The Accelerated Evolution of Lagging Strand Genes Is Independent of Sequence Context.

abstract：:Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we i...

journal_title：Genome biology and evolution

authors： Yoshida K,Ravinet M,Makino T,Toyoda A,Kokita T,Mori S,Kitano J

更新日期：2020-04-01 00:00:00

abstract：:Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the ...

journal_title：Genome biology and evolution

authors： Wolf JB,Künstner A,Nam K,Jakobsson M,Ellegren H

更新日期：2009-08-13 00:00:00

abstract：:Coliphage phi1, which was isolated for phage therapy in the Republic of Georgia, is closely related to the T-like myovirus RB49. The approximately 275 open reading frames encoded by each phage have an average level of amino acid identity of 95.8%. RB49 lacks 7 phi1 genes while 10 phi1 genes are missing from RB49. Most...

journal_title：Genome biology and evolution

authors： Arbiol C,Comeau AM,Kutateladze M,Adamia R,Krisch HM

更新日期：2010-02-01 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：:Only few studies on snake venoms were dedicated to deeply characterize the toxin secretion of animals from the Colubridae family, despite the fact that they represent the majority of snake diversity. As a consequence, some evolutionary trends observed in venom proteins that underpinned the evolutionary histories of sn...

journal_title：Genome biology and evolution

authors： Campos PF,Andrade-Silva D,Zelanis A,Paes Leme AF,Rocha MM,Menezes MC,Serrano SM,Junqueira-de-Azevedo Ide L

更新日期：2016-08-16 00:00:00

abstract：:In the experimental evolution of microbes such as Escherichia coli, many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus ea...

journal_title：Genome biology and evolution

authors： Sprouffske K,Aguilar-Rodríguez J,Wagner A

更新日期：2016-05-09 00:00:00

abstract：:Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf ...

journal_title：Genome biology and evolution

authors： Arakawa T,Kagami H,Katsuyama T,Kitazaki K,Kubo T

更新日期：2020-12-06 00:00:00

abstract：:Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given t...

journal_title：Genome biology and evolution

authors： Díaz-Viraqué F,Pita S,Greif G,de Souza RCM,Iraola G,Robello C

更新日期：2019-07-01 00:00:00

abstract：:Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two-component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cu...

journal_title：Genome biology and evolution

authors： Kabbara S,Hérivaux A,Dugé de Bernonville T,Courdavault V,Clastre M,Gastebois A,Osman M,Hamze M,Cock JM,Schaap P,Papon N

更新日期：2019-01-01 00:00:00

abstract：:Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer's yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high quality long read genomes of non-domesticated yeast strains isolated from primeval forests...

journal_title：Genome biology and evolution

authors： Bendixsen DP,Gettle N,Gilchrist C,Zhang Z,Stelkens R

更新日期：2021-01-11 00:00:00

abstract：:The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary pr...

journal_title：Genome biology and evolution

authors： Brown AP,Arias-Rodriguez L,Yee MC,Tobler M,Kelley JL

更新日期：2018-11-01 00:00:00

abstract：:Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV...

journal_title：Genome biology and evolution

authors： Simons ND,Eick GN,Ruiz-Lopez MJ,Hyeroba D,Omeja PA,Weny G,Zheng H,Shankar A,Frost SDW,Jones JH,Chapman CA,Switzer WM,Goldberg TL,Sterner KN,Ting N

更新日期：2019-06-01 00:00:00

abstract：:The propensity of protein sites to be occupied by any of the 20 amino acids is known as site-specific amino acid preferences (SSAP). Under the assumption that SSAP are conserved among homologs, they can be used to parameterize evolutionary models for the reconstruction of accurate phylogenetic trees. However, simulati...

journal_title：Genome biology and evolution

authors： Ferrada E

更新日期：2019-01-01 00:00:00

abstract：:RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded p...

journal_title：Genome biology and evolution

authors： Dong S,Zhao C,Zhang S,Wu H,Mu W,Wei T,Li N,Wan T,Liu H,Cui J,Zhu R,Goffinet B,Liu Y

更新日期：2019-11-01 00:00:00

abstract：:Mitochondrial DNA (mtDNA) mutations underlie a variety of human genetic disorders and are associated with the aging process. mtDNA polymorphisms are widely used in a variety of evolutionary applications. Although mtDNA mutation spectra are known to differ between distantly related model organisms, the extent to which ...

journal_title：Genome biology and evolution

authors： Howe DK,Baer CF,Denver DR

更新日期：2009-12-23 00:00:00

abstract：:Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. Recently, an antibiotic-resistant strain of this serovar was implicated in a large 2011 multistate outbreak resulting from consumption of contaminated ground turkey that involved 136 confirmed...

journal_title：Genome biology and evolution

authors： Hoffmann M,Zhao S,Pettengill J,Luo Y,Monday SR,Abbott J,Ayers SL,Cinar HN,Muruvanda T,Li C,Allard MW,Whichard J,Meng J,Brown EW,McDermott PF

更新日期：2014-05-01 00:00:00

abstract：:Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and loss...

journal_title：Genome biology and evolution

authors： Vandewege MW,Mangum SF,Gabaldón T,Castoe TA,Ray DA,Hoffmann FG

更新日期：2016-02-09 00:00:00

abstract：:The family Actinomycetaceae comprises several important pathogens that impose serious threat to human health and cause substantial infections of economically important animals. However, the phylogeny and evolutionary dynamic of this family are poorly characterized. Here, we provide detailed description of the genome c...

journal_title：Genome biology and evolution

authors： Zhao K,Li W,Kang C,Du L,Huang T,Zhang X,Wu M,Yue B

更新日期：2014-09-22 00:00:00

abstract：:Nemerteans are one of few animal groups that have evolved the ability to utilize toxins for both defense and subduing prey, but little is known about specific nemertean toxins. In particular, no study has identified specific toxin genes even though peptide toxins are known from some nemertean species. Information abou...

journal_title：Genome biology and evolution

authors： Whelan NV,Kocot KM,Santos SR,Halanych KM

更新日期：2014-11-27 00:00:00

abstract：:Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by mult...

journal_title：Genome biology and evolution

authors： Reyes-Bermudez A,Villar-Briones A,Ramirez-Portilla C,Hidaka M,Mikheyev AS

更新日期：2016-03-23 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：:Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model ...

journal_title：Genome biology and evolution

authors： Riba A,Fumagalli MR,Caselle M,Osella M

更新日期：2020-11-03 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：:The selective pressures acting on viruses that replicate under enhanced mutation rates are largely unknown. Here, we describe resistance of foot-and-mouth disease virus to the mutagen 5-fluorouracil (FU) through a single polymerase substitution that prevents an excess of A to G and U to C transitions evoked by FU on t...

journal_title：Genome biology and evolution

authors： de la Higuera I,Ferrer-Orta C,de Ávila AI,Perales C,Sierra M,Singh K,Sarafianos SG,Dehouck Y,Bastolla U,Verdaguer N,Domingo E

更新日期：2017-05-01 00:00:00

abstract：:Clashes between transcription and replication complexes can cause point mutations and chromosome rearrangements on heavily transcribed genes. In eukaryotic ribosomal RNA genes, the system that prevents transcription-replication conflicts also causes frequent copy number variation. Such fast mutational dynamics do not ...

journal_title：Genome biology and evolution

authors： Colizzi ES,Hogeweg P

更新日期：2019-11-01 00:00:00

abstract：:The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a ...

journal_title：Genome biology and evolution

authors： Liu Y,Liu S,Zhang N,Chen,Que P,Liu N,Höglund J,Zhang Z,Wang B

更新日期：2019-12-01 00:00:00

abstract：:The contribution of the transposons' promoter in the horizontal transfer process is quite overlooked in the scientific literature. To shed light on this aspect we have mimicked the horizontal transfer process in laboratory and assayed in a wide range of hosts (fly, human, yeast and bacteria) the promoter activity of t...

journal_title：Genome biology and evolution

authors： Palazzo A,Caizzi R,Viggiano L,Marsano RM

更新日期：2017-06-01 00:00:00

abstract：:Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic re...

journal_title：Genome biology and evolution

authors： Pich I Roselló O,Kondrashov FA

更新日期：2014-07-28 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：: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