abstract：:The mechanistic basis of regulatory variation and the prevailing evolutionary forces shaping that variation are known to differ between sexes and between chromosomes. Regulatory variation of gene expression can be due to functional changes within a gene itself (cis) or in other genes elsewhere in the genome (trans). T...

journal_title：Genome biology and evolution

authors： Graze RM,McIntyre LM,Morse AM,Boyd BM,Nuzhdin SV,Wayne ML

更新日期：2014-04-01 00:00:00

abstract：:Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired sh...

journal_title：Genome biology and evolution

authors： Guo W,Grewe F,Cobo-Clark A,Fan W,Duan Z,Adams RP,Schwarzbach AE,Mower JP

更新日期：2014-03-01 00:00:00

abstract：:Mitochondrial ORFans (open reading frames having no detectable homology and with unknown function) were discovered in bivalve molluscs with doubly uniparental inheritance (DUI) of mitochondria. In these animals, two mitochondrial lineages are present, one transmitted through eggs (F-type), the other through sperm (M-t...

journal_title：Genome biology and evolution

authors： Milani L,Ghiselli F,Maurizii MG,Nuzhdin SV,Passamonti M

更新日期：2014-02-01 00:00:00

abstract：:Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophu...

journal_title：Genome biology and evolution

authors： García-Pérez R,Ibáñez C,Godínez JM,Aréchiga N,Garin I,Pérez-Suárez G,de Paz O,Juste J,Echevarría JE,Bravo IG

更新日期：2014-01-01 00:00:00

abstract：:Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most...

journal_title：Genome biology and evolution

authors： Zhang F,Broughton RE

更新日期：2013-01-01 00:00:00

abstract：:The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...

journal_title：Genome biology and evolution

authors： Li C,Wang Z,Zhang J

更新日期：2013-01-01 00:00:00

abstract：:Evolution of prokaryotes involves extensive loss and gain of genes, which lead to substantial differences in the gene repertoires even among closely related organisms. Through a wide range of phylogenetic depths, gene frequency distributions in prokaryotic pangenomes bear a characteristic, asymmetrical U-shape, with a...

journal_title：Genome biology and evolution

authors： Lobkovsky AE,Wolf YI,Koonin EV

更新日期：2013-01-01 00:00:00

abstract：:Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all...

journal_title：Genome biology and evolution

authors： Wissler L,Gadau J,Simola DF,Helmkampf M,Bornberg-Bauer E

更新日期：2013-01-01 00:00:00

abstract：:Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic a...

journal_title：Genome biology and evolution

authors： Andres J,Arsène-Ploetze F,Barbe V,Brochier-Armanet C,Cleiss-Arnold J,Coppée JY,Dillies MA,Geist L,Joublin A,Koechler S,Lassalle F,Marchal M,Médigue C,Muller D,Nesme X,Plewniak F,Proux C,Ramírez-Bahena MH,Schenowitz C

更新日期：2013-01-01 00:00:00

abstract：:Hemerythrins and hemocyanins are respiratory proteins present in some of the most ecologically diverse animal lineages; however, the precise evolutionary history of their enzymatic domains (hemerythrin, hemocyanin M, and tyrosinase) is still not well understood. We survey a wide dataset of prokaryote and eukaryote gen...

journal_title：Genome biology and evolution

authors： Martín-Durán JM,de Mendoza A,Sebé-Pedrós A,Ruiz-Trillo I,Hejnol A

更新日期：2013-01-01 00:00:00

abstract：:The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effect...

journal_title：Genome biology and evolution

authors： Nabholz B,Uwimana N,Lartillot N

更新日期：2013-01-01 00:00:00

abstract：:Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic an...

journal_title：Genome biology and evolution

authors： Eveleigh RJ,Meehan CJ,Archibald JM,Beiko RG

更新日期：2013-01-01 00:00:00

abstract：:The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard tha...

journal_title：Genome biology and evolution

authors： Kelly JK,Koseva B,Mojica JP

更新日期：2013-01-01 00:00:00

abstract：:Conservation of function can be accompanied by obvious similarity of homologous sequences which may persist for billions of years (Iyer LM, Leipe DD, Koonin EV, Aravind L. 2004. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 146:11-31.). However, presumably homologous segments of ...

journal_title：Genome biology and evolution

authors： Vakhrusheva OA,Bazykin GA,Kondrashov AS

更新日期：2013-01-01 00:00:00

abstract：:Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations b...

journal_title：Genome biology and evolution

authors： Shen JJ,Dushoff J,Bewick AJ,Chain FJ,Evans BJ

更新日期：2013-01-01 00:00:00

abstract：:In general, proteins do not work alone; they form macromolecular complexes to play fundamental roles in diverse cellular functions. On the basis of their iterative clustering procedure and frequency of occurrence in the macromolecular complexes, the protein subunits have been categorized as core and attachment. Core p...

journal_title：Genome biology and evolution

authors： Chakraborty S,Ghosh TC

更新日期：2013-01-01 00:00:00

abstract：:Plastid genomes are an invaluable resource for plant biological studies. However, the number of completely sequenced plant plastid genomes is still small compared with the vast number of species. To provide an alternative generalized approach, we designed a set of 138 pairs of universal primers for amplifying (termed ...

journal_title：Genome biology and evolution

authors： Dong W,Xu C,Cheng T,Lin K,Zhou S

更新日期：2013-01-01 00:00:00

abstract：:Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and "Candidatus Methanomethylophilus alvus," provide in...

journal_title：Genome biology and evolution

authors： Borrel G,O'Toole PW,Harris HM,Peyret P,Brugère JF,Gribaldo S

更新日期：2013-01-01 00:00:00

abstract：:Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont...

journal_title：Genome biology and evolution

authors： Bennett GM,Moran NA

更新日期：2013-01-01 00:00:00

abstract：:The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metaz...

journal_title：Genome biology and evolution

authors： Grau-Bové X,Sebé-Pedrós A,Ruiz-Trillo I

更新日期：2013-01-01 00:00:00

abstract：:It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of gene...

journal_title：Genome biology and evolution

authors： Hernández-López A,Chabrol O,Royer-Carenzi M,Merhej V,Pontarotti P,Raoult D

更新日期：2013-01-01 00:00:00

abstract：:Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of geni...

journal_title：Genome biology and evolution

authors： Smith DR,Hua J,Archibald JM,Lee RW

更新日期：2013-01-01 00:00:00

abstract：:Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene clu...

journal_title：Genome biology and evolution

authors： Nikaido M,Suzuki H,Toyoda A,Fujiyama A,Hagino-Yamagishi K,Kocher TD,Carleton K,Okada N

更新日期：2013-01-01 00:00:00

abstract：:The ribonuclease (RNase) A superfamily is a vertebrate-specific gene family. Because of a massive expansion that occurred during the early mammalian evolution, extant mammals in general have much more RNase genes than nonmammalian vertebrates. Mammalian RNases have been associated with diverse physiological functions ...

journal_title：Genome biology and evolution

authors： Goo SM,Cho S

更新日期：2013-01-01 00:00:00

abstract：:Protein metabolism is one of the most costly processes in the cell and is therefore expected to be under the effective control of natural selection. We stimulated yeast strains to overexpress each single gene product to approximately 1% of the total protein content. Consistent with previous reports, we found that exce...

journal_title：Genome biology and evolution

authors： Tomala K,Korona R

更新日期：2013-01-01 00:00:00

abstract：:Although the morphological and physiological changes involved in pregnancy in live-bearing reptiles are well studied, the genetic mechanisms that underlie these changes are not known. We used the viviparous African Ocellated Skink, Chalcides ocellatus, as a model to identify a near complete gene expression profile ass...

journal_title：Genome biology and evolution

authors： Brandley MC,Young RL,Warren DL,Thompson MB,Wagner GP

更新日期：2012-01-01 00:00:00

abstract：:Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. ...

journal_title：Genome biology and evolution

authors： Baymann F,Schoepp-Cothenet B,Lebrun E,van Lis R,Nitschke W

更新日期：2012-01-01 00:00:00

abstract：:MicroRNAs (miRNAs) are small RNA molecules involved in the regulation of mammalian gene expression. Together with other transcription regulators, miRNAs modulate the expression of genes and thereby potentially contribute to tissue and species diversity. To identify miRNAs that are differentially expressed between tiss...

journal_title：Genome biology and evolution

authors： Dannemann M,Prüfer K,Lizano E,Nickel B,Burbano HA,Kelso J

更新日期：2012-01-01 00:00:00

abstract：:Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene co...

journal_title：Genome biology and evolution

authors： Brockman SA,McFadden CS

更新日期：2012-01-01 00:00:00

abstract：:Gibbons (Hylobatidae) shared a common ancestor with the other hominoids only 15-18 million years ago. Nevertheless, gibbons show very distinctive features that include heavily rearranged chromosomes. Previous observations indicate that this phenomenon may be linked to the attenuated epigenetic repression of transposab...

journal_title：Genome biology and evolution

authors： Carbone L,Harris RA,Mootnick AR,Milosavljevic A,Martin DI,Rocchi M,Capozzi O,Archidiacono N,Konkel MK,Walker JA,Batzer MA,de Jong PJ

更新日期：2012-01-01 00:00:00

abstract：:Chlorarachniophytes are unicellular marine algae with plastids (chloroplasts) of secondary endosymbiotic origin. Chlorarachniophyte cells retain the remnant nucleus (nucleomorph) and cytoplasm (periplastidial compartment, PPC) of the green algal endosymbiont from which their plastid was derived. To characterize the di...

journal_title：Genome biology and evolution

authors： Hopkins JF,Spencer DF,Laboissiere S,Neilson JA,Eveleigh RJ,Durnford DG,Gray MW,Archibald JM

更新日期：2012-01-01 00:00:00

abstract：:Recent whole-genome approaches to microbial phylogeny have emphasized partitioning genes into functional classes, often focusing on differences between a stable core of genes and a variable shell. To rigorously address the effects of partitioning and combining genes in genome-level analyses, we developed a novel techn...

journal_title：Genome biology and evolution

authors： Narechania A,Baker RH,Sit R,Kolokotronis SO,DeSalle R,Planet PJ

更新日期：2012-01-01 00:00:00

abstract：:The presence of spliceosomal introns in eukaryotic genes poses a major puzzle for the study of genome evolution. Intron densities vary enormously among distant lineages. However, the mechanisms driving intron gains are poorly understood and very few intron gains and losses have been documented over short evolutionary ...

journal_title：Genome biology and evolution

authors： Croll D,McDonald BA

更新日期：2012-01-01 00:00:00

abstract：:Intronic DNA is a major component of eukaryotic genes and genomes and can be subject to selective constraint and have functions in gene regulation. Intron size is of particular interest given that it is thought to be the target of a variety of evolutionary forces and has been suggested to be linked ultimately to vario...

journal_title：Genome biology and evolution

authors： Zhang Q,Edwards SV

更新日期：2012-01-01 00:00:00

abstract：:The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be ass...

journal_title：Genome biology and evolution

authors： Arber W

更新日期：2011-01-01 00:00:00

abstract：:The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-p...

journal_title：Genome biology and evolution

authors： Baldo L,Santos ME,Salzburger W

更新日期：2011-01-01 00:00:00

abstract：:Dosage compensation--equalizing gene expression levels in response to differences in gene dose or copy number--is classically considered to play a critical role in the evolution of heteromorphic sex chromosomes. As the X and Y diverge through degradation and gene loss on the Y (or the W in female-heterogametic ZW taxa...

journal_title：Genome biology and evolution

authors： Walters JR,Hardcastle TJ

更新日期：2011-01-01 00:00:00

abstract：:Theory suggests that biological modularity and robustness allow for maintenance of fitness under mutational change, and when this change is adaptive, for evolvability. Empirical demonstrations that these traits promote evolvability in nature remain scant however. This is in part because modularity, robustness, and evo...

journal_title：Genome biology and evolution

authors： Rorick MM,Wagner GP

更新日期：2011-01-01 00:00:00

abstract：:The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can c...

journal_title：Genome biology and evolution

authors： Doroghazi JR,Buckley DH

更新日期：2011-01-01 00:00:00

abstract：:Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to...

journal_title：Genome biology and evolution

authors： Fujita MK,Edwards SV,Ponting CP

更新日期：2011-01-01 00:00:00