Mobile regulatory cassettes mediate modular shuffling in T4-type phage genomes.

abstract：:Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morph...

journal_title：Genome biology and evolution

authors： Huang Z,Duan W,Song X,Tang J,Wu P,Zhang B,Hou X

更新日期：2015-12-31 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：:Pathogens and hosts are in an ongoing arms race and genes involved in host-pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, ...

journal_title：Genome biology and evolution

authors： Sperschneider J,Gardiner DM,Thatcher LF,Lyons R,Singh KB,Manners JM,Taylor JM

更新日期：2015-05-19 00:00:00

abstract：:Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species' genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales...

journal_title：Genome biology and evolution

authors： R Marcelino V,Cremen MC,Jackson CJ,Larkum AA,Verbruggen H

更新日期：2016-10-05 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：:Tandem repeats (TRs) are highly dynamic regions of the genome. Mutations at these loci represent a significant source of genetic variation and can facilitate rapid adaptation. Bumblebees are important pollinating insects occupying a wide range of habitats. However, to date, molecular mechanisms underlying the potentia...

journal_title：Genome biology and evolution

authors： Zhao X,Su L,Schaack S,Sadd BM,Sun C

更新日期：2018-12-01 00:00:00

abstract：:Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trema...

journal_title：Genome biology and evolution

authors： Zajac N,Zoller S,Seppälä K,Moi D,Dessimoz C,Jokela J,Hartikainen H,Glover N

更新日期：2021-01-23 00:00:00

abstract：:The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 45...

journal_title：Genome biology and evolution

authors： Do HD,Kim JS,Kim JH

更新日期：2014-06-19 00:00:00

abstract：:Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats...

journal_title：Genome biology and evolution

authors： Zoldoš V,Biruš I,Muratovic E,Šatovic Z,Vojta A,Robin O,Pustahija F,Bogunic F,Vicic Bockor V,Siljak-Yakovlev S

更新日期：2018-01-01 00:00:00

abstract：:Plasma membrane NADPH oxidases (NOXs) are key producers of reactive oxygen species under both normal and stress conditions in plants and they form functional subfamilies. Studies of these subfamilies indicated that they show considerable evolutionary selection. We performed a comparative genomic analysis that identifi...

journal_title：Genome biology and evolution

authors： Chang YL,Li WY,Miao H,Yang SQ,Li R,Wang X,Li WQ,Chen KM

更新日期：2016-02-23 00:00:00

abstract：:Population-level differences in the number of copies of genes resulting from gene duplication and loss have recently been recognized as an important source of variation in eukaryotes. However, except for a small number of cases, the phenotypic effects of this variation are unknown. Data from the Saccharomyces Genome R...

journal_title：Genome biology and evolution

authors： Ames RM,Rash BM,Hentges KE,Robertson DL,Delneri D,Lovell SC

更新日期：2010-01-01 00:00:00

abstract：:Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multitissue transcriptome data set from great tit (Parus major), we analyzed patterns of molecular evolution between two pas...

journal_title：Genome biology and evolution

authors： Gossmann TI,Santure AW,Sheldon BC,Slate J,Zeng K

更新日期：2014-08-01 00:00:00

abstract：:Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, howe...

journal_title：Genome biology and evolution

authors： Naidoo T,Xu J,Vicente M,Malmström H,Soodyall H,Jakobsson M,Schlebusch CM

更新日期：2020-07-01 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：: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：:Many viroids and RNA viruses have genomes that exhibit secondary structure, with paired nucleotides forming stems and loops. Such structures violate a key assumption of most methods of phylogenetic reconstruction, that sequence change is independent among sites. However, phylogenetic analyses of these transmissible ag...

journal_title：Genome biology and evolution

authors： Patiño-Galindo JÁ,González-Candelas F,Pybus OG

更新日期：2018-02-01 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：:Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with d...

journal_title：Genome biology and evolution

authors： Vegesna R,Tomaszkiewicz M,Ryder OA,Campos-Sánchez R,Medvedev P,DeGiorgio M,Makova KD

更新日期：2020-06-01 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：: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：:piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. More...

journal_title：Genome biology and evolution

authors： Kofler R

更新日期：2020-05-01 00:00:00

abstract：:Constitutive defense mechanisms are critical to the understanding of defense mechanisms in conifers because they constitute the first barrier to attacks by insect pests. In interior spruce, trees that are putatively resistant and susceptible to attacks by white pine weevil (Pissodes strobi) typically exhibit constitut...

journal_title：Genome biology and evolution

authors： Verne S,Jaquish B,White R,Ritland C,Ritland K

更新日期：2011-01-01 00:00:00

abstract：:Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isol...

journal_title：Genome biology and evolution

authors： Öztürk B,Werner J,Meier-Kolthoff JP,Bunk B,Spröer C,Springael D

更新日期：2020-06-01 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：:Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abioti...

journal_title：Genome biology and evolution

authors： Mohd-Assaad N,McDonald BA,Croll D

更新日期：2018-04-01 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：:Mitochondrial interactions with the nuclear genome represent one of life's most important co-evolved mutualisms. In many organisms, mitochondria are maternally inherited, and in these cases, co-transmission between the mitochondrial and nuclear genes differs across different parts of the nuclear genome, with genes on ...

journal_title：Genome biology and evolution

authors： Dean R,Zimmer F,Mank JE

更新日期：2014-05-01 00:00:00

abstract：:Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally...

journal_title：Genome biology and evolution

authors： Glinsky GV

更新日期：2016-09-19 00:00:00

abstract：:Because of its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconi...

journal_title：Genome biology and evolution

authors： Ye D,Zaidi AA,Tomaszkiewicz M,Anthony K,Liebowitz C,DeGiorgio M,Shriver MD,Makova KD

更新日期：2018-05-01 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