Abstract：
BACKGROUND:The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodological reliance on accurate gene trees, which are difficult to obtain for duplicated genes. RESULTS:In this work, we detected exons with an accumulation of high-quality nucleotide differences between the human assembly and shotgun sequencing reads from single human and macaque individuals. Comparing the observed rates of nucleotide differences between coding exons and their flanking intronic sequences with a likelihood-ratio test, we identified 74 exons with evidence for rapid coding sequence evolution during the evolution of humans and Old World monkeys. Fifty-five percent of rapidly evolving exons were either partially or totally duplicated, which is a significant enrichment of the 6% rate observed across all human coding exons. CONCLUSIONS:Our results provide a more comprehensive view of the action of selection upon segmental duplications, which are the most complex regions of our genomes. In light of these findings, we suggest that segmental duplications could be subjected to rapid evolution more frequently than previously thought.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Lorente-Galdos B,Bleyhl J,Santpere G,Vives L,Ramírez O,Hernandez J,Anglada R,Cooper GM,Navarro A,Eichler EE,Marques-Bonet Tdoi
10.1186/gb-2013-14-1-r9subject
Has Abstractpub_date
2013-01-29 00:00:00pages
R9issue
1eissn
1474-7596issn
1474-760Xpii
gb-2013-14-1-r9journal_volume
14pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract：:We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-7-preprint0005
更新日期：2002-05-29 00:00:00
abstract：:Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb4154
更新日期：2014-01-27 00:00:00
abstract：:Two recent studies have added microarrays to the toolkit used to analyze the origins of replication in yeast chromosomes, providing a fuller picture of how genomic DNA replication is organized. ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2002-3-6-reviews1016
更新日期：2002-01-01 00:00:00
abstract：BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2002-3-7-research0036
更新日期：2002-06-25 00:00:00
abstract：:Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is l...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/s13059-016-1127-5
更新日期：2016-12-20 00:00:00
abstract：:A report on the Cold Spring Harbor Laboratory meeting on the Evolution of Developmental Diversity, Cold Spring Harbor, NY, USA, 17-21 April 2002. ...
journal_title：Genome biology
pub_type：
doi：10.1186/gb-2002-3-8-reports4023
更新日期：2002-07-15 00:00:00
abstract：:Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. Thi...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-015-0706-1
更新日期：2015-07-23 00:00:00
abstract：:Recent work has identified the human NOD-like receptor NLRX1 as a negative regulator of intracellular signaling leading to type I interferon production. Here we discuss these findings and the questions and implications they raise regarding the function of NOD-like receptors in the antiviral response. ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2008-9-4-217
更新日期：2008-04-25 00:00:00
abstract：:Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data and compare its performance to the currently adopted approa...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2009-10-6-r64
更新日期：2009-01-01 00:00:00
abstract：BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2008-9-12-r183
更新日期：2008-01-01 00:00:00
abstract：:We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surpris...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2010-11-9-r96
更新日期：2010-01-01 00:00:00
abstract：BACKGROUND:Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS:We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated t...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-10-r218
更新日期：2007-01-01 00:00:00
abstract：:Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA pathway. Will these findings limit the therapeutic use of such hairpins? ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2006-7-8-231
更新日期：2006-01-01 00:00:00
abstract：:Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...
journal_title：Genome biology
pub_type： 评论,杂志文章
doi：10.1186/s13059-014-0516-x
更新日期：2014-11-08 00:00:00
abstract：:The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-017-1232-0
更新日期：2017-05-12 00:00:00
abstract：BACKGROUND:The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it r...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-016-1072-3
更新日期：2016-10-11 00:00:00
abstract：BACKGROUND:Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene e...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-017-1302-3
更新日期：2017-09-15 00:00:00
abstract：BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2006-7-11-r112
更新日期：2006-01-01 00:00:00
abstract：:DNA shuffling has proven to be a powerful technique for the directed evolution of proteins. A mix of theoretical and applied research has now provided insights into how recombination can be guided to more efficiently generate proteins and even organisms with altered functions. ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2002-3-8-reviews1021
更新日期：2002-07-31 00:00:00
abstract：BACKGROUND:Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signat...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-019-1746-8
更新日期：2019-07-15 00:00:00
abstract：BACKGROUND:Cultivable archaeal species are assigned to two phyla -- the Crenarchaeota and the Euryarchaeota -- by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellul...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2005-6-5-r42
更新日期：2005-01-01 00:00:00
abstract：:The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2. ...
journal_title：Genome biology
pub_type： 评论,杂志文章
doi：10.1186/s13059-015-0793-z
更新日期：2015-10-26 00:00:00
abstract：BACKGROUND:Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome-wide expression profiling to assess novel functions of the Caenorhabditis elegans HP...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2011-12-12-r123
更新日期：2011-12-20 00:00:00
abstract：:Genomic and proteomic studies have identified hundreds of proteins from mitochondria. A recent study has added a functional twist to these systematic approaches and identified novel mitochondrial modifiers and regulators. ...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2008-9-2-209
更新日期：2008-01-01 00:00:00
abstract：:How the mechanisms of dosage compensation distinguish the sex chromosomes from the autosomes has been something of a mystery. A recent study in Caenorhabditis elegans has identified clusters of two common DNA motifs as a cis-acting code for the recruitment of the DCC, the protein complex that mediates dosage compensat...
journal_title：Genome biology
pub_type： 杂志文章,评审
doi：10.1186/gb-2007-8-2-204
更新日期：2007-01-01 00:00:00
abstract：BACKGROUND:Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? RESULTS:A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped ...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2007-8-7-r152
更新日期：2007-01-01 00:00:00
abstract：BACKGROUND:Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known how common this mechanism is. We provide transcriptional evidence of widespread alternate splicing in the Toll-like rece...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/gb-2006-7-2-r10
更新日期：2006-01-01 00:00:00
abstract：:A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February to 4 March 2011. ...
journal_title：Genome biology
pub_type：
doi：10.1186/gb-2011-12-4-304
更新日期：2011-01-01 00:00:00
abstract：BACKGROUND:Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying me...
journal_title：Genome biology
pub_type： 杂志文章
doi：10.1186/s13059-018-1457-6
更新日期：2018-07-17 00:00:00
abstract：:A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...
journal_title：Genome biology
pub_type：
doi：10.1186/gb-2012-13-1-312
更新日期：2012-01-30 00:00:00
