Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates.

Identifying the genes underlying adaptation, their distribution in genomes and the evolutionary forces shaping genomic diversity are key challenges in evolutionary biology. Very few studies have investigated the abundance and distribution of selective sweeps in species with high-quality reference genomes, outside a handful of model species. Pathogenic fungi are tractable eukaryote models for investigating the genomics of adaptation. By sequencing 53 genomes of two species of anther-smut fungi and mapping them against a high-quality reference genome, we showed that selective sweeps were abundant and scattered throughout the genome in one species, affecting near 17% of the genome, but much less numerous and in different genomic regions in its sister species, where they left footprints in only 1% of the genome. Polymorphism was negatively correlated with linkage disequilibrium levels in the genomes, consistent with recurrent positive and/or background selection. Differential expression in planta and in vitro, and functional annotation, suggested that many of the selective sweeps were probably involved in adaptation to the host plant. Examples include glycoside hydrolases, pectin lyases and an extracellular membrane protein with CFEM domain. This study thus provides candidate genes for being involved in plant-pathogen interaction (effectors), which have remained elusive for long in this otherwise well-studied system. Their identification will foster future functional and evolutionary studies, in the plant and in the anther-smut pathogens, being model species of natural plant-pathogen associations. In addition, our results suggest that positive selection can have a pervasive impact in shaping genomic variability in pathogens and selfing species, broadening our knowledge of the occurrence and frequency of selective events in natural populations.

DNA demethylation and hypermethylation are both required for late nodule development in Medicago.

Plant epigenetic regulations are involved in transposable element silencing, developmental processes and responses to the environment1-7. They often involve modifications of DNA methylation, particularly through the DEMETER (DME) demethylase family and RNA-dependent DNA methylation (RdDM)8. Root nodules host rhizobia that can fix atmospheric nitrogen for the plant's benefit in nitrogen-poor soils. The development of indeterminate nodules, as in Medicago truncatula, involves successive waves of gene activation9-12, control of which raises interesting questions. Using laser capture microdissection (LCM) coupled to RNA-sequencing (SYMbiMICS data11), we previously identified 4,309 genes (termed NDD) activated in the nodule differentiation and nitrogen fixation zones, 36% of which belong to co-regulated genomic regions dubbed symbiotic islands13. We found MtDME to be upregulated in the differentiation zone and required for nodule development, and we identified 474 differentially methylated regions hypomethylated in the nodule by analysing ~2% of the genome4. Here, we coupled LCM and whole-genome bisulfite sequencing for a comprehensive view of DNA methylation, integrated with gene expression at the tissue level. Furthermore, using CRISPR-Cas9 mutagenesis of MtDRM2, we showed the importance of RdDM for CHH hypermethylation and nodule development. We thus proposed a model of DNA methylation dynamics during nodule development.

The composite genome of the legume symbiont Sinorhizobium meliloti.

The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

Sequencing the Sinorhizobium meliloti genome.

The Sinorhizobium meliloti genome consists of three replicons. This bacterium forms an intricate symbiotic relationship with the roots of certain legumes and is considered as an agriculturally important nitrogen-fixer. A consortium of 6 European laboratories was organized to sequence its single chromosome (3.7 Mb), whereas the other two elements (pSyma 1.4 Mb and pSymb 1.7 Mb) will be sequenced by other groups.

[Biliary colonic ileus: an unusual cause of colonic obstruction]. / L'iléus biliaire colique: une cause rare d'occlusion colique.

We report a rare case of colonic gallstone obstruction in a patient with cholecystocolic fistula. Diagnosis of this condition is usually difficult and only achieved at surgery. We review the radiological findings, particularly the CT findings, helpful for diagnosis: ectopic gallstone, biliary gas and fistula. Early preoperative diagnosis could reduce morbidity and mortality. Treatment is surgical with enterolithotomy. There is some controversy over the need to repair the fistula.

The ProDom database of protein domain families.

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail (prodom@toulouse.inra.fr) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the graphical user interface which allows for interactive analysis of protein homology relationships. Recent improvements to the server include: ProDom search by keyword; links to PROSITE and PDB entries; more sensitive ProDom similarity search with BLAST or WU-BLAST; alignments of query sequences with homologous ProDom domain families; and links to the SWISS-MODEL server (http: //www.expasy.ch/swissmod/SWISS-MODEL.html ) for homology based 3-D domain modelling where possible.

Recent improvements of the ProDom database of protein domain families.

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. The current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. ProDom can be searched on the World Wide Web to study domain arrangements within either known families or new proteins, with the help of a user-friendly graphical interface (http://www.toulouse.inra.fr/prodom.html). Recent improvements to the ProDom server include: ProDom queries under the SRS Sequence Retrieval System; links to the PredictProtein server; phylogenetic trees and condensed multiple alignments for a better representation of large domain families, with zooming in and out capabilities. In addition, a similar server was set up to display the outcome of whole genome domain analysis as applied to 17 completed microbial genomes (http://www.toulouse.inra.fr/prodomCG.html ).

Whole genome protein domain analysis using a new method for domain clustering.

We present the outcome of a systematic analysis of protein domain shuffling in 17 completed microbial genomes. This analysis has been performed using MKDOM Version 2, a completely new version of the domain clustering program MKDOM based on PSI-BLAST recursive homology searches. It allows to delineate the most frequent protein domain building blocks, which domains are found specifically in Bacteria, Archaea or yeast, and which domains are shared between two or all three domains of life. The latter are good candidates as the basic protein building blocks underlying all forms of cellular life. Statistics of multi-domain proteins indicate that some organisms such as Bacillus subtilis or Mycobacterium tuberculosis contain an abnormally high number of large multi-domain proteins. We also provide examples of highly shuffled or circularly permutated domains. A WWW graphical interface has been made available to interactively browse domain arrangements of proteins in all 17 genomes, at http:@www.toulouse.inra.fr/prodomCG.html.

Browsing protein families via the 'Rich Family Description' format.

MOTIVATION: Multiple alignments of protein sequences are the basis of structural and functional analysis of protein families. It is however difficult even for an expert biologist to comprehend an alignment of more than 50 to 100 homologous sequences. RESULTS: This paper presents a browser for the analysis of multiple alignments of large numbers of protein sequences. Phylogenetic trees and consensus sequences are computed and used to summarise the alignments; these data are stored in a structure called Rich Family Description. Summary alignments and trees are displayed in HTML pages and can be developed or reduced by the user. This browser is used to display the ProDom domain families on the Web. Its zooming facilities allow extracting information from alignments of more than 1000 homologous sequences.

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.

ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www. toulouse.inra.fr/prodom.html ). ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse. inra.fr/prodomCG.html ). Recent improvements to the ProDom database and its server include: scaling up to include sequences from TrEMBL, addition of Pfam-A entries to the set of expert validated families, assignment of stable accession numbers, consistency indicators for domain families, domain arrangements of sub-families and links to Pfam-A.

Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome.

MOTIVATION: Quick and easy gene mapping by the use of a panel of cytogenetically characterized somatic cell hybrids is possible, even if some discordant experimental results arise. RESULTS: An interactive program is proposed and is made available on a WWW site to users of a somatic cell hybrid panel. Assignments to chromosomes and subchromosomal regions are based on likelihood calculations and Bayes' theorem, and a confidence level is provided. The method is illustrated in the case of the pig genome.

XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences.

MOTIVATION: To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis. RESULTS: This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization of any set of protein sequences. The algorithm is an automatic method to identify putative domains from sequence comparisons. The graphical tool displays the proteins as a set of linked boxes, corresponding to its domains. The method has been tested on a family of bacterial proteins and on whole genomes. It is currently applied to the complete SWISS-PROT database to build the PRODOM database. AVAILABILITY: XDOM is available free of charge by anonymous ftp:¿¿ftp://ftp.toulouse.inra.fr/pub/xdom¿ ¿. The ProDom database can be consulted at ¿¿http://protein.toulouse.inra.fr/prodom.html¿¿.

A high-density physical map of Sinorhizobium meliloti 1021 chromosome derived from bacterial artificial chromosome library.

As part of the European Sinorhizobium meliloti (strain 1021) chromosome sequencing project, four genomic bacterial artificial chromosome (BAC) libraries have been constructed, one of which was mainly used for chromosome mapping. This library consists of 1,824 clones with an average insert size of 80 kilobases and represents approximately 20-fold total genome coverage [6.8 megabases (Mbs)]. PCR screening of 384 BAC clones with 447 chromosomal markers (PCR primer pairs), consisting of 73 markers representing 118 genes (40 individual genes and 78 genes clustered in 23 operons), two markers from the rrn operon (three loci), four markers from insertion sequences (approximately 16 loci) and 368 sequence-tagged sites allowed the identification of 252 chromosomal BAC clones and the construction of a high-density physical map of the whole 3.7-Mb chromosome of S. meliloti. An average of 5.5 overlapping and colinear BAC clones per marker, correlated with a low rate of deleted or rearranged clones (0.8%) indicate a solid BAC contigation and a correct mapping. Systematic BLASTX analysis of sequence-tagged site marker sequences allowed prediction of a biological function for a number of putative ORFs. Results are available at. This map, whose resolution averages one marker every 9 kilobases, should provide a valuable tool for further sequencing, functional analysis, and positional cloning.

The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.

Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N(2)-fixing bacterium Sinorhizobium meliloti revealed that the replicon has a high gene density with a total of 1,570 protein-coding regions, with few insertion elements and regions duplicated elsewhere in the genome. The only copies of an essential arg-tRNA gene and the minCDE genes are located on pSymB. Almost 20% of the pSymB sequence carries genes encoding solute uptake systems, most of which were of the ATP-binding cassette family. Many previously unsuspected genes involved in polysaccharide biosynthesis were identified and these, together with the two known distinct exopolysaccharide synthesis gene clusters, show that 14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other recognizable gene clusters include many involved in catabolic activities such as protocatechuate utilization and phosphonate degradation. The functions of these genes are consistent with the notion that pSymB plays a major role in the saprophytic competence of the bacteria in the soil environment.

Genome sequence of the plant pathogen Ralstonia solanacearum.

Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.

InterPro--an integrated documentation resource for protein families, domains and functional sites.

MOTIVATION: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. RESULTS: Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries (i.e. those that have no counterpart in the companion resources) are assigned unique accession numbers. Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL).

Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021.

Sinorhizobium meliloti is an alpha-proteobacterium that forms agronomically important N(2)-fixing root nodules in legumes. We report here the complete sequence of the largest constituent of its genome, a 62.7% GC-rich 3,654,135-bp circular chromosome. Annotation allowed assignment of a function to 59% of the 3,341 predicted protein-coding ORFs, the rest exhibiting partial, weak, or no similarity with any known sequence. Unexpectedly, the level of reiteration within this replicon is low, with only two genes duplicated with more than 90% nucleotide sequence identity, transposon elements accounting for 2.2% of the sequence, and a few hundred short repeated palindromic motifs (RIME1, RIME2, and C) widespread over the chromosome. Three regions with a significantly lower GC content are most likely of external origin. Detailed annotation revealed that this replicon contains all housekeeping genes except two essential genes that are located on pSymB. Amino acid/peptide transport and degradation and sugar metabolism appear as two major features of the S. meliloti chromosome. The presence in this replicon of a large number of nucleotide cyclases with a peculiar structure, as well as of genes homologous to virulence determinants of animal and plant pathogens, opens perspectives in the study of this bacterium both as a free-living soil microorganism and as a plant symbiont.