Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.

abstract：:Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-in...

journal_title：Genome biology and evolution

authors： Salmela H,Stark T,Stucki D,Fuchs S,Freitak D,Dey A,Kent CF,Zayed A,Dhaygude K,Hokkanen H,Sundström L

更新日期：2016-03-09 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：:Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. ...

journal_title：Genome biology and evolution

authors： Baymann F,Schoepp-Cothenet B,Lebrun E,van Lis R,Nitschke W

更新日期：2012-01-01 00:00:00

abstract：:The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a ...

journal_title：Genome biology and evolution

authors： Liu Y,Liu S,Zhang N,Chen,Que P,Liu N,Höglund J,Zhang Z,Wang B

更新日期：2019-12-01 00:00:00

abstract：:Bartonella is a genetically diverse group of vector-borne bacteria. Over 40 species have been characterized to date, mainly from mammalian reservoirs and arthropod vectors. Rodent reservoirs harbor one of the largest Bartonella diversity described to date, and novel species and genetic variants are continuously identi...

journal_title：Genome biology and evolution

authors： Gutiérrez R,Markus B,Carstens Marques de Sousa K,Marcos-Hadad E,Mugasimangalam RC,Nachum-Biala Y,Hawlena H,Covo S,Harrus S

更新日期：2018-11-01 00:00:00

abstract：:Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insert...

journal_title：Genome biology and evolution

authors： Jiang X,Tang H,Ye Z,Lynch M

更新日期：2017-02-01 00:00:00

abstract：:Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given t...

journal_title：Genome biology and evolution

authors： Díaz-Viraqué F,Pita S,Greif G,de Souza RCM,Iraola G,Robello C

更新日期：2019-07-01 00:00:00

abstract：:Insertion sequences (ISs) are mobile genetic elements in bacterial genomes. In general, intergenic IS elements are probably less deleterious for their hosts than intragenic ISs, simply because they have a lower likelihood of disrupting native genes. However, since promoters, Shine-Dalgarno sequences, and transcription...

journal_title：Genome biology and evolution

authors： Plague GR

更新日期：2010-01-01 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：: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：:Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N2O) emissions. Despite extensive efforts, fungal contributions to N2O emissions remain uncertain. For example, the majority of N2O emitted from antibiotic-ame...

journal_title：Genome biology and evolution

authors： Higgins SA,Schadt CW,Matheny PB,Löffler FE

更新日期：2018-09-01 00:00:00

abstract：:piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. More...

journal_title：Genome biology and evolution

authors： Kofler R

更新日期：2020-05-01 00:00:00

abstract：:Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly...

journal_title：Genome biology and evolution

authors： Abascal F,Tress ML,Valencia A

更新日期：2015-04-29 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：:The evolution of a mechanically resilient epidermis was a key adaptation in the transition of amniotes to a fully terrestrial lifestyle. Skin appendages usually form via a specialized type of programmed cell death known as cornification which is characterized by the formation of an insoluble cornified envelope (CE). M...

journal_title：Genome biology and evolution

authors： Davis AC,Greenwold MJ,Sawyer RH

更新日期：2019-03-01 00:00:00

abstract：:Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (blac...

journal_title：Genome biology and evolution

authors： Thorpe P,Escudero-Martinez CM,Cock PJA,Eves-van den Akker S,Bos JIB

更新日期：2018-10-01 00:00:00

abstract：:Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called "selfish" genetic elements will proliferate when the host e...

journal_title：Genome biology and evolution

authors： Phillips WS,Coleman-Hulbert AL,Weiss ES,Howe DK,Ping S,Wernick RI,Estes S,Denver DR

更新日期：2015-06-24 00:00:00

abstract：:Different genes and proteins evolve at very different rates. To identify the factors that explain these differences is an important aspect of research in molecular evolution. One such factor is the role a protein plays in a large molecular network. Here, we analyze the evolutionary rates of enzyme-coding genes in the ...

journal_title：Genome biology and evolution

authors： Aguilar-Rodríguez J,Wagner A

更新日期：2018-11-01 00:00:00

abstract：:Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age...

journal_title：Genome biology and evolution

authors： Liu J,Robinson-Rechavi M

更新日期：2018-09-01 00:00:00

abstract：:Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 tar...

journal_title：Genome biology and evolution

authors： Hein A,Brenner S,Knoop V

更新日期：2019-03-01 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：:Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0-3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning m...

journal_title：Genome biology and evolution

authors： Taylor-Brown A,Pillonel T,Greub G,Vaughan L,Nowak B,Polkinghorne A

更新日期：2018-10-01 00:00:00

abstract：:All vertically transmitted bacterial symbionts undergo a process of genome reduction over time, resulting in tiny, gene-dense genomes. Comparison of genomes of ancient bacterial symbionts gives only limited information about the early stages in the transition from a free-living to symbiotic lifestyle because many chan...

journal_title：Genome biology and evolution

authors： Burke GR,Moran NA

更新日期：2011-01-01 00:00:00

abstract：:Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene clu...

journal_title：Genome biology and evolution

authors： Nikaido M,Suzuki H,Toyoda A,Fujiyama A,Hagino-Yamagishi K,Kocher TD,Carleton K,Okada N

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：: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：: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：: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：: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：:Mitochondrial evolution has given rise to a complex array of organelles, ranging from classical aerobic mitochondria to mitochondrial remnants known as hydrogenosomes and mitosomes. The latter are found in anaerobic eukaryotes, and these highly derived organelles often retain only scant evidence of their mitochondrial...

journal_title：Genome biology and evolution

authors： Pérez-Brocal V,Shahar-Golan R,Clark CG

更新日期：2010-07-12 00:00:00