Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus.

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：: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：:Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid a...

journal_title：Genome biology and evolution

authors： Shao GM,Li XY,Wang Y,Wang ZW,Li Z,Zhang XJ,Zhou L,Gui JF

更新日期：2018-09-01 00:00:00

abstract：:All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome a...

journal_title：Genome biology and evolution

authors： Fort P,Kajava AV,Delsuc F,Coux O

更新日期：2015-05-04 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：: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：:Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustai...

journal_title：Genome biology and evolution

authors： Boon E,Halary S,Bapteste E,Hijri M

更新日期：2015-01-07 00:00:00

abstract：:Hemerythrins and hemocyanins are respiratory proteins present in some of the most ecologically diverse animal lineages; however, the precise evolutionary history of their enzymatic domains (hemerythrin, hemocyanin M, and tyrosinase) is still not well understood. We survey a wide dataset of prokaryote and eukaryote gen...

journal_title：Genome biology and evolution

authors： Martín-Durán JM,de Mendoza A,Sebé-Pedrós A,Ruiz-Trillo I,Hejnol A

更新日期：2013-01-01 00:00:00

abstract：:Experimental evolution allows the observation of change over time as laboratory populations evolve in response to novel, controlled environments. Microbial evolution experiments take advantage of cryopreservation to archive experimental populations in glycerol media, creating a frozen, living "fossil" record. Prior re...

journal_title：Genome biology and evolution

authors： Wing KM,Phillips MA,Baker AR,Burke MK

更新日期：2020-08-01 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：:The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary ...

journal_title：Genome biology and evolution

authors： Wetzel ME,Olsen GJ,Chakravartty V,Farrand SK

更新日期：2015-11-19 00:00:00

abstract：:DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here, ...

journal_title：Genome biology and evolution

authors： Kvist J,Gonçalves Athanàsio C,Shams Solari O,Brown JB,Colbourne JK,Pfrender ME,Mirbahai L

更新日期：2018-08-01 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：:Throughout the animal kingdom chemical senses are one of the primary means by which organisms make sense of their environment. To achieve perception of complex chemosensory stimuli large repertoires of olfactory and gustatory receptors are employed in bony vertebrates, which are characterized by high evolutionary dyna...

journal_title：Genome biology and evolution

authors： Sharma K,Syed AS,Ferrando S,Mazan S,Korsching SI

更新日期：2019-02-01 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：: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：:MicroRNAs (miRNAs) are small RNA molecules involved in the regulation of mammalian gene expression. Together with other transcription regulators, miRNAs modulate the expression of genes and thereby potentially contribute to tissue and species diversity. To identify miRNAs that are differentially expressed between tiss...

journal_title：Genome biology and evolution

authors： Dannemann M,Prüfer K,Lizano E,Nickel B,Burbano HA,Kelso J

更新日期：2012-01-01 00:00:00

abstract：:Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of geni...

journal_title：Genome biology and evolution

authors： Smith DR,Hua J,Archibald JM,Lee RW

更新日期：2013-01-01 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 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：: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：:Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic an...

journal_title：Genome biology and evolution

authors： Eveleigh RJ,Meehan CJ,Archibald JM,Beiko RG

更新日期：2013-01-01 00:00:00

abstract：:Nested genes are the most common form of protein-coding overlap in eukaryotic genomes. Previous studies have shown that nested genes accumulate rapidly over evolutionary time, typically via the insertion of short young duplicate genes into long introns. However, the evolutionary relationship between nested genes remai...

journal_title：Genome biology and evolution

authors： Assis R

更新日期：2016-10-23 00:00:00

abstract：:Arbuscular mycorrhizal fungi (AMF) represent an ecologically important and evolutionarily intriguing group of symbionts of land plants, currently thought to have propagated clonally for over 500 Myr. AMF produce multinucleate spores and may exchange nuclei through anastomosis, but meiosis has never been observed in th...

journal_title：Genome biology and evolution

authors： Halary S,Malik SB,Lildhar L,Slamovits CH,Hijri M,Corradi N

更新日期：2011-01-01 00:00:00

abstract：:Many organisms have a global mechanism for dosage compensation (DC) operating along the entire male X chromosome, which equalizes gene expression on the male X with that on the two Xs in females and/or on autosomes. At the initial stage of sex chromosome evolution, however, gene-by-gene (or localized) DC may also be n...

journal_title：Genome biology and evolution

authors： Nozawa M,Ikeo K,Gojobori T

更新日期：2018-08-01 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：:Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila...

journal_title：Genome biology and evolution

authors： Mahajan S,Bachtrog D

更新日期：2015-01-18 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：: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：:The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...

journal_title：Genome biology and evolution

authors： Li C,Wang Z,Zhang J

更新日期：2013-01-01 00:00:00