A Journey across Genomes Uncovers the Origin of Ubiquinone in Cyanobacteria.

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：:Only few studies on snake venoms were dedicated to deeply characterize the toxin secretion of animals from the Colubridae family, despite the fact that they represent the majority of snake diversity. As a consequence, some evolutionary trends observed in venom proteins that underpinned the evolutionary histories of sn...

journal_title：Genome biology and evolution

authors： Campos PF,Andrade-Silva D,Zelanis A,Paes Leme AF,Rocha MM,Menezes MC,Serrano SM,Junqueira-de-Azevedo Ide L

更新日期：2016-08-16 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：:Although the morphological and physiological changes involved in pregnancy in live-bearing reptiles are well studied, the genetic mechanisms that underlie these changes are not known. We used the viviparous African Ocellated Skink, Chalcides ocellatus, as a model to identify a near complete gene expression profile ass...

journal_title：Genome biology and evolution

authors： Brandley MC,Young RL,Warren DL,Thompson MB,Wagner GP

更新日期：2012-01-01 00:00:00

abstract：:In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as...

journal_title：Genome biology and evolution

authors： Link V,Aguilar-Gómez D,Ramírez-Suástegui C,Hurst LD,Cortez D

更新日期：2017-09-01 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：:The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metaz...

journal_title：Genome biology and evolution

authors： Grau-Bové X,Sebé-Pedrós A,Ruiz-Trillo I

更新日期：2013-01-01 00:00:00

abstract：:Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species' genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales...

journal_title：Genome biology and evolution

authors： R Marcelino V,Cremen MC,Jackson CJ,Larkum AA,Verbruggen H

更新日期：2016-10-05 00:00:00

abstract：:Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. Although previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical r...

journal_title：Genome biology and evolution

authors： Metzger BPH,Wittkopp PJ,Coolon JD

更新日期：2017-04-01 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：:It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a compa...

journal_title：Genome biology and evolution

authors： Sillo F,Garbelotto M,Friedman M,Gonthier P

更新日期：2015-11-01 00:00:00

abstract：:Positive selection and purifying selection reduce levels of variation at linked neutral loci. One consequence of these processes is that the amount of neutral diversity and the meiotic recombination rate are predicted to be positively correlated across the genome-a prediction met in some species but not others. To bet...

journal_title：Genome biology and evolution

authors： Kartje ME,Jing P,Payseur BA

更新日期：2020-04-01 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：: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：: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：:Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally...

journal_title：Genome biology and evolution

authors： Glinsky GV

更新日期：2016-09-19 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

abstract：:OAS (2'-5'-oligoadenylate synthases) proteins and cyclic GMP-AMP synthase (cGAS, gene symbol: MB21D1) patrol the cytoplasm for the presence of foreign nucleic acids. Upon binding to double-stranded RNA or double-stranded DNA, OAS proteins and cGAS produce nucleotide second messengers to activate RNase L and STING (sti...

journal_title：Genome biology and evolution

authors： Mozzi A,Pontremoli C,Forni D,Clerici M,Pozzoli U,Bresolin N,Cagliani R,Sironi M

更新日期：2015-03-09 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：: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：:Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isol...

journal_title：Genome biology and evolution

authors： Öztürk B,Werner J,Meier-Kolthoff JP,Bunk B,Spröer C,Springael D

更新日期：2020-06-01 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：:Gene duplication is the primary source of new genes, but the mechanisms underlying the functional divergence and retention of duplicate genes are not well understood. Because eukaryotic proteins are localized to subcellular structures and localization can be altered by a single amino acid replacement, it was recently ...

journal_title：Genome biology and evolution

authors： Qian W,Zhang J

更新日期：2009-07-22 00:00:00

abstract：:Cyanobacteria are dominant primary producers of various ecosystems and they colonize marine as well as freshwater and terrestrial habitats. On the basis of their oxygenic photosynthesis they are known to synthesize a high number of secondary metabolites, which makes them promising for biotechnological applications. St...

journal_title：Genome biology and evolution

authors： Will SE,Henke P,Boedeker C,Huang S,Brinkmann H,Rohde M,Jarek M,Friedl T,Seufert S,Schumacher M,Overmann J,Neumann-Schaal M,Petersen J

更新日期：2019-01-01 00:00:00

abstract：:Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints tha...

journal_title：Genome biology and evolution

authors： Daub JT,Dupanloup I,Robinson-Rechavi M,Excoffier L

更新日期：2015-05-13 00:00:00

abstract：:"Candidatus Endomicrobium trichonymphae" (Bacteria; Elusimicrobia) is an obligate intracellular symbiont of the cellulolytic protist genus Trichonympha in the termite gut. A previous genome analysis of "Ca Endomicrobium trichonymphae" phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in the...

journal_title：Genome biology and evolution

authors： Izawa K,Kuwahara H,Kihara K,Yuki M,Lo N,Itoh T,Ohkuma M,Hongoh Y

更新日期：2016-10-13 00:00:00

abstract：:Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragr...

journal_title：Genome biology and evolution

authors： Zhang W,Xu J,Bennetzen JL,Messing J

更新日期：2016-06-13 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：:In general, proteins do not work alone; they form macromolecular complexes to play fundamental roles in diverse cellular functions. On the basis of their iterative clustering procedure and frequency of occurrence in the macromolecular complexes, the protein subunits have been categorized as core and attachment. Core p...

journal_title：Genome biology and evolution

authors： Chakraborty S,Ghosh TC

更新日期：2013-01-01 00:00:00

abstract：:The study of microbe domestication has witnessed major advances that contribute to a better understanding of the emergence of artificially selected phenotypes and set the foundations of their rational improvement for biotechnology. Several features make Saccharomyces cerevisiae an ideal model for such a study, notably...

journal_title：Genome biology and evolution

authors： Barbosa R,Pontes A,Santos RO,Montandon GG,de Ponzzes-Gomes CM,Morais PB,Gonçalves P,Rosa CA,Sampaio JP

更新日期：2018-08-01 00:00:00