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1.
Nature ; 464(7285): 59-65, 2010 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-20203603

RESUMEN

To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.


Asunto(s)
Tracto Gastrointestinal/microbiología , Genómica , Metagenoma/genética , Adulto , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Bacterias/metabolismo , Estudios de Cohortes , Mapeo Contig , Dinamarca , Heces/microbiología , Genes Bacterianos/genética , Genes Esenciales/genética , Genoma Bacteriano/genética , Salud , Humanos , Enfermedades Inflamatorias del Intestino/genética , Obesidad/genética , Sistemas de Lectura Abierta/genética , Sobrepeso/genética , Análisis de Secuencia de ADN , España
2.
PLoS Biol ; 8(11): e1000533, 2010 Nov 09.
Artículo en Inglés | MEDLINE | ID: mdl-21085693

RESUMEN

DNA methylation plays an important role in biological processes in human health and disease. Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells. Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project. PBMC constitute an important source for clinical blood tests world-wide. We found that 68.4% of CpG sites and <0.2% of non-CpG sites were methylated, demonstrating that non-CpG cytosine methylation is minor in human PBMC. Analysis of the PBMC methylome revealed a rich epigenomic landscape for 20 distinct genomic features, including regulatory, protein-coding, non-coding, RNA-coding, and repeat sequences. Integration of our methylome data with the YH genome sequence enabled a first comprehensive assessment of allele-specific methylation (ASM) between the two haploid methylomes of any individual and allowed the identification of 599 haploid differentially methylated regions (hDMRs) covering 287 genes. Of these, 76 genes had hDMRs within 2 kb of their transcriptional start sites of which >80% displayed allele-specific expression (ASE). These data demonstrate that ASM is a recurrent phenomenon and is highly correlated with ASE in human PBMCs. Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies.


Asunto(s)
Metilación de ADN , Leucocitos Mononucleares/metabolismo , Alelos , Islas de CpG , Haploidia , Humanos , ARN no Traducido/genética , Alineación de Secuencia
3.
Nat Genet ; 42(11): 1027-30, 2010 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-20972441

RESUMEN

We have resequenced a group of six elite maize inbred lines, including the parents of the most productive commercial hybrid in China. This effort uncovered more than 1,000,000 SNPs, 30,000 indel polymorphisms and 101 low-sequence-diversity chromosomal intervals in the maize genome. We also identified several hundred complete genes that show presence/absence variation among these resequenced lines. We discuss the potential roles of complementation of presence/absence variations and other deleterious mutations in contributing to heterosis. High-density SNP and indel polymorphism markers reported here are expected to be a valuable resource for future genetic studies and the molecular breeding of this important crop.


Asunto(s)
Variación Genética , Estudio de Asociación del Genoma Completo , Polimorfismo de Nucleótido Simple , Zea mays/genética , Cromosomas de las Plantas/genética , ADN de Plantas/genética , Genes de Plantas/genética , Endogamia
4.
Science ; 326(5951): 433-6, 2009 Oct 16.
Artículo en Inglés | MEDLINE | ID: mdl-19713493

RESUMEN

A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.


Asunto(s)
Bombyx/genética , Genes de Insecto , Variación Genética , Genoma de los Insectos , Análisis de Secuencia de ADN , Animales , Bombyx/clasificación , Sistema Digestivo/metabolismo , Glándulas Exocrinas/metabolismo , Femenino , Expresión Génica , Mutación INDEL , Desequilibrio de Ligamiento , Masculino , Filogenia , Polimorfismo de Nucleótido Simple , Análisis de Componente Principal , Selección Genética , Testículo/metabolismo
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