Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

<p>Abstract</p> <p>Background</p> <p>The <it>Ralstonia solanacearum </it>species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, which have major socio-economic impacts. Pathogenicity is an ancestral trait in <it>R. solanacearum </it>and strains with high genetic variation can be subdivided into four phylotypes, correlating to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB), Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome sequences strains representative of this phylogenetic diversity can help determine which traits allow this bacterium to be such a pathogen of so many different plant species and how the bacteria survive in many different habitats.</p> <p>Results</p> <p>The genomes of three tomato bacterial wilt pathogens, CFBP2957 (phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were sequenced and manually annotated. These genomes were compared with those of three previously sequenced <it>R. solanacearum </it>strains: GMI1000 (tomato, phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The major genomic features (size, G+C content, number of genes) were conserved across all of the six sequenced strains. Despite relatively high genetic distances (calculated from average nucleotide identity) and many genomic rearrangements, more than 60% of the genes of the megaplasmid and 70% of those on the chromosome are syntenic. The three new genomic sequences revealed the presence of several previously unknown traits, probably acquired by horizontal transfers, within the genomes of <it>R. solanacearum</it>, including a type IV secretion system, a rhi-type anti-mitotic toxin and two small plasmids. Genes involved in virulence appear to be evolving at a faster rate than the genome as a whole.</p> <p>Conclusions</p> <p>Comparative analysis of genome sequences and gene content confirmed the differentiation of <it>R. solanacearum </it>species complex strains into four phylotypes. Genetic distances between strains, in conjunction with CGH analysis of a larger set of strains, revealed differences great enough to consider reclassification of the <it>R. solanacearum </it>species complex into three species. The data are still too fragmentary to link genomic classification and phenotypes, but these new genome sequences identify a pan-genome more representative of the diversity in the <it>R. solanancearum </it>species complex.</p

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

A utilisé MicroScope PlatformInternational audienceMicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest

The MUSE

We present the second data release of the MUSE Hubble Ultra-Deep Field surveys, which includes the deepest spectroscopic survey ever performed. The MUSE data, with their 3D content, amazing depth, wide spectral range, and excellent spatial and medium spectral resolution, are rich in information. Their location in the Hubble ultra-deep field area, which benefits from an exquisite collection of ancillary panchromatic information, is a major asset. This update of the first release incorporates a new 141-h adaptive-optics-assisted MUSE eXtremely Deep Field (MXDF; 1 arcmin diameter field of view) in addition to the reprocessed 10-h mosaic (3 × 3 arcmin2) and the single 31-h deep field (1 × 1 arcmin2). All three data sets were processed and analyzed homogeneously using advanced data reduction and analysis methods. The 3σ point-source flux limit of an unresolved emission line reaches 3.1 × 10−19 and 6.3 × 10−20 erg s−1 cm−2 at 10- and 141-h depths, respectively. We have securely identified and measured the redshift of 2221 sources, an increase of 41% compared to the first release. With the exception of eight stars, the collected sample consists of 25 nearby galaxies (z < 0.25), 677 [O I

The MUSE Hubble Ultra Deep Field surveys: Data release II

We present the second data release of the MUSE Hubble UDF surveys, which includes the deepest spectroscopic survey ever performed. The MUSE data, with their 3D content, amazing depth, wide spectral range, and excellent spatial and medium spectral resolution, are rich in information. This update of the first release incorporates a new 141-hour adaptive-optics-assisted MXDF field (1' diameter FoV) in addition to the reprocessed 10-hour mosaic (3'x3') and the single 31-hour deep field (1'x1'). We have securely identified and measured the redshift of 2221 sources, an increase of 41% compared to the first release. With the exception of 8 stars, the collected sample consists of 25 nearby galaxies (z 3, the difference is even more striking, with a factor of 65 increase (1308 vs 20). We compared the measured redshifts against three published photometric redshift catalogs and find the photo-z accuracy to be lower than the constraints provided by photo-z fitting codes. 80% of the galaxies have an HST counterpart. They are on average faint, with a median magnitude of 25.7 and 28.7 for the OII and Ly-alpha emitters, respectively. SED fits show that these galaxies tend to be low-mass star-forming galaxies, with a median stellar mass of 6.2 10**8 M and a median SFR of 0.4 M/yr. 20% of our catalog, or 424 galaxies, have no HST counterpart. The vast majority of these new sources are high EQW z>2.8 LAEs that are detected by MUSE thanks to their bright and asymmetric broad Ly-alpha line. We release advanced data products, specific software, and a web interface to select and download data sets

The MUSE Hubble Ultra Deep Field surveys: Data release II

We present the second data release of the MUSE Hubble UDF surveys, which includes the deepest spectroscopic survey ever performed. The MUSE data, with their 3D content, amazing depth, wide spectral range, and excellent spatial and medium spectral resolution, are rich in information. This update of the first release incorporates a new 141-hour adaptive-optics-assisted MXDF field (1' diameter FoV) in addition to the reprocessed 10-hour mosaic (3'x3') and the single 31-hour deep field (1'x1'). We have securely identified and measured the redshift of 2221 sources, an increase of 41% compared to the first release. With the exception of 8 stars, the collected sample consists of 25 nearby galaxies (z 3, the difference is even more striking, with a factor of 65 increase (1308 vs 20). We compared the measured redshifts against three published photometric redshift catalogs and find the photo-z accuracy to be lower than the constraints provided by photo-z fitting codes. 80% of the galaxies have an HST counterpart. They are on average faint, with a median magnitude of 25.7 and 28.7 for the OII and Ly-alpha emitters, respectively. SED fits show that these galaxies tend to be low-mass star-forming galaxies, with a median stellar mass of 6.2 10**8 M and a median SFR of 0.4 M/yr. 20% of our catalog, or 424 galaxies, have no HST counterpart. The vast majority of these new sources are high EQW z>2.8 LAEs that are detected by MUSE thanks to their bright and asymmetric broad Ly-alpha line. We release advanced data products, specific software, and a web interface to select and download data sets

The MUSE Hubble Ultra Deep Field surveys: Data release II

International audienceWe present the second data release of the MUSE Hubble UDF surveys, which includes the deepest spectroscopic survey ever performed. The MUSE data, with their 3D content, amazing depth, wide spectral range, and excellent spatial and medium spectral resolution, are rich in information. This update of the first release incorporates a new 141-hour adaptive-optics-assisted MXDF field (1' diameter FoV) in addition to the reprocessed 10-hour mosaic (3'x3') and the single 31-hour deep field (1'x1'). We have securely identified and measured the redshift of 2221 sources, an increase of 41% compared to the first release. With the exception of 8 stars, the collected sample consists of 25 nearby galaxies (z 3, the difference is even more striking, with a factor of 65 increase (1308 vs 20). We compared the measured redshifts against three published photometric redshift catalogs and find the photo-z accuracy to be lower than the constraints provided by photo-z fitting codes. 80% of the galaxies have an HST counterpart. They are on average faint, with a median magnitude of 25.7 and 28.7 for the OII and Ly-alpha emitters, respectively. SED fits show that these galaxies tend to be low-mass star-forming galaxies, with a median stellar mass of 6.2 10**8 M and a median SFR of 0.4 M/yr. 20% of our catalog, or 424 galaxies, have no HST counterpart. The vast majority of these new sources are high EQW z>2.8 LAEs that are detected by MUSE thanks to their bright and asymmetric broad Ly-alpha line. We release advanced data products, specific software, and a web interface to select and download data sets

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least 4 m. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the 6.5 m James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 yr, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit