Barclay G. Barrell

ACT: the Artemis comparison tool

The Artemis Comparison Tool (ACT) allows an interactive visualisation of comparisons between complete genome sequences and associated annotations. The comparison data can be generated with several different programs; BLASTN, TBLASTX or Mummer comparisons between genomic DNA sequences, or orthologue tables generated by reciprocal FASTA comparison between protein sets. It is possible to identify regions of similarity, insertions and rearrangements at any level from the whole genome to base-pair differences. ACT uses Artemis components to display the sequences and so inherits powerful searching and analysis tools. ACT is part of the Artemis distribution and is similarly open source, written in Java and can run on any Java enabled platform, including UNIX, Macintosh and Windows.

The genome of the blood fluke Schistosoma mansoni

Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363u2009megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.

Comparative genomic analysis of three Leishmania species that cause diverse human disease.

Leishmania parasites cause a broad spectrum of clinical disease. Here we report the sequencing of the genomes of two species of Leishmania: Leishmania infantum and Leishmania braziliensis. The comparison of these sequences with the published genome of Leishmania major reveals marked conservation of synteny and identifies only ∼200 genes with a differential distribution between the three species. L. braziliensis, contrary to Leishmania species examined so far, possesses components of a putative RNA-mediated interference pathway, telomere-associated transposable elements and spliced leader–associated SLACS retrotransposons. We show that pseudogene formation and gene loss are the principal forces shaping the different genomes. Genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage.

Artemis and ACT

Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis

Background Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. Methodology/Principal Findings The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, ∼40% of the ∼2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three ∼90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. Conclusions/Significance The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

Candida dubliniensis is the closest known relative of Candida albicans, the most pathogenic yeast species in humans. However, despite both species sharing many phenotypic characteristics, including the ability to form true hyphae, C. dubliniensis is a significantly less virulent and less versatile pathogen. Therefore, to identify C. albicans-specific genes that may be responsible for an increased capacity to cause disease, we have sequenced the C. dubliniensis genome and compared it with the known C. albicans genome sequence. Although the two genome sequences are highly similar and synteny is conserved throughout, 168 species-specific genes are identified, including some encoding known hyphal-specific virulence factors, such as the aspartyl proteinases Sap4 and Sap5 and the proposed invasin Als3. Among the 115 pseudogenes confirmed in C. dubliniensis are orthologs of several filamentous growth regulator (FGR) genes that also have suspected roles in pathogenesis. However, the principal differences in genomic repertoire concern expansion of the TLO gene family of putative transcription factors and the IFA family of putative transmembrane proteins in C. albicans, which represent novel candidate virulence-associated factors. The results suggest that the recent evolutionary histories of C. albicans and C. dubliniensis are quite different. While gene families instrumental in pathogenesis have been elaborated in C. albicans, C. dubliniensis has lost genomic capacity and key pathogenic functions. This could explain why C. albicans is a more potent pathogen in humans than C. dubliniensis.

Subtelomeric sequence from the right arm of Schizosaccharomyces pombe chromosome I contains seven permease genes

The sequence has been determined of 80 888u2009bp of contiguous subtelomeric DNA, including the isp5 gene, from the right arm of chromosome I of Schizosaccharomyces pombe; 27 open reading frames (ORFs) longer than 100 codons are present, giving a density of one gene per 3.0u2009kb. Seven of the predicted proteins are members of the major facilitator superfamily (MFS) of transport proteins, including four amino acid permease homologues, bringing this family of amino acid permease sequences to 17 in Sz. pombe, and a phylogenetic analysis is presented. Also encoded is an allantoate permease homologue, a sulphate permease homologue and a probable urea active transporter. Predicted non‐membrane proteins include a 1‐aminocyclopropane‐1‐carboxylate deaminase (ACC deaminase), a class III aminotransferase, serine acetyltransferase, protein‐L‐isoaspartate O‐methyltransferase, α‐glucosidase, α‐galactosidase, esterase/lipase, oxidoreductase of the short‐chain dehydrogenase/reductase (SDR) family, aldehyde dehydrogenase, formamidase, amidase, flavohaemoprotein, a putative translation initiation inhibitor and a protein with similarity to a filamentous fungal conidiation‐specific protein. The remaining six ORFs are likely to encode proteins, either because they have sequence similarity with hypothetical proteins or because they are known to be transcribed. Introns are scarce in the sequenced region: only three ORFs contain introns, with only one having multiple introns. The sequenced region also contains a single Tf1 transposon long terminal repeat (LTR). The sequence is derived from cosmid clones c869, c922 and c1039 and has been submitted to the EMBL database under entries SPAC869 (Accession No. AL132779), SPAC922 (AL133522) and SPAC1039 (AL133521). Copyright

DNA sequencing and analysis of a 67.4 kb region from the right arm of Schizosaccharomyces pombe chromosome II reveals 28 open reading frames including the genes his5, pol5, ppa2, rip1, rpb8 and skb1.

67u2009393u2009bp of contiguous DNA located between markers cdc18 and cdc14 on the right arm of fission yeast chromosome II has been sequenced as part of the European Union Schizosaccharomyces pombe genome sequencing project. The complete sequence, contained in cosmid clones c15C4 and c21H7, has been determined on both strands. Sequence analysis shows that it contains 28 open reading frames capable of coding for proteins, 16 split by one or more introns, but no tRNA, rRNA or transposon sequences. The gene density is one per 2·4u2009kb. Six genes have been previously described (his5, pol5, ppa2, rip1, rpb8 and skb1) and 22 are novel. Of the novel genes, 14 have significant similarity with proteins of known function, three have similarities with proteins of unknown function and five show no extensive similarities with known proteins. Sequence similarities suggest that three of the novel genes encode ATP‐dependent RNA helicases, two encode transcription factor components and others encode a G‐protein, a dehydrogenase, a Rab escort protein, an Abc1‐like protein, a lipase, an ATP‐binding transport protein, an amino acid permease, an acid phosphatase and a mannosyltransferase. The sequence has been submitted to the EMBL database under entries: SPBC15C4 (Accession No. AL023290), SPBC21H7 (AL023286), SPBC14C8 (part)(AL022305) and SPBC16H5 (part)(AL022104). Copyright

Detailed Structure of Pneumocystis carinii Chromosome Ends

Pnewnocystis carinii has three gene families, MSG, MSR and PRTl, the members of which tend to be grouped together in clusters located at chromosome ends (reviewed in reference 6). Each of these gene families encodes a family of surface proteins, which are known as Major Surface Glycoprotein (MSG), MSG-Related (MSR). and Protease (PRTl). Determining the size and composition of these gene arrays is important for understanding their evolution and function. A question of particular interest is the possibility of co-expression of a specific MSG gene and a specific PRT1. because MSG proteins may be processed by proteases e n d e d by PRTl genes [3. 7.1. Prior to the work described here. segments of the genome that contain members of these gene families had been characterird. but an entire cluster had not yet been isolated. As part of the Pneumocystis Genome Project. the Sanger Center (http://www.sanger.ac.uk) determined the sequence of gene arrays contained within two cosmids, 3G5 and 1B2. Both cloned gene clusters contained members of all three gene families, but the order of the genes in the two clones was different. In addition to full size MSG and MSR genes, both gene clusters contained what appear to be fragments of MSG or MSR genes. The library contained additional cosmids that shared with 1B2. and with each other. a core region of about 15 kilobases at the telomere-distal end of the sequence. Surprisingly, two of these 1B2related cosmids mapped to one chromosome, and another mapped to a different chromosome. These linkage data show that the same gene array can be at the ends of two different chromosomes.

Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere-distal to his5.

One hundred and fourteen kilobase pairs (kb) of contiguous genomic sequence have been determined immediately distal to the his5 genetic marker located about 0.9u2009Mb from the centromere on the long arm of Schizosaccharomyces pombe chromosome 2. The sequence is contained in overlapping cosmid clones c16H5, c12D12, c24C6 and c19G7, of which 20u2009kb are identical to previously reported sequence from clone c21H7. The remaining 93u2009781u2009bp of sequence contains 10 known genes (cdc14, cdm1, cps1, gpa1, msh2, pck2, rip1, rps30‐2, sad1 and ubl1), 32 open reading frames (ORFs) capable of coding for proteins of at least 100 amino acid residues in length, one 5S rRNA gene, one tRNAPro gene, one lone Tf1‐type long terminal repeat (LTR) and one lone Tf2‐type LTR. There is a density of one protein‐coding gene per 2.2u2009kb and 22 of the 42 ORFs (52%) incorporate one or more introns. Twenty‐one of the novel ORFs show sequence similarities which suggest functions of their products, including a cyclin C, a MADS box transcription factor, mad2‐like protein, telomere binding protein, topoisomerase II‐associated protein, ATP‐dependent DEAH box RNA helicase, G10 protein, ubiquitin‐activating e1‐like enzyme, nucleoporin, prolyl‐tRNA synthetase, peptidylprolyl isomerase, δ‐1‐pyrroline‐5‐carboxylate dehydrogenase, protein transport protein, coatomer epsilon, TCP‐1 chaperonin, β‐subunit of 6‐phosphofructokinase, aminodeoxychorismate lyase, a phosphate transport protein and a thioredoxin. The sequence has been submitted to the EMBL database under Accession Nos AL021839, AL022104, AL031786 and AL035085. Copyright