Abstract:
:Codon usage bias in Drosophila melanogaster genes has been attributed to negative selection of those codons whose cellular tRNA abundance restricts rates of mRNA translation. Previous studies, which involved limited numbers of genes, can now be compared against analyses of the entire gene complements of 12 Drosophila species whose genome sequences have become available. Using large numbers (6138) of orthologs represented in all 12 species, we establish that the codon preferences of more closely related species are better correlated. Differences between codon usage biases are attributed, in part, to changes in mutational biases. These biases are apparent from the strong correlation (r = 0.92, P < 0.001) among these genomes' intronic G + C contents and exonic G + C contents at degenerate third codon positions. To perform a cross-species comparison of selection on codon usage, while accounting for changes in mutational biases, we calibrated each genome in turn using the codon usage bias indices of highly expressed ribosomal protein genes. The strength of translational selection was predicted to have varied between species largely according to their phylogeny, with the D. melanogaster group species exhibiting the strongest degree of selection.
journal_name
Geneticsjournal_title
Geneticsauthors
Heger A,Ponting CPdoi
10.1534/genetics.107.070466subject
Has Abstractpub_date
2007-11-01 00:00:00pages
1337-48issue
3eissn
0016-6731issn
1943-2631pii
177/3/1337journal_volume
177pub_type
杂志文章相关文献
GENETICS文献大全abstract::Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host transla...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.114.162842
更新日期:2014-05-01 00:00:00
abstract::In diploid eukaryotes, repair of double-stranded DNA breaks by homologous recombination often leads to loss of heterozygosity (LOH). Most previous studies of mitotic recombination in Saccharomyces cerevisiae have focused on a single chromosome or a single region of one chromosome at which LOH events can be selected. I...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.111.137927
更新日期:2012-04-01 00:00:00
abstract::The eight enzymes of the tricarboxylic acid (TCA) cycle are encoded by at least 15 different nuclear genes in Saccharomyces cerevisiae. We have constructed a set of yeast strains defective in these genes as part of a comprehensive analysis of the interactions among the TCA cycle proteins. The 15 major TCA cycle genes ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1999-05-01 00:00:00
abstract::Drosophila adult leg development provides an ideal model system for characterizing the molecular mechanisms of hormone-triggered morphogenesis. A pulse of the steroid hormone ecdysone at the onset of metamorphosis triggers the rapid transformation of a flat leg imaginal disc into an immature adult leg, largely through...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2003-11-01 00:00:00
abstract::Currently used tests of Hardy-Weinberg proportions do not take into account the nature of the alternative hypothesis, which is generally a heterozygote deficiency. Different exact tests, appropriate for small sample size and large number of alleles, are proposed in this perspective, and their properties are evaluated ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1995-08-01 00:00:00
abstract::Chromatin is organized and compacted in the nucleus through the association of histones and other proteins, which together control genomic activity. Two broad types of chromatin can be distinguished: euchromatin, which is generally transcriptionally active, and heterochromatin, which is repressed. Here we examine the ...
journal_title:Genetics
pub_type: 杂志文章,评审
doi:10.1534/genetics.117.300386
更新日期:2018-02-01 00:00:00
abstract::Previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for association with 31 tra...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.108.090134
更新日期:2008-10-01 00:00:00
abstract::Genes with unstable transcripts often encode proteins that play important regulatory roles. ATL2 is a member of a multigene family coding highly related RING-H2 zinc-finger proteins that may function as E3 ubiquitin ligases. ATL2 mRNA accumulation occurs rapidly and transiently after incubation with elicitors of patho...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.028043
更新日期:2004-06-01 00:00:00
abstract::The developmental gene optomotor-blind (omb) encodes a T-box-containing transcription factor that has multiple roles in Drosophila development. Previous genetic analyses established that omb plays a key role in establishing the abdominal pigmentation pattern of Drosophila melanogaster. In this report we examine patter...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.032078
更新日期:2004-12-01 00:00:00
abstract::There are many types of DNA damage that are repaired by a multiplicity of different repair pathways. All damage and repair occur in the context of chromatin, and histone modifications are involved in many repair processes. We have analyzed the roles of H2A and its modifications in repair by mutagenizing modifiable res...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.106.063792
更新日期:2007-05-01 00:00:00
abstract::Seventeen lines, each homozygous for a different X chromosome but all with a common autosomal genetic blackground, were constructed and assayed for abdominal bristle number to determine whether dosage compensation operates for sex-linked genes affecting this character. --The regression coefficient of male mean on fema...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1977-01-01 00:00:00
abstract::Adaptation from de novo mutation can produce so-called soft selective sweeps, where adaptive alleles of independent mutational origin sweep through the population at the same time. Population genetic theory predicts that such soft sweeps should be likely if the product of the population size and the mutation rate towa...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.114.165571
更新日期:2014-10-01 00:00:00
abstract::Smg1 is a key component of nonsense-mediated decay (NMD) in Caenorhabditis elegans and mammals. Here we report that two nonsense alleles of the ortholog of Smg1 do not affect NMD in Drosophila melanogaster. ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.105.045674
更新日期:2005-09-01 00:00:00
abstract::To inquire whether the loci identified by recombination-defective and disjunction-defective meiotic mutants in Drosophila are also utilized during mitotic cell division, the effects of 18 meiotic mutants (representing 13 loci) on mitotic chromosome stability have been examined genetically. To do this, meiotic-mutant-b...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1978-11-01 00:00:00
abstract::We have used a novel method to activate the DNA damage S-phase checkpoint response in Saccharomyces cerevisiae to slow lagging-strand DNA replication by exposing cells expressing a drug-sensitive DNA polymerase δ (L612M-DNA pol δ) to the inhibitory drug phosphonoacetic acid (PAA). PAA-treated pol3-L612M cells arrest a...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.111.131938
更新日期:2011-12-01 00:00:00
abstract::Yeast DNA fragments that confer multiple drug resistance when amplified were isolated. Cells containing a yeast genomic library cloned in the high copy autonomously replicating vector, YEp24, were plated on medium containing cycloheximide. Five out of 100 cycloheximide-resistant colonies were cross-resistant to the un...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1990-05-01 00:00:00
abstract::Male Drosophila heterozygous for an SD-bearing second chromosome and a normal homolog preferentially transmit the SD chromosome to their offspring. The distorted transmission involves the induced dysfunction of the sperm that receive the SD+ chromosome. The loci on the SD chromosome responsible for causing distortion ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1989-04-01 00:00:00
abstract::Heterologous yeast artificial chromosomes (YACs) do not recombine with each other and missegregate in 25% of meiosis I events. Recombination hot spots in the yeast Saccharomyces cerevisiae have previously been shown to be associated with sites of meiosis-induced double-strand breaks (DSBs). A 6-kb fragment containing ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1994-12-01 00:00:00
abstract::Mutations in the Saccharomyces cerevisiae SPT8 gene were previously isolated as suppressors of retrotransposon insertion mutations in the 5' regions of the HIS4 and LYS2 genes. Mutations in SPT8 confer phenotypes similar to those caused by particular mutations in SPT15, which encodes the TATA-binding protein (TBP). Th...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1994-07-01 00:00:00
abstract::Filamentous fungi undergo cytokinesis by forming crosswalls termed septa. Here, we describe the genetic and physiological controls governing septation in Aspergillus nidulans. Germinating conidia do not form septa until the completion of their third nuclear division. The first septum is invariantly positioned at the b...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1994-02-01 00:00:00
abstract::The no-on-transient-A (nonA) gene of Drosophila melanogaster influences vision, courtship song, and viability. The nonA-encoded polypeptide is inferred to bind single-stranded nucleic acids. Although sequence-analysis of NONA implies that it belongs to a special interspecific family of this protein type, it does conta...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1996-05-01 00:00:00
abstract::Two large experiments were conducted in order to evaluate the heterozygous effects of irradiated chromosomes on viability. Mutations were accumulated on several hundred second chromosomes by delivering doses of 2,500r over either two or four generations for total X-ray exposures of 5,000r or 10,000r. Chromosomes treat...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1976-10-01 00:00:00
abstract::RNA interference (RNAi) in tissue culture cells has emerged as an excellent methodology for identifying gene functions systematically and in an unbiased manner. Here, we describe how RNAi high-throughput screening (HTS) in Drosophila cells are currently being performed and emphasize the strengths and weaknesses of the...
journal_title:Genetics
pub_type: 杂志文章,评审
doi:10.1534/genetics.106.069963
更新日期:2007-01-01 00:00:00
abstract::Determining the patterns of DNA sequence variation in the human genome is a useful first step toward identifying the genetic basis of a common disease. A haplotype map (HapMap), aimed at describing these variation patterns across the entire genome, has been recently developed by the International HapMap Consortium. In...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.029603
更新日期:2004-09-01 00:00:00
abstract::The ability of a virus population to colonize a novel host is predicted to depend on the equilibrium frequency of potential colonists (i.e., genotypes capable of infecting the novel host) in the source population. In this study, we investigated the determinants of the equilibrium frequency of potential colonists in th...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.106.064634
更新日期:2007-06-01 00:00:00
abstract::The identification of genes affecting sociality can give insights into the maintenance and development of sociality and personality. In this study, we used the combination of an advanced intercross between wild and domestic chickens with a combined QTL and eQTL genetical genomics approach to identify genes for social ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.118.300810
更新日期:2018-05-01 00:00:00
abstract::Fifty-eight isochromosomal lines sampled from two natural populations of Drosophila pseudoobscura in California and one from Bogota, Colombia, were examined using four-cutter restriction mapping. A 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. Thi...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1989-10-01 00:00:00
abstract::A canon of population genetics concerns the properties of FST, a descriptor of spatial genetic structure. Interest for FST arose from Wright's early insights linking FST to dispersal parameters as well as to his concept of effective population size (e.g., Wright 1938, 1951). Although there is continued interest in thi...
journal_title:Genetics
pub_type: 评论,杂志文章
doi:10.1534/genetics.113.152132
更新日期:2013-07-01 00:00:00
abstract::In Drosophila and other insects egg production is related to the nutrients available. Somehow the nutritional status of the environment is translated into hormonal signs that can be "read" by each individual egg chamber, influencing the decision to either develop into an egg or die. We have shown that BR-C is a contro...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.103.024323
更新日期:2004-08-01 00:00:00
abstract::Differential gene expression across cell types underlies development and cell physiology in multicellular organisms. Caenorhabditis elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates to the difficulty to obtain comprehensive tissue-specific gene transcri...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.120.303774
更新日期:2020-12-01 00:00:00