Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species.

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：:Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree...

journal_title：Genome biology and evolution

authors： Hillmann F,Forbes G,Novohradská S,Ferling I,Riege K,Groth M,Westermann M,Marz M,Spaller T,Winckler T,Schaap P,Glöckner G

更新日期：2018-02-01 00:00:00

abstract：:Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to p...

journal_title：Genome biology and evolution

authors： Ely ZA,Moon JM,Sliwoski GR,Sangha AK,Shen XX,Labella AL,Meiler J,Capra JA,Rokas A

更新日期：2019-09-01 00:00:00

abstract：:Cnidarians represent one of the few groups of venomous animals that lack a centralized venom transmission system. Instead, they are equipped with stinging capsules collectively known as nematocysts. Nematocysts vary in abundance and type across different tissues; however, the venom composition in most species remains ...

journal_title：Genome biology and evolution

authors： Macrander J,Broe M,Daly M

更新日期：2016-08-25 00:00:00

abstract：:Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic a...

journal_title：Genome biology and evolution

authors： Andres J,Arsène-Ploetze F,Barbe V,Brochier-Armanet C,Cleiss-Arnold J,Coppée JY,Dillies MA,Geist L,Joublin A,Koechler S,Lassalle F,Marchal M,Médigue C,Muller D,Nesme X,Plewniak F,Proux C,Ramírez-Bahena MH,Schenowitz C

更新日期：2013-01-01 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：: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：: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：:Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability o...

journal_title：Genome biology and evolution

authors： Vizueta J,Rozas J,Sánchez-Gracia A

更新日期：2018-04-01 00:00:00

abstract：:Mitochondrial (mt) genomes are intensively studied in Ascomycota and Basidiomycota, but they are poorly documented in basal fungal lineages. In this study, we sequenced the complete mtDNA of Rhizophagus sp. DAOM 213198, a close relative to Rhizophagus irregularis, a widespread, ecologically and economical relevant spe...

journal_title：Genome biology and evolution

authors： Nadimi M,Stefani FO,Hijri M

更新日期：2014-12-19 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：:Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with d...

journal_title：Genome biology and evolution

authors： Vegesna R,Tomaszkiewicz M,Ryder OA,Campos-Sánchez R,Medvedev P,DeGiorgio M,Makova KD

更新日期：2020-06-01 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：:Bitter taste perception likely evolved as a protective mechanism against the ingestion of harmful compounds in food. The evolution of the taste receptor type 2 (TAS2R) gene family, which encodes the chemoreceptors that are directly responsible for the detection of bitter compounds, has therefore been of considerable i...

journal_title：Genome biology and evolution

authors： Davis JK,Lowman JJ,Thomas PJ,ten Hallers BF,Koriabine M,Huynh LY,Maney DL,de Jong PJ,Martin CL,NISC Comparative Sequencing Program.,Thomas JW

更新日期：2010-07-12 00:00:00

abstract：:Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment (LTEE) with Escherichia coli have also diversified extensively in nature. ...

journal_title：Genome biology and evolution

authors： Maddamsetti R,Hatcher PJ,Green AG,Williams BL,Marks DS,Lenski RE

更新日期：2017-04-01 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：: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：: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：: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：:Glycosaminoglycans are sulfated polysaccharide molecules, essential for many biological processes. The 6-O sulfation of glycosaminoglycans is carried out by carbohydrate 6-O sulfotransferases (C6OSTs), previously named Gal/GalNAc/GlcNAc 6-O sulfotransferases. Here, for the first time, we present a detailed phylogeneti...

journal_title：Genome biology and evolution

authors： Ocampo Daza D,Haitina T

更新日期：2020-07-01 00:00:00

abstract：:Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here...

journal_title：Genome biology and evolution

authors： Sarver BA,Demboski JR,Good JM,Forshee N,Hunter SS,Sullivan J

更新日期：2017-01-01 00:00:00

abstract：:Intronic DNA is a major component of eukaryotic genes and genomes and can be subject to selective constraint and have functions in gene regulation. Intron size is of particular interest given that it is thought to be the target of a variety of evolutionary forces and has been suggested to be linked ultimately to vario...

journal_title：Genome biology and evolution

authors： Zhang Q,Edwards SV

更新日期：2012-01-01 00:00:00

abstract：:The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expressio...

journal_title：Genome biology and evolution

authors： Irwin NAT,Keeling PJ

更新日期：2019-03-01 00:00:00

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：:SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, De...

journal_title：Genome biology and evolution

authors： Nishihara H,Plazzi F,Passamonti M,Okada N

更新日期：2016-02-12 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：:We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene cont...

journal_title：Genome biology and evolution

authors： Guillory WX,Onyshchenko A,Ruck EC,Parks M,Nakov T,Wickett NJ,Alverson AJ

更新日期：2018-06-01 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：:The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, ...

journal_title：Genome biology and evolution

authors： Carretero-Paulet L,Chang TH,Librado P,Ibarra-Laclette E,Herrera-Estrella L,Rozas J,Albert VA

更新日期：2015-01-09 00:00:00

abstract：:Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. This study utilized wh...

journal_title：Genome biology and evolution

authors： Miyoshi-Akiyama T,Tada T,Ohmagari N,Viet Hung N,Tharavichitkul P,Pokhrel BM,Gniadkowski M,Shimojima M,Kirikae T

更新日期：2017-12-01 00:00:00