RESUMEN
We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.
Asunto(s)
Cromosomas/genética , ADN Protozoario/genética , Trypanosoma brucei brucei/genética , Animales , Antígenos de Protozoos/genética , Mapeo Cromosómico , ADN Protozoario/química , Duplicación de Gen , Genes Protozoarios/genética , Datos de Secuencia Molecular , Seudogenes/genética , Recombinación Genética , Análisis de Secuencia de ADNRESUMEN
Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.
Asunto(s)
Cryptococcus neoformans/genética , Genoma Fúngico , Empalme Alternativo , Pared Celular/metabolismo , Cromosomas Fúngicos/genética , Biología Computacional , Cryptococcus neoformans/patogenicidad , Cryptococcus neoformans/fisiología , Elementos Transponibles de ADN , Proteínas Fúngicas/metabolismo , Biblioteca de Genes , Genes Fúngicos , Humanos , Intrones , Datos de Secuencia Molecular , Fenotipo , Polimorfismo Genético , Polimorfismo de Nucleótido Simple , Polisacáridos/metabolismo , ARN sin Sentido , Análisis de Secuencia de ADN , Transcripción Genética , Virulencia , Factores de Virulencia/metabolismoRESUMEN
As part of a collaborative project aimed at sequencing and functionally analysing the entire genome of Pseudomonas putida strain KT2440, a physical clone map was produced as an initial resource. To this end, a high-coverage cosmid library was arrayed and ordered by clone hybridizations. Restriction fragments generated by rare-cutting enzymes and plasmids containing the rrn operon and 23S rDNA of Pseudomonas aeruginosa were used as probes and, parts of the cosmids were end-sequenced. This provided the information necessary for merging and comparing the macro-restriction map, cosmid clone order and sequence information, thereby assuring co-linearity of the eventual sequence assembly with the actual genome. A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non-coding portions.
Asunto(s)
Cósmidos/genética , ADN Bacteriano/genética , Biblioteca de Genes , Genoma Bacteriano , Pseudomonas putida/genética , Clonación Molecular , Mapeo Contig , Hibridación de Ácido Nucleico , Análisis de Secuencia por Matrices de Oligonucleótidos , Operón de ARNr/genéticaRESUMEN
Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.