Abstract:
BACKGROUND:Regions of the genome that are under evolutionary constraint across multiple species have previously been used to identify functional sequences in the human genome. Furthermore, it is known that there is an inverse relationship between evolutionary constraint and the allele frequency of a mutation segregating in human populations, implying a direct relationship between interspecies divergence and fitness in humans. Here we utilise this relationship to test differences in the accumulation of putatively deleterious mutations both between populations and on the individual level. RESULTS:Using whole genome and exome sequencing data from Phase 1 of the 1000 Genome Project for 1,092 individuals from 14 worldwide populations we show that minor allele frequency (MAF) varies as a function of constraint around both coding regions and non-coding sites genome-wide, implying that negative, rather than positive, selection primarily drives the distribution of alleles among individuals via background selection. We find a strong relationship between effective population size and the depth of depression in MAF around the most conserved genes, suggesting that populations with smaller effective size are carrying more deleterious mutations, which also translates into higher genetic load when considering the number of putatively deleterious alleles segregating within each population. Finally, given the extreme richness of the data, we are now able to classify individual genomes by the accumulation of mutations at functional sites using high coverage 1000 Genomes data. Using this approach we detect differences between 'healthy' individuals within populations for the distributions of putatively deleterious rare alleles they are carrying. CONCLUSIONS:These findings demonstrate the extent of background selection in the human genome and highlight the role of population history in shaping patterns of diversity between human individuals. Furthermore, we provide a framework for the utility of personal genomic data for the study of genetic fitness and diseases.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Hodgkinson A,Casals F,Idaghdour Y,Grenier JC,Hernandez RD,Awadalla Pdoi
10.1186/1471-2164-14-495subject
Has Abstractpub_date
2013-07-23 00:00:00pages
495issn
1471-2164pii
1471-2164-14-495journal_volume
14pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Lung aging is characterized by a number of structural alterations including fibrosis, chronic inflammation and the alteration of inflammatory cell composition. Chronic exposure to cigarette smoke (CS) is known to induce similar alterations and may contribute to premature lung aging. Additionally, aging and C...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6712-z
更新日期:2020-04-09 00:00:00
abstract:BACKGROUND:Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers as external clinical signs. However, there is no information about the changes produced by the wounds...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4349-3
更新日期:2017-12-02 00:00:00
abstract:BACKGROUND:Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of Ty3/gypsy retrotrans...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-142
更新日期:2013-03-04 00:00:00
abstract:BACKGROUND:The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequenc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-524
更新日期:2013-07-31 00:00:00
abstract:BACKGROUND:Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are develo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S5-S3
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-86
更新日期:2006-04-21 00:00:00
abstract:BACKGROUND:Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation. RESULTS:Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondri...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06846-x
更新日期:2020-06-24 00:00:00
abstract:BACKGROUND:The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5888-6
更新日期:2019-06-17 00:00:00
abstract:BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-323
更新日期:2006-12-25 00:00:00
abstract:BACKGROUND:Adenosine to inosine (A-to-I) RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several hu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-608
更新日期:2010-10-28 00:00:00
abstract:BACKGROUND:Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem D...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-178
更新日期:2012-05-10 00:00:00
abstract:BACKGROUND:Malaria is the most important parasitic disease in the world with approximately two million people dying every year, mostly due to Plasmodium falciparum infection. During its complex life cycle in the Anopheles vector and human host, the parasite requires the coordinated and modulated expression of diverse s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-34
更新日期:2010-01-15 00:00:00
abstract:BACKGROUND:Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: elements of different families do not cooperate, but they independently fight for their survival in ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-219
更新日期:2008-05-14 00:00:00
abstract:BACKGROUND:Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1755-2
更新日期:2015-07-22 00:00:00
abstract:BACKGROUND:Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5872-1
更新日期:2019-06-07 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs affecting the expression of target genes via translational repression or mRNA degradation mechanisms. With the increasing availability of mRNA and miRNA expression data, it might be possible to assess functional targets using the fact that a miRNA might down-regul...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-218
更新日期:2009-05-12 00:00:00
abstract:BACKGROUND:Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3945-6
更新日期:2017-07-24 00:00:00
abstract:BACKGROUND:Improvements in poultry production within the past 50 years have led to increased muscle yield and growth rate, which may be contributing to an increased rate and development of new muscle disorders in chickens. Previously reported muscle disorders and conditions are generally associated with poor meat quali...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1623-0
更新日期:2015-05-21 00:00:00
abstract:BACKGROUND:Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were use...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-34
更新日期:2007-01-29 00:00:00
abstract:BACKGROUND:The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expression in the equine endometrium in response to the introduction of bacterial pathogens and the infl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2139-3
更新日期:2015-11-14 00:00:00
abstract:BACKGROUND:The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found in fast neutron populations has been hindered, however, by the wide range of mutations generated and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5998-1
更新日期:2019-08-06 00:00:00
abstract:BACKGROUND:Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anopheline species, only a few species from different branches of the mosquito evolutionary tree tran...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-207
更新日期:2012-05-30 00:00:00
abstract:BACKGROUND:Mitochondria are organelles that fulfill a fundamental role in cell bioenergetics, as well as in other processes like cell signaling and death. Small non-coding RNAs (sncRNA) are now being considered as pivotal post-transcriptional regulators, widening the landscape of their diversity and functions. In mamma...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5020-3
更新日期:2018-08-28 00:00:00
abstract:BACKGROUND:The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constrain...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-202
更新日期:2010-03-26 00:00:00
abstract:BACKGROUND:Alcohol dehydrogenases (ADHs) in plants are encoded by a multigene family. ADHs participate in growth, development, and adaptation in many plant species, but the evolution and function of the ADH gene family in sugarcane is still unclear. RESULTS:In the present study, 151 ADH genes from 17 species including...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06929-9
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5693-2
更新日期:2019-05-07 00:00:00
abstract:BACKGROUND:Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4876-6
更新日期:2018-06-25 00:00:00
abstract:BACKGROUND:The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-152
更新日期:2011-03-16 00:00:00
abstract:BACKGROUND:The circadian rhythms regulate physiological functions and metabolism. Circadian Time (CT) is a unit to quantify the rhythm of endogenous circadian clock, independent of light influence. To understand the gene expression changes throughout CT, C57BL/6 J mice were maintained under constant darkness (DD) for 6...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6639-4
更新日期:2020-03-12 00:00:00
abstract:BACKGROUND:Aluminium (Al) toxicity is the main factor limiting the crop production in acid soils and barley (Hordeum vulgare L.) is one of the most Al-sensitive of the small-grained cereals. The major gene for Al tolerance in barley is HvAACT1 (HvMATE) on chromosome 4H which encodes a multidrug and toxic compound extru...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2551-3
更新日期:2016-03-05 00:00:00