Dataset Information

Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

ABSTRACT:

Background

Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed.

Methods/principal findings

Here, we show that equivalent length, or L(e), a quantity determined by the variance of fluctuating part of the distribution of the k-mer frequencies in a genome, characterizes the latter's global structure. We computed the L(e)s of 865 complete chromosomes and found that they have nearly universal but (k-dependent) values. The differences among the L(e) of a chromosome and those of its coding and non-coding parts were found to be slight.

Conclusions

We verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative "point" mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (1-5) x 10(-3)/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

SUBMITTER: Chen HD

PROVIDER: S-EPMC2854691 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

Chen Hong-Da HD Fan Wen-Lang WL Kong Sing-Guan SG Lee Hoong-Chien HC

PloS one 20100414 4

<h4>Background</h4>Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed.<h4>Methods/principal findings</h4>Here, we show that equivalent length, or L(e), a quantity determined by the variance of fluctuating part of the distribution of the k-mer frequencies in a genome, characterizes the latter's global structure. We computed the L(e)s of 865 complete chromosomes and found t ...[more]

PMID: 20418954

Similar Datasets

Project description:Transvaginal measurement of cervical length (CL) has been advocated as a screening tool to prevent preterm birth, but controversy remains regarding the overall utility of universal screening.We aimed to evaluate the acceptability of a universal CL screening program. Additionally we evaluated risk factors associated with declining screening and subsequent delivery outcomes of women who accepted or declined screening.This was a retrospective cohort study of transvaginal CL screening at a single institution from July 1, 2011, through December 31, 2014. Institutional protocol recommended transvaginal CL measurement at the time of anatomic survey between 17-23 weeks in all women with singleton, viable pregnancies, without current or planned cerclage, with patients able to opt out. Patients with CL ?20 mm were considered to have clinically significant cervical shortening and were offered treatment. We assessed acceptance rate, risk factors for declining CL screening, and the trend of acceptance of CL screening over time. We also calculated the prevalence of CL ?25, ?20, and ?15 mm, and estimated the association between CL screening and spontaneous preterm birth.Of 12,740 women undergoing anatomic survey during the study period, 10,871 (85.3%; 95% confidence interval [CI], 84.7-85.9%) underwent CL screening. Of those, 215 (2.0%) had a CL ?25 mm and 131 (1.2%) had a CL ?20 mm. After the first 6 months of implementation, there was no change in rates of acceptance of CL screening over time (P for trend = .15). Women were more likely to decline CL screening if they were African American (adjusted odds ratio [aOR], 2.17; 95% CI, 1.93-2.44), obese (aOR, 1.18; 95% CI, 1.06-1.31), multiparous (aOR, 1.45; 95% CI, 1.29-1.64), age <35 years (aOR, 1.24; 95% CI, 1.08-1.43), or smokers (aOR, 1.42; 95% CI, 1.20-1.68). Rates of spontaneous preterm birth <28 weeks were higher in those who declined CL screening (aOR, 2.01; 95% CI, 1.33-3.02).Universal CL screening was implemented successfully with 85% of women screened. Overall incidence of short cervix was low and women with significant risk factors for preterm birth were more likely to decline screening. Patients who declined CL screening were more likely to be African American, obese, multiparous, age <35 years, and smokers. Rates of early, but not late, spontaneous preterm birth were significantly higher among women who did not undergo CL screening.

Dataset Information

Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

Background

Methods/principal findings

Conclusions

Publications

Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets