Genome-Wide Patterns of Gene Expression in a Wild Primate Indicate Species-Specific Mechanisms Associated with Tolerance to Natural Simian Immunodeficiency Virus Infection.

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：:North Borneo (NB) is home to more than 40 native populations. These natives are believed to have undergone local adaptation in response to environmental challenges such as the mosquito-abundant tropical rainforest. We attempted to trace the footprints of natural selection from the genomic data of NB native populations...

journal_title：Genome biology and evolution

authors： Hoh BP,Zhang X,Deng L,Yuan K,Yew CW,Saw WY,Hoque MZ,Aghakhanian F,Phipps ME,Teo YY,Subbiah VK,Xu S

更新日期：2020-12-06 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：: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：: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：: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：:Amoebiasis is the third-most common cause of mortality worldwide from a parasitic disease. Although the primary etiological agent of amoebiasis is the obligate human parasite Entamoeba histolytica, other members of the genus Entamoeba can infect humans and may be pathogenic. Here, we present the first annotated refere...

journal_title：Genome biology and evolution

authors： Wilson IW,Weedall GD,Lorenzi H,Howcroft T,Hon CC,Deloger M,Guillén N,Paterson S,Clark CG,Hall N

更新日期：2019-03-01 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：: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：: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：:Animals interact with a diverse array of both beneficial and detrimental microorganisms. In insects, these symbioses in many cases allow feeding on nutritionally unbalanced diets. It is, however, still not clear how are obligate symbioses maintained at the cellular level for up to several hundred million years. Exact ...

journal_title：Genome biology and evolution

authors： Husnik F,Hypsa V,Darby A

更新日期：2020-04-01 00:00:00

abstract：:Many algal groups acquired complex plastids by the uptake of green and red algae through multiple secondary endosymbioses. As a result of gene loss and transfer during the endosymbiotic processes, algal endosymbiont nuclei disappeared in most cases. However, chlorarachniophytes and cryptophytes still possess a relict ...

journal_title：Genome biology and evolution

authors： Suzuki S,Shirato S,Hirakawa Y,Ishida K

更新日期：2015-05-22 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：:A major mode of gene expression evolution is based on changes in cis-regulatory elements (CREs) whose function critically depends on the presence of transcription factor-binding sites (TFBS). Because CREs experience extensive TFBS turnover even with conserved function, alignment-based studies of CRE sequence evolution...

journal_title：Genome biology and evolution

authors： Otto W,Stadler PF,López-Giraldéz F,Townsend JP,Lynch VJ,Wagner GP

更新日期：2009-05-25 00:00:00

abstract：:Theory suggests that biological modularity and robustness allow for maintenance of fitness under mutational change, and when this change is adaptive, for evolvability. Empirical demonstrations that these traits promote evolvability in nature remain scant however. This is in part because modularity, robustness, and evo...

journal_title：Genome biology and evolution

authors： Rorick MM,Wagner GP

更新日期：2011-01-01 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：: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：: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：:The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-p...

journal_title：Genome biology and evolution

authors： Baldo L,Santos ME,Salzburger W

更新日期：2011-01-01 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：: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：:Vomeronasal sensitivity is important for detecting intraspecific pheromonal cues as well as environmental odorants and is involved in mating, social interaction, and other daily activities of many vertebrates. Two large families of seven-transmembrane G-protein-coupled receptors, V1rs and V2rs, bind to various ligands...

journal_title：Genome biology and evolution

authors： Park SH,Podlaha O,Grus WE,Zhang J

更新日期：2011-01-01 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：:The presence of spliceosomal introns in eukaryotic genes poses a major puzzle for the study of genome evolution. Intron densities vary enormously among distant lineages. However, the mechanisms driving intron gains are poorly understood and very few intron gains and losses have been documented over short evolutionary ...

journal_title：Genome biology and evolution

authors： Croll D,McDonald BA

更新日期：2012-01-01 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 family Actinomycetaceae comprises several important pathogens that impose serious threat to human health and cause substantial infections of economically important animals. However, the phylogeny and evolutionary dynamic of this family are poorly characterized. Here, we provide detailed description of the genome c...

journal_title：Genome biology and evolution

authors： Zhao K,Li W,Kang C,Du L,Huang T,Zhang X,Wu M,Yue B

更新日期：2014-09-22 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：: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：:MicroRNAs (miRNAs) are short endogenous RNA molecules that regulate gene expression at the posttranscriptional level and have been shown to play critical roles during animal development. The identification and comparison of miRNAs in metazoan species are therefore paramount for our understanding of the evolution of bo...

journal_title：Genome biology and evolution

authors： Marco A,Hui JH,Ronshaugen M,Griffiths-Jones S

更新日期：2010-01-01 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