Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.

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：:Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to be greater than that of the mitochondrial genome. This assumption is based on early, pioneering studies of land plant molecular evolution, which uncovered higher rates of synonymous substitution in plastid versus mitochondrial ...

journal_title：Genome biology and evolution

authors： Smith DR

更新日期：2015-04-13 00:00:00

abstract：:Parasites are sometimes able to manipulate the behavior of their hosts. However, the molecular cues underlying this phenomenon are poorly documented. We previously reported that the parasitoid wasp Leptopilina boulardi which develops from Drosophila larvae is often infected by an inherited DNA virus. In addition to be...

journal_title：Genome biology and evolution

authors： Lepetit D,Gillet B,Hughes S,Kraaijeveld K,Varaldi J

更新日期：2016-12-01 00:00:00

abstract：:Nucleomorphs are the remnant nuclei of algal endosymbionts that were engulfed by nonphotosynthetic host eukaryotes. These peculiar organelles are found in cryptomonad and chlorarachniophyte algae, where they evolved from red and green algal endosymbionts, respectively. Despite their independent origins, cryptomonad an...

journal_title：Genome biology and evolution

authors： Tanifuji G,Onodera NT,Wheeler TJ,Dlutek M,Donaher N,Archibald JM

更新日期：2011-01-01 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：: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：: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：: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：:Chaperonins promote protein folding and are known to play a role in the maintenance of cellular stability under stress conditions. The group I bacterial chaperonin complex comprises GroEL, that forms a barrel-like oligomer, and GroES that forms the lid. In most eubacteria the GroES/GroEL chaperonin is encoded by a sin...

journal_title：Genome biology and evolution

authors： Weissenbach J,Ilhan J,Bogumil D,Hülter N,Stucken K,Dagan T

更新日期：2017-01-01 00:00:00

abstract：:The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed tempo...

journal_title：Genome biology and evolution

authors： Lynch M,Ho WC

更新日期：2020-04-01 00:00:00

abstract：:Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male dete...

journal_title：Genome biology and evolution

authors： Meisel RP,Scott JG,Clark AG

更新日期：2015-07-02 00:00:00

abstract：:Organisms show striking differences in genome structure; however, the functional implications and fundamental forces that govern these differences remain obscure. The intron-exon organization of nuclear genes is involved in a particularly large variety of structures and functional roles. We performed a 22-species stud...

journal_title：Genome biology and evolution

authors： Irimia M,Maeso I,Burguera D,Hidalgo-Sánchez M,Puelles L,Roy SW,Garcia-Fernàndez J,Ferran JL

更新日期：2011-01-01 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：: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：: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：: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：: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：: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：:Acetyl-CoA carboxylase (ACCase) is the key regulator of fatty acid biosynthesis. In most plants, ACCase exists in two locations (cytosol and plastids) and in two forms (homomeric and heteromeric). Heteromeric ACCase comprises four subunits, three of them (ACCA-C) are nuclear encoded (nr) and the fourth (ACCD) is usual...

journal_title：Genome biology and evolution

authors： Sudianto E,Chaw SM

更新日期：2019-06-01 00:00:00

abstract：:African trypanosomiasis is a vector-borne disease of humans and livestock caused by African trypanosomes (Trypanosoma spp.). Survival in the vertebrate bloodstream depends on antigenic variation of Variant Surface Glycoproteins (VSGs) coating the parasite surface. In T. brucei, a model for antigenic variation, monoall...

journal_title：Genome biology and evolution

authors： Abbas AH,Silva Pereira S,D'Archivio S,Wickstead B,Morrison LJ,Hall N,Hertz-Fowler C,Darby AC,Jackson AP

更新日期：2018-09-01 00:00:00

abstract：:Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolut...

journal_title：Genome biology and evolution

authors： Lu MR,Lai CK,Liao BY,Tsai IJ

更新日期：2020-07-01 00:00:00

abstract：:Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model fo...

journal_title：Genome biology and evolution

authors： Tvedte ES,Walden KKO,McElroy KE,Werren JH,Forbes AA,Hood GR,Logsdon JM,Feder JL,Robertson HM

更新日期：2019-10-01 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：:Klebsiella pneumoniae clonal group (CG) 258, comprising sequence types (STs) 258, 11, and closely related variants, is associated with dissemination of the K. pneumoniae carbapenemase (KPC). Hospital outbreaks of KPC CG258 infections have been observed globally and are very difficult to treat. As a consequence, there ...

journal_title：Genome biology and evolution

authors： Wyres KL,Gorrie C,Edwards DJ,Wertheim HF,Hsu LY,Van Kinh N,Zadoks R,Baker S,Holt KE

更新日期：2015-04-10 00:00:00

abstract：:The Arabidopsis DA1 genes appear to have multiple functions in regulating organ size and abiotic stress response, but the biological roles of its closely related genes remain unknown. Evolutionary analyses might provide some clues to aid in an understanding of their functional diversification. In this work, we charact...

journal_title：Genome biology and evolution

authors： Zhao M,He L,Gu Y,Wang Y,Chen Q,He C

更新日期：2014-04-01 00:00:00

abstract：:One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the main...

journal_title：Genome biology and evolution

authors： Willemsen A,Zwart MP,Higueras P,Sardanyés J,Elena SF

更新日期：2016-10-12 00:00:00

abstract：:The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, ...

journal_title：Genome biology and evolution

authors： Carretero-Paulet L,Chang TH,Librado P,Ibarra-Laclette E,Herrera-Estrella L,Rozas J,Albert VA

更新日期：2015-01-09 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：: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：:Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems. However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small ...

journal_title：Genome biology and evolution

authors： Gottlieb Y,Lalzar I,Klasson L

更新日期：2015-05-28 00:00:00