RESUMEN
Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X-Y crossing-over unleashed a second dynamic: selfish X-Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X-Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X-Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.
Asunto(s)
Análisis de Secuencia de ADN/veterinaria , Cromosoma X/genética , Cromosoma Y/genética , Animales , Bovinos , Linaje de la Célula , Intercambio Genético , Evolución Molecular , Femenino , Amplificación de Genes , Humanos , Masculino , Ratones , Especificidad de Órganos , Testículo/químicaRESUMEN
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
Asunto(s)
Genes de Insecto/genética , Genoma de los Insectos/genética , Tribolium/genética , Animales , Composición de Base , Tipificación del Cuerpo/genética , Sistema Enzimático del Citocromo P-450/genética , Elementos Transponibles de ADN/genética , Crecimiento y Desarrollo/genética , Humanos , Insecticidas/farmacología , Neurotransmisores/genética , Oogénesis/genética , Filogenia , Proteoma/genética , Interferencia de ARN , Receptores Acoplados a Proteínas G/genética , Receptores Odorantes/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Gusto/genética , Telómero/genética , Tribolium/clasificación , Tribolium/embriología , Tribolium/fisiología , Visión Ocular/genéticaRESUMEN
BACKGROUND: Enterococci are among the leading causes of hospital-acquired infections in the United States and Europe, with Enterococcus faecalis and Enterococcus faecium being the two most common species isolated from enterococcal infections. In the last decade, the proportion of enterococcal infections caused by E. faecium has steadily increased compared to other Enterococcus species. Although the underlying mechanism for the gradual replacement of E. faecalis by E. faecium in the hospital environment is not yet understood, many studies using genotyping and phylogenetic analysis have shown the emergence of a globally dispersed polyclonal subcluster of E. faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references. RESULTS: In this study, we report the complete genome sequence of the E. faecium strain TX16, also known as DO, which belongs to multilocus sequence type (ST) 18, and was the first E. faecium strain ever sequenced. Whole genome comparison of the TX16 genome with 21 E. faecium draft genomes confirmed that most clinical, outbreak, and hospital-associated (HA) strains (including STs 16, 17, 18, and 78), in addition to strains of non-hospital origin, group in the same clade (referred to as the HA clade) and are evolutionally considerably more closely related to each other by phylogenetic and gene content similarity analyses than to isolates in the community-associated (CA) clade with approximately a 3-4% average nucleotide sequence difference between the two clades at the core genome level. Our study also revealed that many genomic loci in the TX16 genome are unique to the HA clade. 380 ORFs in TX16 are HA-clade specific and antibiotic resistance genes are enriched in HA-clade strains. Mobile elements such as IS16 and transposons were also found almost exclusively in HA strains, as previously reported. CONCLUSIONS: Our findings along with other studies show that HA clonal lineages harbor specific genetic elements as well as sequence differences in the core genome which may confer selection advantages over the more heterogeneous CA E. faecium isolates. Which of these differences are important for the success of specific E. faecium lineages in the hospital environment remain(s) to be determined.
Asunto(s)
ADN Bacteriano/química , ADN Bacteriano/genética , Enterococcus faecium/genética , Genoma Bacteriano , Análisis de Secuencia de ADN , Enterococcus faecium/aislamiento & purificación , Humanos , Datos de Secuencia MolecularRESUMEN
After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
Asunto(s)
Cromosomas Humanos Par 3/genética , Animales , Secuencia de Bases , Rotura Cromosómica/genética , Inversión Cromosómica/genética , Mapeo Contig , Islas de CpG/genética , ADN Complementario/genética , Evolución Molecular , Etiquetas de Secuencia Expresada , Proyecto Genoma Humano , Humanos , Macaca mulatta/genética , Datos de Secuencia Molecular , Pan troglodytes/genética , Análisis de Secuencia de ADN , Sintenía/genéticaRESUMEN
Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.
Asunto(s)
Cromosomas Humanos Par 12/genética , Animales , Composición de Base , Islas de CpG/genética , Evolución Molecular , Etiquetas de Secuencia Expresada , Genes/genética , Humanos , Desequilibrio de Ligamiento/genética , Repeticiones de Microsatélite/genética , Datos de Secuencia Molecular , Mutagénesis Insercional/genética , Pan troglodytes/genética , Análisis de Secuencia de ADN , Eliminación de Secuencia/genética , Elementos de Nucleótido Esparcido Corto/genética , Sintenía/genéticaRESUMEN
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
Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9%) of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits) during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies.
Asunto(s)
Genoma/genética , Treponema/genética , Humanos , Datos de Secuencia Molecular , Análisis de Secuencia de ADNRESUMEN
BACKGROUND: Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV). Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and 594 (ATCC 14018) were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9. PRINCIPAL FINDINGS: Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species. CONCLUSIONS: Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism.
Asunto(s)
Gardnerella vaginalis/genética , Gardnerella vaginalis/metabolismo , Genómica , Vaginosis Bacteriana/microbiología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Femenino , Gardnerella vaginalis/clasificación , Gardnerella vaginalis/patogenicidad , Humanos , Masculino , Datos de Secuencia Molecular , Filogenia , Vagina/microbiología , VirulenciaRESUMEN
BACKGROUND: Enterococcus faecalis has emerged as a major hospital pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF, which is commonly used for molecular manipulation and virulence studies. RESULTS: The 2,739,625 base pair chromosome of OG1RF was found to contain approximately 232 kilobases unique to this strain compared to V583, the only publicly available sequenced strain. Almost no mobile genetic elements were found in OG1RF. The 64 areas of divergence were classified into three categories. First, OG1RF carries 39 unique regions, including 2 CRISPR loci and a new WxL locus. Second, we found nine replacements where a sequence specific to V583 was substituted by a sequence specific to OG1RF. For example, the iol operon of OG1RF replaces a possible prophage and the vanB transposon in V583. Finally, we found 16 regions that were present in V583 but missing from OG1RF, including the proposed pathogenicity island, several probable prophages, and the cpsCDEFGHIJK capsular polysaccharide operon. OG1RF was more rapidly but less frequently lethal than V583 in the mouse peritonitis model and considerably outcompeted V583 in a murine model of urinary tract infections. CONCLUSION: E. faecalis OG1RF carries a number of unique loci compared to V583, but the almost complete lack of mobile genetic elements demonstrates that this is not a defining feature of the species. Additionally, OG1RF's effects in experimental models suggest that mediators of virulence may be diverse between different E. faecalis strains and that virulence is not dependent on the presence of mobile genetic elements.
Asunto(s)
Enterococcus faecalis/genética , Genoma Bacteriano , Animales , Antibacterianos , Proteínas Bacterianas/genética , Biopelículas , ADN Bacteriano/química , Farmacorresistencia Bacteriana , Enterococcus faecalis/efectos de los fármacos , Enterococcus faecalis/patogenicidad , Ácido Fusídico/farmacología , Variación Genética , Genómica , Secuencias Repetitivas Esparcidas , Proteínas de la Membrana/genética , Ratones , Operón , Secuencias Repetitivas de Ácidos Nucleicos , Rifampin/farmacología , Homología de Secuencia de Ácido NucleicoRESUMEN
BACKGROUND: Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, gamma-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species. PRINCIPAL FINDINGS: The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species. SIGNIFICANCE: This study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.
Asunto(s)
Bacillus/genética , Reparación del ADN , Farmacorresistencia Bacteriana/genética , Peróxido de Hidrógeno/farmacología , Bacillus/efectos de los fármacos , Bacillus/efectos de la radiación , Rayos gamma , Genes Bacterianos , Genoma Bacteriano , Estrés Oxidativo , Análisis de Secuencia de ADN , Esporas Bacterianas/efectos de los fármacos , Esporas Bacterianas/genética , Esporas Bacterianas/efectos de la radiación , Rayos UltravioletaRESUMEN
The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.