abstract：:Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model s...

journal_title：Genome biology and evolution

authors： Chen ZH,Zhang M,Lv FH,Ren X,Li WR,Liu MJ,Nam K,Bruford MW,Li MH

更新日期：2018-04-01 00:00:00

abstract：:Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with ...

journal_title：Genome biology and evolution

authors： Klinger CM,Paoli L,Newby RJ,Wang MY,Carroll HD,Leblond JD,Howe CJ,Dacks JB,Bowler C,Cahoon AB,Dorrell RG,Richardson E

更新日期：2018-04-01 00:00:00

abstract：:Each animal microRNA (miRNA) targets many genes for repression. Down-regulation of most of these targets is weak and has no detectable individual phenotypic effect. Whether this extensive weak repression is biologically relevant is a central issue in the debate on miRNA functionality. In the "small (target) pool" view...

journal_title：Genome biology and evolution

authors： Zhao Y,Lin P,Liufu Z,Yang H,Lyu Y,Shen X,Wu CI,Tang T

更新日期：2018-04-01 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：:Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) a...

journal_title：Genome biology and evolution

authors： Gilbert MJ,Duim B,van der Graaf-van Bloois L,Wagenaar JA,Zomer AL

更新日期：2018-03-01 00:00:00

abstract：:Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a si...

journal_title：Genome biology and evolution

authors： Bitarello BD,de Filippo C,Teixeira JC,Schmidt JM,Kleinert P,Meyer D,Andrés AM

更新日期：2018-03-01 00:00:00

abstract：:Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homol...

journal_title：Genome biology and evolution

authors： Murillo T,Ramírez-Vargas G,Riedel T,Overmann J,Andersen JM,Guzmán-Verri C,Chaves-Olarte E,Rodríguez C

更新日期：2018-03-01 00:00:00

abstract：:Plants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example is secreted fungal effector proteins and their host targets, w...

journal_title：Genome biology and evolution

authors： Schweizer G,Münch K,Mannhaupt G,Schirawski J,Kahmann R,Dutheil JY

更新日期：2018-02-01 00:00:00

abstract：:Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree...

journal_title：Genome biology and evolution

authors： Hillmann F,Forbes G,Novohradská S,Ferling I,Riege K,Groth M,Westermann M,Marz M,Spaller T,Winckler T,Schaap P,Glöckner G

更新日期：2018-02-01 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：: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：:The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relat...

journal_title：Genome biology and evolution

authors： Nilsson MA,Zheng Y,Kumar V,Phillips MJ,Janke A

更新日期：2018-01-01 00:00:00

abstract：:Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we d...

journal_title：Genome biology and evolution

authors： Laenen L,Vergote V,Kafetzopoulou LE,Wawina TB,Vassou D,Cook JA,Hugot JP,Deboutte W,Kang HJ,Witkowski PT,Köppen-Rung P,Krüger DH,Licková M,Stang A,Striešková L,Szemeš T,Markowski J,Hejduk J,Kafetzopoulos D,Van Ranst

更新日期：2018-01-01 00:00:00

abstract：:Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies ...

journal_title：Genome biology and evolution

authors： Brito PH,Chevreux B,Serra CR,Schyns G,Henriques AO,Pereira-Leal JB

更新日期：2018-01-01 00:00:00

abstract：:Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. This study utilized wh...

journal_title：Genome biology and evolution

authors： Miyoshi-Akiyama T,Tada T,Ohmagari N,Viet Hung N,Tharavichitkul P,Pokhrel BM,Gniadkowski M,Shimojima M,Kirikae T

更新日期：2017-12-01 00:00:00

abstract：:Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availabil...

journal_title：Genome biology and evolution

authors： Wilhelmsson PKI,Mühlich C,Ullrich KK,Rensing SA

更新日期：2017-12-01 00:00:00

abstract：:The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic in...

journal_title：Genome biology and evolution

authors： Freese HM,Sikorski J,Bunk B,Scheuner C,Meier-Kolthoff JP,Spröer C,Gram L,Overmann J

更新日期：2017-12-01 00:00:00

abstract：:Geosmithia morbida is an emerging fungal pathogen which serves as a model for examining the evolutionary processes behind pathogenicity because it is one of two known pathogens within a genus of mostly saprophytic, beetle-associated, fungi. This pathogen causes thousand cankers disease in black walnut trees and is vec...

journal_title：Genome biology and evolution

authors： Schuelke TA,Wu G,Westbrook A,Woeste K,Plachetzki DC,Broders K,MacManes MD

更新日期：2017-12-01 00:00:00

abstract：:Kallikrein related peptidase 8 (KLK8; also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we...

journal_title：Genome biology and evolution

authors： Hecker N,Sharma V,Hiller M

更新日期：2017-11-01 00:00:00

abstract：:Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochon...

journal_title：Genome biology and evolution

authors： Degli Esposti M

更新日期：2017-11-01 00:00:00

abstract：:Amoebae have been considered as a genetic "melting pot" for its symbionts, facilitating genetic exchanges of the bacteria that co-inhabit the same host. To test the "melting pot" hypothesis, we analyzed six genomes of amoeba endosymbionts within Rickettsiales, four of which belong to Holosporaceae family and two to Ca...

journal_title：Genome biology and evolution

authors： Wang Z,Wu M

更新日期：2017-11-01 00:00:00

abstract：:The root-knot nematodes (genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding...

journal_title：Genome biology and evolution

authors： Szitenberg A,Salazar-Jaramillo L,Blok VC,Laetsch DR,Joseph S,Williamson VM,Blaxter ML,Lunt DH

更新日期：2017-10-01 00:00:00

abstract：:Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of posit...

journal_title：Genome biology and evolution

authors： Aird SD,Arora J,Barua A,Qiu L,Terada K,Mikheyev AS

更新日期：2017-10-01 00:00:00

abstract：:In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as...

journal_title：Genome biology and evolution

authors： Link V,Aguilar-Gómez D,Ramírez-Suástegui C,Hurst LD,Cortez D

更新日期：2017-09-01 00:00:00

abstract：:Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls...

journal_title：Genome biology and evolution

authors： Evkaikina AI,Berke L,Romanova MA,Proux-Wéra E,Ivanova AN,Rydin C,Pawlowski K,Voitsekhovskaja OV

更新日期：2017-09-01 00:00:00

abstract：:Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide th...

journal_title：Genome biology and evolution

authors： Nielsen TK,Rasmussen M,Demanèche S,Cecillon S,Vogel TM,Hansen LH

更新日期：2017-09-01 00:00:00

abstract：:Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagasca...

journal_title：Genome biology and evolution

authors： Bankoff RJ,Jerjos M,Hohman B,Lauterbur ME,Kistler L,Perry GH

更新日期：2017-07-01 00:00:00

abstract：:Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with novel mechanisms of action. Favipiravir is an antiviral drug that acts by increasing the genome-wide mutation rate of influenza A virus (IAV). Potential synergistic b...

journal_title：Genome biology and evolution

authors： Ormond L,Liu P,Matuszewski S,Renzette N,Bank C,Zeldovich K,Bolon DN,Kowalik TF,Finberg RW,Jensen JD,Wang JP

更新日期：2017-07-01 00:00:00

abstract：:Campylobacter sputorum is a nonthermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase neg...

journal_title：Genome biology and evolution

authors： Miller WG,Yee E,Chapman MH,Bono JL

更新日期：2017-06-01 00:00:00

abstract：:Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two ...

journal_title：Genome biology and evolution

authors： Luchetti A,Plazzi F,Mantovani B

更新日期：2017-06-01 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：:Adaptive prediction is a capability of diverse organisms, including microbes, to sense a cue and prepare in advance to deal with a future environmental challenge. Here, we investigated the timeframe over which adaptive prediction emerges when an organism encounters an environment with novel structure. We subjected yea...

journal_title：Genome biology and evolution

authors： López García de Lomana A,Kaur A,Turkarslan S,Beer KD,Mast FD,Smith JJ,Aitchison JD,Baliga NS

更新日期：2017-06-01 00:00:00

abstract：:As most genes are shared between females and males, DNA methylation is assumed to play a crucial role in sex-biased gene expression. DNA methylation exclusively occurs at CpG dinucleotides, and therefore, we would expect that CpG density around transcription start sites (TSSs) relate to sex-biased gene expression. Her...

journal_title：Genome biology and evolution

authors： Tamagawa K,Makino T,Kawata M

更新日期：2017-05-01 00:00:00

abstract：:Discoba (Excavata) is an evolutionarily important group of eukaryotes that includes Jakobida, with the most bacterial-like mitochondrial genomes known, and Euglenozoa, many of which have extensively fragmented mitochondrial genomes. However, little is known about the mitochondrial genomes of Heterolobosea, the third m...

journal_title：Genome biology and evolution

authors： Yang J,Harding T,Kamikawa R,Simpson AGB,Roger AJ

更新日期：2017-05-01 00:00:00

abstract：:The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently charac...

journal_title：Genome biology and evolution

authors： MacArthur I,Anastasi E,Alvarez S,Scortti M,Vázquez-Boland JA

更新日期：2017-05-01 00:00:00

abstract：:Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting...

journal_title：Genome biology and evolution

authors： Fares MA,Sabater-Muñoz B,Toft C

更新日期：2017-05-01 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：:Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment (LTEE) with Escherichia coli have also diversified extensively in nature. ...

journal_title：Genome biology and evolution

authors： Maddamsetti R,Hatcher PJ,Green AG,Williams BL,Marks DS,Lenski RE

更新日期：2017-04-01 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：: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