Abstract:
:Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutational drift, is the major determinant of variation across species. Here, we find that in addition to GC content, interspecies codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding and show that domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain of life with high accuracy. We then wondered whether the inclusion of codon usage codon autocorrelation patterns, which reflects the nonrandom distribution of codon occurrences throughout a transcript, might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to previous reports. Instead, our results suggest that codon autocorrelation patterns are a by-product of codon optimality throughout a sequence, where highly expressed genes display autocorrelated "optimal" codons, whereas lowly expressed genes display autocorrelated "nonoptimal" codons.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Novoa EM,Jungreis I,Jaillon O,Kellis Mdoi
10.1093/molbev/msz124subject
Has Abstractpub_date
2019-10-01 00:00:00pages
2328-2339issue
10eissn
0737-4038issn
1537-1719pii
5492082journal_volume
36pub_type
杂志文章abstract::Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss126
更新日期:2012-10-01 00:00:00
abstract::A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg139
更新日期:2003-08-01 00:00:00
abstract::The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here, we have studied the 3D organization and regulation of zebrafish globin gene domain and compared its organization and regulation with tho...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx100
更新日期:2017-06-01 00:00:00
abstract::Most mitochondrial proteins are synthesized in the cytosol of eukaryotic cells as precursor proteins carrying N-terminal extensions called transit peptides or presequences, which mediate their specific transport into mitochondria. However, plant cells possess a second potential target organelle for such transit peptid...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp087
更新日期:2009-08-01 00:00:00
abstract::In Arabidopsis, stem cell homeostasis in the shoot apical meristem (SAM) is controlled by a feedback loop between WUS and CLV functions. We have identified WUS orthologues in maize and rice by a detailed phylogenetic analysis of the WOX gene family and subsequent cloning. A single WUS orthologue is present in the rice...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl125
更新日期:2006-12-01 00:00:00
abstract::Partial and complete genome duplications occurred during evolution and resulted in the creation of new genes and gene families. We identified a novel and intricate human gene family located primarily in regions of segmental duplications on human chromosome 1. We named it NBPF, for neuroblastoma breakpoint family, beca...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi222
更新日期:2005-11-01 00:00:00
abstract::The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelate...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp120
更新日期:2009-09-01 00:00:00
abstract::Full-length mariner-like elements (MLEs) were identified from both a parasitoid wasp, Ascogaster reticulatus, and its moth host, Adoxophyes honmai. MLEs were detected in two related Tortricid moths, but not in another Ascogaster species. The MLEs of A. reticulatus and A. honmai were 97.6% identical in DNA sequence. Th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003735
更新日期:2001-10-01 00:00:00
abstract::Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an addi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025716
更新日期:1997-10-01 00:00:00
abstract::That natural selection affects molecular evolution at synonymous sites in protein-coding sequences is well established and is thought to predominantly reflect selection for translational efficiency/accuracy mediated through codon bias. However, a recently developed maximum likelihood framework, when applied to 18 codi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm196
更新日期:2007-12-01 00:00:00
abstract::Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERN...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa038
更新日期:2020-06-01 00:00:00
abstract::Heme biosynthesis represents one of the most essential metabolic pathways in living organisms, providing the precursors for cytochrome prosthetic groups, photosynthetic pigments, and vitamin B(12). Using genomic data, we have compared the heme pathway in the diatom Thalassiosira pseudonana and the red alga Cyanidiosch...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi230
更新日期:2005-12-01 00:00:00
abstract::Employing comparative analysis of the cDNA-coding sequences of the unique preprorelaxin of the Afro-lorisiform Galago crassicaudatus and the Malagasy lemur Varecia variegata and the relaxin-like factor (RLF) of G. crassicaudatus, we demonstrated distinct differences in the dynamics of molecular remodeling of both horm...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003815
更新日期:2001-03-01 00:00:00
abstract::We implement an isolation with migration model for three species, with migration occurring between two closely related species while an out-group species is used to provide further information concerning gene trees and model parameters. The model is implemented in the likelihood framework for analyzing multilocus geno...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss118
更新日期:2012-10-01 00:00:00
abstract::We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction-enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040101
更新日期:1994-03-01 00:00:00
abstract::The phylogenetic relationships of the biflagellate protist group Apusomonadidae have been unclear despite the availability of some molecular data. We analyzed sequences from 6 nuclear encoded genes-small-subunit rRNA, large-subunit rRNA, alpha-tubulin, beta-tubulin, actin, and heat shock protein 90-to infer the phylog...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl120
更新日期:2006-12-01 00:00:00
abstract::Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be hi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq229
更新日期:2011-01-01 00:00:00
abstract::Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw048
更新日期:2016-07-01 00:00:00
abstract::The genes of tryptophan biosynthesis are arranged and regulated differently in many microorganisms. Comparison of the transcription regulatory regions of the trp operons of several species of enterobacteria reveals that those sequences and structures believed to be essential for repression and attenuation control are ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040307
更新日期:1984-02-01 00:00:00
abstract::The brine shrimp Artemia has three extracellular hemoglobins (Hbs) that are developmentally expressed and exhibit distinct oxygen-binding characteristics (Heip, Moens, and Kondo 1978; Heip et al. 1978 ). These Hbs are composed of two polymers, each of which comprises nine covalently linked globin domains. Although the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004189
更新日期:2002-08-01 00:00:00
abstract::Vertebrate eye lenses mostly contain two abundant types of proteins, the alpha-crystallins and the beta/gamma-crystallins. In addition, certain housekeeping enzymes are highly expressed as crystallins in various taxa. We now observed an unusual approximately 41-kd protein that makes up 16% to 18% of the total protein ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg116
更新日期:2003-06-01 00:00:00
abstract::Here, we address a much-debated topic: is there or is there not an organismal tree of gamma-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj113
更新日期:2006-05-01 00:00:00
abstract::The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa257
更新日期:2021-01-23 00:00:00
abstract::Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic chang...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr142
更新日期:2011-11-01 00:00:00
abstract::Here, we present a study of the molecular evolution of the pheromone receptor genes (pre-1 and pre-2) in Neurospora taxa with different mating systems. We focus on comparisons between heterothallic and homothallic taxa, reproducing sexually by outcrossing and by intrahaploid selfing, respectively. Our general aim was ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss193
更新日期:2012-12-01 00:00:00
abstract::Protamines are small, highly basic DNA-binding proteins found in the sperm of animals. Interestingly, the proportion of arginine residues in one type of protamine, protamine P1, is about 50% in mammals. Upon closer examination, it was found that both the total number of amino acids and the positions of arginine residu...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026307
更新日期:2000-02-01 00:00:00
abstract::Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the mus...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj070
更新日期:2006-03-01 00:00:00
abstract::Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst271
更新日期:2014-04-01 00:00:00
abstract::Although evolutionary studies of gene function often rely on RNA interference, the ideal approach would use reverse genetics to create null mutations for cross-species comparisons and forward genetics to identify novel genes in each species. We have used transcription activator-like effector nucleases (TALENs) to faci...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst213
更新日期:2014-02-01 00:00:00
abstract::As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic vari...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg092
更新日期:2003-06-01 00:00:00