RESUMEN
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
Asunto(s)
Evolución Molecular , Genoma , Genómica , Ratas Endogámicas BN/genética , Animales , Composición de Base , Centrómero/genética , Cromosomas de los Mamíferos/genética , Islas de CpG/genética , Elementos Transponibles de ADN/genética , ADN Mitocondrial/genética , Duplicación de Gen , Humanos , Intrones/genética , Masculino , Ratones , Modelos Moleculares , Mutagénesis , Polimorfismo de Nucleótido Simple/genética , Sitios de Empalme de ARN/genética , ARN no Traducido/genética , Ratas , Secuencias Reguladoras de Ácidos Nucleicos/genética , Retroelementos/genética , Análisis de Secuencia de ADN , Telómero/genéticaRESUMEN
The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon Ignicoccus. Ribosomal protein and rRNA-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom Nanoarchaeota. The N. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. It is the smallest microbial genome sequenced to date, and also one of the most compact, with 95% of the DNA predicted to encode proteins or stable RNAs. Its limited biosynthetic and catabolic capacity indicates that N. equitans' symbiotic relationship to Ignicoccus is parasitic, making it the only known archaeal parasite. Unlike the small genomes of bacterial parasites that are undergoing reductive evolution, N. equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome.
Asunto(s)
Archaea/genética , Evolución Biológica , Genoma Arqueal , Arabidopsis/microbiología , Archaea/clasificación , Archaea/patogenicidad , ADN de Archaea/genética , Biblioteca de Genes , FilogeniaRESUMEN
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.
Asunto(s)
Genoma Humano , Genoma , Análisis de Secuencia de ADN , Takifugu/genética , Animales , Evolución Biológica , Biología Computacional , Secuencia Conservada , Elementos Transponibles de ADN , Evolución Molecular , Exones , Proteínas de Peces/química , Proteínas de Peces/genética , Duplicación de Gen , Orden Génico , Genómica , Humanos , Intrones , Mapeo Físico de Cromosoma , Proteínas/química , Proteínas/genética , Proteoma , Secuencias Repetitivas de Ácidos Nucleicos , SinteníaRESUMEN
Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.