylogenetic affiliation of individual prokaryotic cells on various mineral surfaces (e.g. carbonates, basaltic glass) when combined with a newly developed protocol based on fluorescence in situ hybridization coupled to ultra-small immunogold. The possibility to associate simultaneously the phylogenetic identification of microorganisms with the chemical and structural characteristics of associated mineral phases (i.e. inorganic substrate and biomineralizations), offers great interest for assessing the geochemical impact of subsurface microbial communities and unraveling microbe-mineral interactions in the deep biosphere

High-resolution imaging of sulfur oxidation states, trace elements, and organic molecules distribution in individual microfossils and contempo rary microbial filaments

International audienceOwing to the delicate nature of fossil microorganisms and inherent difficulties for discriminating true fossils from artifacts, an important challenge is to extract unequivocal biogenic information from individual microfossils using high-resolution, nondestructive and sensitive techniques. Here, we use combined synchrotron (X-ray microfluorescence, X-ray absorption near-edge structure and infrared microspectroscopies) and particle-induced X-ray emission analyses to image the spatial distribution at a μm-scale of a variety of potential biogenic markers (major and trace elements, C-H bonds, and sulfur-oxidation states) in individual prokaryotic microfossils. In particular, we analyzed iron-oxide fossil filaments of putative biogenic origin encapsulated with amorphous silica from a fragment of an inactive hydrothermal chimney of the East Pacific Rise. In order to test the biogenic origin of the markers studied, we performed the same analyses on filamentous bacteria corresponding most likely to the ɛ-Proteobacteria, and collected from substrates exposed to a hydrothermal fluid vent at the Mid-Atlantic Ridge. In both types of fossil and contemporary filaments, the occurrence of CH2 groups and of three sulfur species (sulfate, sulfite, organic S) showing heterogeneous distribution that underline the cytoplasm of individual cells in the case of the present-day filament, suggests that the original microorganisms were actively metabolizing sulfur. These results show the large potential of combining high-resolution synchrotron techniques to analyze individual microfossils for extracting unequivocal biogenic information. Furthermore, they also suggest that cooccurrence of different sulfur oxidation states within single microfossils could constitute a biogenic metabolic marker indicating S-metabolizing activities

A Snapshot of the Emerging Tomato Genome Sequence

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 \u201cInternational Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation\u201d 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 3c40,000, 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

The tomato genome sequence provides insights into fleshy fruit evolution

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 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 pimpinellifolium2, 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