Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies.

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：:Mitochondrial ORFans (open reading frames having no detectable homology and with unknown function) were discovered in bivalve molluscs with doubly uniparental inheritance (DUI) of mitochondria. In these animals, two mitochondrial lineages are present, one transmitted through eggs (F-type), the other through sperm (M-t...

journal_title：Genome biology and evolution

authors： Milani L,Ghiselli F,Maurizii MG,Nuzhdin SV,Passamonti M

更新日期：2014-02-01 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 genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors...

journal_title：Genome biology and evolution

authors： Jackman SD,Warren RL,Gibb EA,Vandervalk BP,Mohamadi H,Chu J,Raymond A,Pleasance S,Coope R,Wildung MR,Ritland CE,Bousquet J,Jones SJ,Bohlmann J,Birol I

更新日期：2015-12-08 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：: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：: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：:Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lo...

journal_title：Genome biology and evolution

authors： Huylmans AK,Toups MA,Macon A,Gammerdinger WJ,Vicoso B

更新日期：2019-04-01 00:00:00

abstract：:The process of transcription is highly stochastic leading to cell-to-cell variations and noise in gene expression levels. However, key essential genes have to be precisely expressed at the correct amount and time to ensure proper cellular development and function. Studies in yeast and bacterial systems have shown that...

journal_title：Genome biology and evolution

authors： Vance KW,Woodcock DJ,Reid JE,Bretschneider T,Ott S,Koentges G

更新日期：2015-09-04 00:00:00

abstract：:Wolbachia is a widely distributed intracellular bacterial endosymbiont among invertebrates. The wStriCN, the Wolbachia strain that naturally infects an agricultural pest Laodelphax striatellus, has a "Jekyll and Hyde" mode of infection pattern with positive and negative effects: It not only kills many offspring by ind...

journal_title：Genome biology and evolution

authors： Bing XL,Zhao DS,Sun JT,Zhang KJ,Hong XY

更新日期：2020-02-01 00:00:00

abstract：:The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary pr...

journal_title：Genome biology and evolution

authors： Brown AP,Arias-Rodriguez L,Yee MC,Tobler M,Kelley JL

更新日期：2018-11-01 00:00:00

abstract：:Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. ...

journal_title：Genome biology and evolution

authors： Coimbra NDR,Goes-Neto A,Azevedo V,Ouangraoua A

更新日期：2020-04-01 00:00:00

abstract：:Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hinderi...

journal_title：Genome biology and evolution

authors： Mukherjee D,Mukherjee A,Ghosh TC

更新日期：2015-11-10 00:00:00

abstract：:Mitochondrial DNA (mtDNA) mutations underlie a variety of human genetic disorders and are associated with the aging process. mtDNA polymorphisms are widely used in a variety of evolutionary applications. Although mtDNA mutation spectra are known to differ between distantly related model organisms, the extent to which ...

journal_title：Genome biology and evolution

authors： Howe DK,Baer CF,Denver DR

更新日期：2009-12-23 00:00:00

abstract：:Explaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct time-scales on potentially interdependent traits, can benefit from ...

journal_title：Genome biology and evolution

authors： Lord E,Pathmanathan JS,Corel E,Makarenkov V,Lopez P,Bouchard F,Bhattacharya D,Antoine PO,Le Guyader H,Lapointe FJ,Bapteste E

更新日期：2019-09-01 00:00:00

abstract：:The universal genetic code defines the translation of nucleotide triplets, called codons, into amino acids. In many Saccharomycetes a unique alteration of this code affects the translation of the CUG codon, which is normally translated as leucine. Most of the species encoding CUG alternatively as serine belong to the ...

journal_title：Genome biology and evolution

authors： Mühlhausen S,Kollmar M

更新日期：2014-07-22 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：:Chlorarachniophytes are unicellular marine algae with plastids (chloroplasts) of secondary endosymbiotic origin. Chlorarachniophyte cells retain the remnant nucleus (nucleomorph) and cytoplasm (periplastidial compartment, PPC) of the green algal endosymbiont from which their plastid was derived. To characterize the di...

journal_title：Genome biology and evolution

authors： Hopkins JF,Spencer DF,Laboissiere S,Neilson JA,Eveleigh RJ,Durnford DG,Gray MW,Archibald JM

更新日期：2012-01-01 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

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：: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：: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：:Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and...

journal_title：Genome biology and evolution

authors： Coronado-Zamora M,Salvador-Martínez I,Castellano D,Barbadilla A,Salazar-Ciudad I

更新日期：2019-05-01 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：:Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Unlike other Xenorhabdus species, Xenorhabdus poinarii is avirulent when injected into insects in the ...

journal_title：Genome biology and evolution

authors： Ogier JC,Pagès S,Bisch G,Chiapello H,Médigue C,Rouy Z,Teyssier C,Vincent S,Tailliez P,Givaudan A,Gaudriault S

更新日期：2014-06-05 00:00:00

abstract：:Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf ...

journal_title：Genome biology and evolution

authors： Arakawa T,Kagami H,Katsuyama T,Kitazaki K,Kubo T

更新日期：2020-12-06 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：:Bacteriophage flux can cause the majority of genetic diversity in free-living bacteria. This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. However, recent studie...

journal_title：Genome biology and evolution

authors： Kent BN,Salichos L,Gibbons JG,Rokas A,Newton IL,Clark ME,Bordenstein SR

更新日期：2011-01-01 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：:Conservation of function can be accompanied by obvious similarity of homologous sequences which may persist for billions of years (Iyer LM, Leipe DD, Koonin EV, Aravind L. 2004. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 146:11-31.). However, presumably homologous segments of ...

journal_title：Genome biology and evolution

authors： Vakhrusheva OA,Bazykin GA,Kondrashov AS

更新日期：2013-01-01 00:00:00