Protein structural modularity and robustness are associated with evolvability.

abstract：:Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called "selfish" genetic elements will proliferate when the host e...

journal_title：Genome biology and evolution

authors： Phillips WS,Coleman-Hulbert AL,Weiss ES,Howe DK,Ping S,Wernick RI,Estes S,Denver DR

更新日期：2015-06-24 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：:Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with ...

journal_title：Genome biology and evolution

authors： Lynch M,Bost D,Wilson S,Maruki T,Harrison S

更新日期：2014-04-30 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：: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：:We previously discovered that lagging strand genes evolve faster in Bacillus subtilis (and potentially other bacteria). Lagging strand genes are transcribed in the head-on orientation with respect to DNA replication, leading to collisions between the two machineries that stall replication and can destabilize genomes. ...

journal_title：Genome biology and evolution

authors： Merrikh CN,Weiss E,Merrikh H

更新日期：2016-12-01 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：: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：:Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether and how this occurs is limited. Here, we present an analysis of the great tit (Parus ...

journal_title：Genome biology and evolution

authors： Hayes K,Barton HJ,Zeng K

更新日期：2020-03-01 00:00:00

abstract：:The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this perio...

journal_title：Genome biology and evolution

authors： Brito AF,Braconi CT,Weidmann M,Dilcher M,Alves JM,Gruber A,Zanotto PM

更新日期：2015-11-27 00:00:00

abstract：:The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host im...

journal_title：Genome biology and evolution

authors： Glander S,He F,Schmitz G,Witten A,Telschow A,de Meaux J

更新日期：2018-09-01 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：:In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive...

journal_title：Genome biology and evolution

authors： De Maeyer D,Weytjens B,De Raedt L,Marchal K

更新日期：2016-01-23 00:00:00

abstract：:Cnidarians represent one of the few groups of venomous animals that lack a centralized venom transmission system. Instead, they are equipped with stinging capsules collectively known as nematocysts. Nematocysts vary in abundance and type across different tissues; however, the venom composition in most species remains ...

journal_title：Genome biology and evolution

authors： Macrander J,Broe M,Daly M

更新日期：2016-08-25 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：:Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,2...

journal_title：Genome biology and evolution

authors： Bertelli C,Cissé OH,Rusconi B,Kebbi-Beghdadi C,Croxatto A,Goesmann A,Collyn F,Greub G

更新日期：2016-08-25 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

abstract：:RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal ...

journal_title：Genome biology and evolution

authors： Kleine Büning M,Meyer D,Austermann-Busch S,Roman-Sosa G,Rümenapf T,Becher P

更新日期：2017-04-01 00:00:00

abstract：:Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2...

journal_title：Genome biology and evolution

authors： Lin YL,Gokcumen O

更新日期：2019-04-01 00:00:00

abstract：:Bitter taste perception likely evolved as a protective mechanism against the ingestion of harmful compounds in food. The evolution of the taste receptor type 2 (TAS2R) gene family, which encodes the chemoreceptors that are directly responsible for the detection of bitter compounds, has therefore been of considerable i...

journal_title：Genome biology and evolution

authors： Davis JK,Lowman JJ,Thomas PJ,ten Hallers BF,Koriabine M,Huynh LY,Maney DL,de Jong PJ,Martin CL,NISC Comparative Sequencing Program.,Thomas JW

更新日期：2010-07-12 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 this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database we...

journal_title：Genome biology and evolution

authors： Silva FJ,Ferreira LC,Campos VP,Cruz-Magalhães V,Barros AF,Andrade JP,Roberts DP,de Souza JT

更新日期：2019-10-01 00:00:00

abstract：:Insertion sequences (ISs) are mobile genetic elements in bacterial genomes. In general, intergenic IS elements are probably less deleterious for their hosts than intragenic ISs, simply because they have a lower likelihood of disrupting native genes. However, since promoters, Shine-Dalgarno sequences, and transcription...

journal_title：Genome biology and evolution

authors： Plague GR

更新日期：2010-01-01 00:00:00

abstract：:Genomic analysis of many nonmodel species has uncovered an incredible diversity of sex chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of sex chromosome evolution. Classic theory predicts that sex chromosomes originate from a pair of homologous ...

journal_title：Genome biology and evolution

authors： Furman BLS,Metzger DCH,Darolti I,Wright AE,Sandkam BA,Almeida P,Shu JJ,Mank JE

更新日期：2020-06-01 00:00:00

abstract：:"Candidatus Endomicrobium trichonymphae" (Bacteria; Elusimicrobia) is an obligate intracellular symbiont of the cellulolytic protist genus Trichonympha in the termite gut. A previous genome analysis of "Ca Endomicrobium trichonymphae" phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in the...

journal_title：Genome biology and evolution

authors： Izawa K,Kuwahara H,Kihara K,Yuki M,Lo N,Itoh T,Ohkuma M,Hongoh Y

更新日期：2016-10-13 00:00:00

abstract：:Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mut...

journal_title：Genome biology and evolution

authors： Katju V,Bergthorsson U

更新日期：2019-01-01 00:00:00

abstract：:Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. Although previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical r...

journal_title：Genome biology and evolution

authors： Metzger BPH,Wittkopp PJ,Coolon JD

更新日期：2017-04-01 00:00:00

abstract：:The major human pathogens Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-dept...

journal_title：Genome biology and evolution

authors： Pita S,Díaz-Viraqué F,Iraola G,Robello C

更新日期：2019-02-01 00:00:00

abstract：:Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age...

journal_title：Genome biology and evolution

authors： Liu J,Robinson-Rechavi M

更新日期：2018-09-01 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